@article{glanzmann_inborn_2024,
	title = {Inborn errors of immunity in {South} {Africa}: genetics and the expanding universe},
	volume = {37},
	shorttitle = {Inborn errors of immunity in {South} {Africa}},
	url = {https://journals.co.za/doi/10.10520/ejc-caci-v37-n1-a2},
	doi = {10.10520/ejc-caci-v37-n1-a2},
	abstract = {Inborn errors of immunity (IEI) represent a diverse group of disorders resulting from monogenic defects in immune system genes. These defects cause individuals to be more susceptible to severe, persistent, unusual and recurrent infections, malignancies and autoimmune/autoinaflmmatory conditions. Recent advances in next-generation sequencing (NGS) technologies have transformed IEI diagnoses, as can be seen in the large increase of new variants identiefid in these disorders. However, many suspected IEI patients still lack a molecular diagnosis, emphasising the need for unbiased investigative approaches. The early diagnosis of IEI enables more effective treatments and ensures more precise genetic counselling, which help families to understand the disease, family planning and informed decision-making about testing. The establishment of registries is critical to capturing data on IEI patients, which can inform clinical care, raise awareness and respond to research questions in the efild. In developing countries such as South Africa, the adoption of NGS technologies has the potential to transform the diagnosis and management of IEI, ultimately improving patient outcomes. This review highlights the signicfiance of NGS technologies in the diagnosis and management of IEI, the importance of genetic counselling and the role of registries in advancing our understanding of these rare disorders, particularly in underserved regions.},
	number = {1},
	urldate = {2024-06-10},
	journal = {Current Allergy \& Clinical Immunology},
	author = {Glanzmann, Brigitte and Scholtz, Denise and van, Coller Ansia and Abraham, Deepthi R. and Du, Toit Maxine and Nortje, Rina and Esser, Monika and Glashoff, Richard and M, öller Marlo and Kinnear, Craig},
	month = mar,
	year = {2024},
	note = {Publisher: Allergy Society of South Africa (ALLSA)},
	keywords = {South Africa, Whole exome sequencing, inborn errors of immunity, targeted gene panels, whole genome sequencing},
	pages = {5--10},
}

Inborn errors of immunity (IEI) represent a diverse group of disorders resulting from monogenic defects in immune system genes. These defects cause individuals to be more susceptible to severe, persistent, unusual and recurrent infections, malignancies and autoimmune/autoinaflmmatory conditions. Recent advances in next-generation sequencing (NGS) technologies have transformed IEI diagnoses, as can be seen in the large increase of new variants identiefid in these disorders. However, many suspected IEI patients still lack a molecular diagnosis, emphasising the need for unbiased investigative approaches. The early diagnosis of IEI enables more effective treatments and ensures more precise genetic counselling, which help families to understand the disease, family planning and informed decision-making about testing. The establishment of registries is critical to capturing data on IEI patients, which can inform clinical care, raise awareness and respond to research questions in the efild. In developing countries such as South Africa, the adoption of NGS technologies has the potential to transform the diagnosis and management of IEI, ultimately improving patient outcomes. This review highlights the signicfiance of NGS technologies in the diagnosis and management of IEI, the importance of genetic counselling and the role of registries in advancing our understanding of these rare disorders, particularly in underserved regions.

@article{moodley_latent_2024,
	title = {Latent tuberculosis infection is associated with an enrichment of short chain fatty acid producing bacteria in the stool of women living with {HIV}},
	doi = {10.21203/rs.3.rs-4182285/v1},
	abstract = {BACKGROUND: Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV.
METHOD: Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST- negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2.
RESULTS: No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were Faecalibacterium-, Blautia-, Gemmiger-, Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, Streptococcus-depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (Acidaminococcus-enrichment and Megamonas-, Alistipes-, and Paraprevotella-depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups.
CONCLUSION: Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Faecalibacterium, Blautia, Gemmiger, Bacteriodes-enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.},
	language = {eng},
	journal = {Research Square},
	author = {Moodley, Suventha and Kroon, Elouise and Naidoo, Charissa C. and Nyawo, Georgina R. and Wu, Benjamin G. and Naidoo, Selisha and Chiyaka, Tinaye L. and Tshivhula, Happy and Singh, Shivani and Li, Yonghua and Warren, Robin M. and Hoal, Eileen G. and Schurr, Erwin and Clemente, Jose and Segal, Leopoldo N. and Möller, Marlo and Theron, Grant},
	month = apr,
	year = {2024},
	pmid = {38645218},
	pmcid = {PMC11030539},
	keywords = {HIV, Short chain fatty acids, latent tuberculosis, microbiota},
	pages = {rs.3.rs--4182285},
}

BACKGROUND: Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV. METHOD: Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST- negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2. RESULTS: No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were Faecalibacterium-, Blautia-, Gemmiger-, Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, Streptococcus-depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (Acidaminococcus-enrichment and Megamonas-, Alistipes-, and Paraprevotella-depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups. CONCLUSION: Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Faecalibacterium, Blautia, Gemmiger, Bacteriodes-enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.

@article{ndong_sima_advancing_2024,
	title = {Advancing pharmacogenetics research in {Africa}: the "{Project} {Africa} {GRADIENT}" initiative},
	volume = {29},
	issn = {1878-5832},
	shorttitle = {Advancing pharmacogenetics research in {Africa}},
	doi = {10.1016/j.drudis.2024.103939},
	language = {eng},
	number = {5},
	journal = {Drug Discovery Today},
	author = {Ndong Sima, Carene Anne Alene and Othman, Houcemeddine and Möller, Marlo and {Project Africa GRADIENT Consortium}},
	month = may,
	year = {2024},
	pmid = {38430965},
	keywords = {Africa, Biomedical Research, Humans, Pharmacogenetics, Project Africa GRADIENT, malaria, pharmacogenetics, precision medicine, tuberculosis},
	pages = {103939},
}

@article{croock_data_2024,
	title = {Data {Harmonization} {Guidelines} to {Combine} {Multi}-platform {Genomic} {Data} from {Admixed} {Populations} and {Boost} {Power} in {Genome}-{Wide} {Association} {Studies}},
	volume = {4},
	issn = {2691-1299},
	doi = {10.1002/cpz1.1055},
	abstract = {Data harmonization involves combining data from multiple independent sources and processing the data to produce one uniform dataset. Merging separate genotypes or whole-genome sequencing datasets has been proposed as a strategy to increase the statistical power of association tests by increasing the effective sample size. However, data harmonization is not a widely adopted strategy due to the difficulties with merging data (including confounding produced by batch effects and population stratification). Detailed data harmonization protocols are scarce and are often conflicting. Moreover, data harmonization protocols that accommodate samples of admixed ancestry are practically non-existent. Existing data harmonization procedures must be modified to ensure the heterogeneous ancestry of admixed individuals is incorporated into additional downstream analyses without confounding results. Here, we propose a set of guidelines for merging multi-platform genetic data from admixed samples that can be adopted by any investigator with elementary bioinformatics experience. We have applied these guidelines to aggregate 1544 tuberculosis (TB) case-control samples from six separate in-house datasets and conducted a genome-wide association study (GWAS) of TB susceptibility. The GWAS performed on the merged dataset had improved power over analyzing the datasets individually and produced summary statistics free from bias introduced by batch effects and population stratification. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Processing separate datasets comprising array genotype data Alternate Protocol 1: Processing separate datasets comprising array genotype and whole-genome sequencing data Alternate Protocol 2: Performing imputation using a local reference panel Basic Protocol 2: Merging separate datasets Basic Protocol 3: Ancestry inference using ADMIXTURE and RFMix Basic Protocol 4: Batch effect correction using pseudo-case-control comparisons.},
	language = {eng},
	number = {6},
	journal = {Current Protocols},
	author = {Croock, Dayna and Swart, Yolandi and Schurz, Haiko and Petersen, Desiree C. and Möller, Marlo and Uren, Caitlin},
	month = jun,
	year = {2024},
	pmid = {38837690},
	keywords = {Case-Control Studies, Genetic Predisposition to Disease, Genome-Wide Association Study, Genomics, Guidelines as Topic, Humans, Tuberculosis, ancestry inference, batch effects, data harmonization, genomic data, merging},
	pages = {e1055},
}

Data harmonization involves combining data from multiple independent sources and processing the data to produce one uniform dataset. Merging separate genotypes or whole-genome sequencing datasets has been proposed as a strategy to increase the statistical power of association tests by increasing the effective sample size. However, data harmonization is not a widely adopted strategy due to the difficulties with merging data (including confounding produced by batch effects and population stratification). Detailed data harmonization protocols are scarce and are often conflicting. Moreover, data harmonization protocols that accommodate samples of admixed ancestry are practically non-existent. Existing data harmonization procedures must be modified to ensure the heterogeneous ancestry of admixed individuals is incorporated into additional downstream analyses without confounding results. Here, we propose a set of guidelines for merging multi-platform genetic data from admixed samples that can be adopted by any investigator with elementary bioinformatics experience. We have applied these guidelines to aggregate 1544 tuberculosis (TB) case-control samples from six separate in-house datasets and conducted a genome-wide association study (GWAS) of TB susceptibility. The GWAS performed on the merged dataset had improved power over analyzing the datasets individually and produced summary statistics free from bias introduced by batch effects and population stratification. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Processing separate datasets comprising array genotype data Alternate Protocol 1: Processing separate datasets comprising array genotype and whole-genome sequencing data Alternate Protocol 2: Performing imputation using a local reference panel Basic Protocol 2: Merging separate datasets Basic Protocol 3: Ancestry inference using ADMIXTURE and RFMix Basic Protocol 4: Batch effect correction using pseudo-case-control comparisons.

@article{moller_power_2024,
	title = {The power of contemporary {African} {DNA}: {Exploring} models of human evolution and health in {Africa}},
	volume = {120},
	copyright = {Copyright (c) 2024},
	issn = {1996-7489},
	shorttitle = {The power of contemporary {African} {DNA}},
	url = {https://sajs.co.za/article/view/17145},
	doi = {10.17159/sajs.2024/17145},
	language = {en},
	number = {1/2},
	urldate = {2024-02-15},
	journal = {South African Journal of Science},
	author = {Möller, Marlo and Hoal, Eileen and Henn, Brenna M.},
	month = jan,
	year = {2024},
	note = {Number: 1/2},
	keywords = {African genomes, genetic diversity, health implications, human evolution, population genomics},
}

@article{ochieng_awareness_2024,
	title = {Awareness, experiences and perceptions regarding genetic testing and the return of genetic and genomics results in a hypothetical research context among patients in {Uganda}: a qualitative study},
	issn = {1473-4257},
	shorttitle = {Awareness, experiences and perceptions regarding genetic testing and the return of genetic and genomics results in a hypothetical research context among patients in {Uganda}},
	doi = {10.1136/jme-2022-108885},
	abstract = {BACKGROUND: Genetic testing presents unique ethical challenges for research and clinical practice, particularly in low-resource settings. To address such challenges, context-specific understanding of ethical, legal and social issues is essential. Return of genetics and genomics research (GGR) results remains an unresolved yet topical issue particularly in African settings that lack appropriate regulation and guidelines. Despite the need to understand what is contextually acceptable, there is a paucity of empirical research and literature on what constitutes appropriate practice with respect to GGR.The study assessed patients' awareness, experiences and perceptions regarding genetic testing and the return of GGR results in a hypothetical context.
METHODS: This cross-sectional study employed a qualitative exploratory approach. Respondents were patients attending the medical outpatient unit of Mulago National Hospital. Three deliberative focus group discussions involving 18 respondents were conducted. Data were analysed through thematic analysis.
RESULTS: Three main themes and several subthemes were identified. Most respondents were aware of genetic testing, supportive of GGR and receiving results. However, only a few had undergone genetic testing due to cost constraints. They articulated the need for adequate information and genetic counselling to inform decision-making. Privacy of results was important to respondents while others were willing to share results.
CONCLUSION: There was general awareness and support for GGR and the return of results. Stigmatisation emerged as a barrier to disclosure of results for some. Global health inequity impacts access and affordability of genetic testing and counselling in Africa and should be addressed as a matter of social justice.},
	language = {eng},
	journal = {Journal of Medical Ethics},
	author = {Ochieng, Joseph and Kwagala, Betty and Barugahare, John and Möller, Marlo and Moodley, Keymanthri},
	month = jan,
	year = {2024},
	pmid = {38290855},
	keywords = {Ethics},
	pages = {jme--2022--108885},
}

BACKGROUND: Genetic testing presents unique ethical challenges for research and clinical practice, particularly in low-resource settings. To address such challenges, context-specific understanding of ethical, legal and social issues is essential. Return of genetics and genomics research (GGR) results remains an unresolved yet topical issue particularly in African settings that lack appropriate regulation and guidelines. Despite the need to understand what is contextually acceptable, there is a paucity of empirical research and literature on what constitutes appropriate practice with respect to GGR.The study assessed patients' awareness, experiences and perceptions regarding genetic testing and the return of GGR results in a hypothetical context. METHODS: This cross-sectional study employed a qualitative exploratory approach. Respondents were patients attending the medical outpatient unit of Mulago National Hospital. Three deliberative focus group discussions involving 18 respondents were conducted. Data were analysed through thematic analysis. RESULTS: Three main themes and several subthemes were identified. Most respondents were aware of genetic testing, supportive of GGR and receiving results. However, only a few had undergone genetic testing due to cost constraints. They articulated the need for adequate information and genetic counselling to inform decision-making. Privacy of results was important to respondents while others were willing to share results. CONCLUSION: There was general awareness and support for GGR and the return of results. Stigmatisation emerged as a barrier to disclosure of results for some. Global health inequity impacts access and affordability of genetic testing and counselling in Africa and should be addressed as a matter of social justice.

@article{schurz_multi-ancestry_2024,
	title = {Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture},
	volume = {13},
	issn = {2050-084X},
	doi = {10.7554/eLife.84394},
	abstract = {The heritability of susceptibility to tuberculosis (TB) disease has been well recognized. Over 100 genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicate. We established the International Tuberculosis Host Genetics Consortium to perform a multi-ancestry meta-analysis of GWAS, including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h2 = 26.3\%, 95\% CI 23.7-29.0\%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p{\textless}5 × 10-8) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value=5.2 × 10-9) but failed to replicate variants previously associated with TB susceptibility. These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressure.},
	language = {eng},
	journal = {eLife},
	author = {Schurz, Haiko and Naranbhai, Vivek and Yates, Tom A. and Gilchrist, James J. and Parks, Tom and Dodd, Peter J. and Möller, Marlo and Hoal, Eileen G. and Morris, Andrew P. and Hill, Adrian V. S. and {International Tuberculosis Host Genetics Consortium}},
	month = jan,
	year = {2024},
	pmid = {38224499},
	pmcid = {PMC10789494},
	keywords = {GWAS, HLA, genetics, genomics, human, meta-analysis, multi-ancestry, tuberculosis},
	pages = {e84394},
}

The heritability of susceptibility to tuberculosis (TB) disease has been well recognized. Over 100 genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicate. We established the International Tuberculosis Host Genetics Consortium to perform a multi-ancestry meta-analysis of GWAS, including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h2 = 26.3%, 95% CI 23.7-29.0%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p\textless5 × 10-8) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value=5.2 × 10-9) but failed to replicate variants previously associated with TB susceptibility. These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressure.

@article{reynolds_persistence_2023,
	title = {Persistence of {Matrilocal} {Postmarital} {Residence} {Across} {Multiple} {Generations} in {Southern} {Africa}},
	volume = {34},
	issn = {1936-4776},
	doi = {10.1007/s12110-023-09452-4},
	abstract = {Factors such as subsistence turnover, warfare, or interaction between different groups can be major sources of cultural change in human populations. Global demographic shifts such as the transition to agriculture during the Neolithic and more recently the urbanization and globalization of the twentieth century have been major catalysts for cultural change. Here, we test whether cultural traits such as patri/matrilocality and postmarital migration persist in the face of social upheaval and gene flow during the past 150 years in postcolonial South Africa. The recent history of South Africa has seen major demographic shifts that resulted in the displacement and forced sedentism of indigenous Khoekhoe and San populations. During the expansion of the colonial frontier, the Khoe-San admixed with European colonists and enslaved individuals from West/Central Africa, Indonesia, and South Asia, introducing novel cultural norms. We conducted demographic interviews among Nama and Cederberg communities representing nearly 3,000 individuals across three generations. Despite the history of colonial expansion, and the subsequent incorporation of Khoe-San and Khoe-San-descendant communities into a colonial society with strong patrilocal norms, patrilocality is the least common postmarital residence pattern in our study populations today. Our results suggest that more recent forces of integration into the market economy are likely the primary drivers of change in the cultural traits examined in our study. Birthplace had a strong effect on an individual's odds of migration, distance moved, and postmarital residence form. These effects are at least partially explained by the population size of the birthplace. Our results suggest that market factors local to birthplaces are important drivers of residence decisions, although the frequency of matrilocal residence and a geographic and temporal cline in migration and residence patterns also indicate the persistence of some historic Khoe-San cultural traits in contemporary groups.},
	language = {eng},
	number = {2},
	journal = {Human Nature (Hawthorne, N.Y.)},
	author = {Reynolds, Austin W. and Grote, Mark N. and Myrick, Justin W. and Al-Hindi, Dana R. and Siford, Rebecca L. and Mastoras, Mira and Möller, Marlo and Henn, Brenna M.},
	month = jun,
	year = {2023},
	pmid = {37310564},
	pmcid = {PMC10353969},
	keywords = {Africa, Southern, Asia, Southern, Colonialism, Cultural evolution, Cultural persistence, Genetics, Population, Humans, Indonesia, Khoe-San, Postmarital residence patterns, Southern Africa},
	pages = {295--323},
}

Factors such as subsistence turnover, warfare, or interaction between different groups can be major sources of cultural change in human populations. Global demographic shifts such as the transition to agriculture during the Neolithic and more recently the urbanization and globalization of the twentieth century have been major catalysts for cultural change. Here, we test whether cultural traits such as patri/matrilocality and postmarital migration persist in the face of social upheaval and gene flow during the past 150 years in postcolonial South Africa. The recent history of South Africa has seen major demographic shifts that resulted in the displacement and forced sedentism of indigenous Khoekhoe and San populations. During the expansion of the colonial frontier, the Khoe-San admixed with European colonists and enslaved individuals from West/Central Africa, Indonesia, and South Asia, introducing novel cultural norms. We conducted demographic interviews among Nama and Cederberg communities representing nearly 3,000 individuals across three generations. Despite the history of colonial expansion, and the subsequent incorporation of Khoe-San and Khoe-San-descendant communities into a colonial society with strong patrilocal norms, patrilocality is the least common postmarital residence pattern in our study populations today. Our results suggest that more recent forces of integration into the market economy are likely the primary drivers of change in the cultural traits examined in our study. Birthplace had a strong effect on an individual's odds of migration, distance moved, and postmarital residence form. These effects are at least partially explained by the population size of the birthplace. Our results suggest that market factors local to birthplaces are important drivers of residence decisions, although the frequency of matrilocal residence and a geographic and temporal cline in migration and residence patterns also indicate the persistence of some historic Khoe-San cultural traits in contemporary groups.

@article{rikhotso_favourable_2023,
	title = {Favourable outcomes in {RR}-{TB} patients using {BPaL} and other {WHO}-recommended second-line anti-{TB} drugs},
	volume = {27},
	issn = {1815-7920},
	doi = {10.5588/ijtld.22.0649},
	abstract = {SETTING: According to reports in South Africa, treatment failure rates for rifampicin-resistant TB (RR-TB) are significant and below the WHO target of ≥70\%. HIV infection and the use of highly active antiretroviral therapy (HAART) influence how patients receiving anti-TB drugs respond to therapy. In the treatment of RR-TB, more recent medications, including bedaquiline, pretomanid and linezolid (BPaL), have shown promising results.OBJECTIVE: To assess treatment outcomes in RR-TB patients using BPaL and other second-line anti-TB drugs as recommended by the WHO in the South African population.DESIGN: The databases Medline, PubMed, Google Scholar and Embase were searched for studies between 2015 and 2022, which investigated BPaL outcomes in South Africa.RESULTS: Of the 27,259 participants, 21\% were on bedaquiline, 1\% were taking pretomanid and 9\% were taking linezolid as part of their background regimen. About 68\% of the patients were HIV-positive, with 59\% of them taking HAART.CONCLUSION: Overall, 66\% of patients taking BPaL drugs as part of their background regimen had favourable treatment outcomes. Additionally, patients with RR-TB who were HIV-positive and taking HAART while receiving BPaL drugs as part of a background regimen had improved treatment outcomes.},
	language = {eng},
	number = {8},
	journal = {The International Journal of Tuberculosis and Lung Disease: The Official Journal of the International Union Against Tuberculosis and Lung Disease},
	author = {Rikhotso, M. C. and Ledwaba, S. E. and Ngandu, J.-P. K. and Mavumengwana, V. and Kinnear, C. J. and Warren, R. and Potgieter, N. and Traoré, A. N.},
	month = aug,
	year = {2023},
	pmid = {37491748},
	pmcid = {PMC10365554},
	keywords = {Antitubercular Agents, Diarylquinolines, HIV Infections, HIV Seropositivity, Humans, Linezolid, Rifampin, Tuberculosis, Tuberculosis, Multidrug-Resistant, World Health Organization},
	pages = {599--605},
}

SETTING: According to reports in South Africa, treatment failure rates for rifampicin-resistant TB (RR-TB) are significant and below the WHO target of ≥70%. HIV infection and the use of highly active antiretroviral therapy (HAART) influence how patients receiving anti-TB drugs respond to therapy. In the treatment of RR-TB, more recent medications, including bedaquiline, pretomanid and linezolid (BPaL), have shown promising results.OBJECTIVE: To assess treatment outcomes in RR-TB patients using BPaL and other second-line anti-TB drugs as recommended by the WHO in the South African population.DESIGN: The databases Medline, PubMed, Google Scholar and Embase were searched for studies between 2015 and 2022, which investigated BPaL outcomes in South Africa.RESULTS: Of the 27,259 participants, 21% were on bedaquiline, 1% were taking pretomanid and 9% were taking linezolid as part of their background regimen. About 68% of the patients were HIV-positive, with 59% of them taking HAART.CONCLUSION: Overall, 66% of patients taking BPaL drugs as part of their background regimen had favourable treatment outcomes. Additionally, patients with RR-TB who were HIV-positive and taking HAART while receiving BPaL drugs as part of a background regimen had improved treatment outcomes.

@article{scholtz_challenges_2023,
	title = {Challenges of {Diagnosing} {Mendelian} {Susceptibility} to {Mycobacterial} {Diseases} in {South} {Africa}},
	volume = {24},
	issn = {1422-0067},
	doi = {10.3390/ijms241512119},
	abstract = {Inborn errors of immunity (IEI) are genetic disorders with extensive clinical presentations. They can range from increased susceptibility to infections to significant immune dysregulation that results in immune impairment. While IEI cases are individually rare, they collectively represent a significant burden of disease, especially in developing countries such as South Africa, where infectious diseases like tuberculosis (TB) are endemic. This is particularly alarming considering that certain high penetrance mutations that cause IEI, such as Mendelian Susceptibility to Mycobacterial Disease (MSMD), put individuals at higher risk for developing TB and other mycobacterial diseases. MSMD patients in South Africa often present with different clinical phenotypes than those from the developed world, therefore complicating the identification of disease-associated variants in this setting with a high burden of infectious diseases. The lack of available data, limited resources, as well as variability in clinical phenotype are the reasons many MSMD cases remain undetected or misdiagnosed. This article highlights the challenges in diagnosing MSMD in South Africa and proposes the use of transcriptomic analysis as a means of potentially identifying dysregulated pathways in affected African populations.},
	language = {eng},
	number = {15},
	journal = {International Journal of Molecular Sciences},
	author = {Scholtz, Denise and Jooste, Tracey and Möller, Marlo and van Coller, Ansia and Kinnear, Craig and Glanzmann, Brigitte},
	month = jul,
	year = {2023},
	pmid = {37569495},
	pmcid = {PMC10418440},
	keywords = {Genetic Predisposition to Disease, Humans, MSMD, Mutation, Mycobacterium Infections, NGS, Phenotype, South Africa, Tuberculosis, genes, inborn errors of immunity, transcriptomics, tuberculosis},
	pages = {12119},
}

Inborn errors of immunity (IEI) are genetic disorders with extensive clinical presentations. They can range from increased susceptibility to infections to significant immune dysregulation that results in immune impairment. While IEI cases are individually rare, they collectively represent a significant burden of disease, especially in developing countries such as South Africa, where infectious diseases like tuberculosis (TB) are endemic. This is particularly alarming considering that certain high penetrance mutations that cause IEI, such as Mendelian Susceptibility to Mycobacterial Disease (MSMD), put individuals at higher risk for developing TB and other mycobacterial diseases. MSMD patients in South Africa often present with different clinical phenotypes than those from the developed world, therefore complicating the identification of disease-associated variants in this setting with a high burden of infectious diseases. The lack of available data, limited resources, as well as variability in clinical phenotype are the reasons many MSMD cases remain undetected or misdiagnosed. This article highlights the challenges in diagnosing MSMD in South Africa and proposes the use of transcriptomic analysis as a means of potentially identifying dysregulated pathways in affected African populations.

@article{soh_prostate_2023,
	title = {Prostate cancer genetic risk and associated aggressive disease in men of {African} ancestry},
	volume = {14},
	issn = {2041-1723},
	doi = {10.1038/s41467-023-43726-w},
	abstract = {African ancestry is a significant risk factor for prostate cancer and advanced disease. Yet, genetic studies have largely been conducted outside the context of Sub-Saharan Africa, identifying 278 common risk variants contributing to a multiethnic polygenic risk score, with rare variants focused on a panel of roughly 20 pathogenic genes. Based on this knowledge, we are unable to determine polygenic risk or differentiate prostate cancer status interrogating whole genome data for 113 Black South African men. To further assess for potentially functional common and rare variant associations, here we interrogate 247,780 exomic variants for 798 Black South African men using a case versus control or aggressive versus non-aggressive study design. Notable genes of interest include HCP5, RFX6 and H3C1 for risk, and MKI67 and KLF5 for aggressive disease. Our study highlights the need for further inclusion across the African diaspora to establish African-relevant risk models aimed at reducing prostate cancer health disparities.},
	language = {eng},
	number = {1},
	journal = {Nature Communications},
	author = {Soh, Pamela X. Y. and Mmekwa, Naledi and Petersen, Desiree C. and Gheybi, Kazzem and van Zyl, Smit and Jiang, Jue and Patrick, Sean M. and Campbell, Raymond and Jaratlerdseri, Weerachai and Mutambirwa, Shingai B. A. and Bornman, M. S. Riana and Hayes, Vanessa M.},
	month = dec,
	year = {2023},
	pmid = {38052806},
	pmcid = {PMC10697980},
	keywords = {Black People, Genetic Predisposition to Disease, Humans, Male, Prostatic Neoplasms, Risk Factors},
	pages = {8037},
}

African ancestry is a significant risk factor for prostate cancer and advanced disease. Yet, genetic studies have largely been conducted outside the context of Sub-Saharan Africa, identifying 278 common risk variants contributing to a multiethnic polygenic risk score, with rare variants focused on a panel of roughly 20 pathogenic genes. Based on this knowledge, we are unable to determine polygenic risk or differentiate prostate cancer status interrogating whole genome data for 113 Black South African men. To further assess for potentially functional common and rare variant associations, here we interrogate 247,780 exomic variants for 798 Black South African men using a case versus control or aggressive versus non-aggressive study design. Notable genes of interest include HCP5, RFX6 and H3C1 for risk, and MKI67 and KLF5 for aggressive disease. Our study highlights the need for further inclusion across the African diaspora to establish African-relevant risk models aimed at reducing prostate cancer health disparities.

@article{ndong_sima_immunogenetics_2023,
	title = {The immunogenetics of tuberculosis ({TB}) susceptibility},
	volume = {75},
	issn = {1432-1211},
	doi = {10.1007/s00251-022-01290-5},
	abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of death due to a single bacterial agent, with approximately 10.6 million people developing active disease and 1.6 million deaths reported globally in 2021. After exposure, some, but not all individuals, will become infected with the bacillus. However, only a small fraction (approximately 5 to 15\%) of these individuals will progress to clinical disease, while in the remainder, infection is seemingly contained, and no signs of clinical disease are shown. Numerous observations have advocated for the role of host genetics in the display of these inter-individual variabilities in infection and disease phenotypes. In this review, we will provide an overview of the approaches, findings and limitations of the very first studies investigating TB genetic susceptibility to more recent studies. Lastly, we highlight several approaches, namely, linkage analyses and association studies, proposed to discover genetic markers associated with TB susceptibility. This review also explored the concept of polygenic risk scores (PRS) for prediction of tuberculosis susceptibility. The identification of host genetic factors influencing TB susceptibility/resistance is paramount to not only better understand the physiopathology of the disease but also explore more effective approaches for the development of both optimal preventive measures (i.e. better vaccines) and treatments of TB disease.},
	language = {eng},
	number = {3},
	journal = {Immunogenetics},
	author = {Ndong Sima, Carene Anne Alene and Smith, Dayna and Petersen, Desiree C. and Schurz, Haiko and Uren, Caitlin and Möller, Marlo},
	month = jun,
	year = {2023},
	pmid = {36512056},
	keywords = {Association studies, Genetic Predisposition to Disease, Genetic susceptibility, Humans, Immunogenetics, Infectious diseases, Meta-analysis, Mycobacterium tuberculosis, Polygenic risk scores, Risk Factors, Tuberculosis, Tuberculosis (TB)},
	pages = {215--230},
}

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of death due to a single bacterial agent, with approximately 10.6 million people developing active disease and 1.6 million deaths reported globally in 2021. After exposure, some, but not all individuals, will become infected with the bacillus. However, only a small fraction (approximately 5 to 15%) of these individuals will progress to clinical disease, while in the remainder, infection is seemingly contained, and no signs of clinical disease are shown. Numerous observations have advocated for the role of host genetics in the display of these inter-individual variabilities in infection and disease phenotypes. In this review, we will provide an overview of the approaches, findings and limitations of the very first studies investigating TB genetic susceptibility to more recent studies. Lastly, we highlight several approaches, namely, linkage analyses and association studies, proposed to discover genetic markers associated with TB susceptibility. This review also explored the concept of polygenic risk scores (PRS) for prediction of tuberculosis susceptibility. The identification of host genetic factors influencing TB susceptibility/resistance is paramount to not only better understand the physiopathology of the disease but also explore more effective approaches for the development of both optimal preventive measures (i.e. better vaccines) and treatments of TB disease.

@article{smith_epidemiological_2023,
	title = {Epidemiological correlates of overweight and obesity in the {Northern} {Cape} {Province}, {South} {Africa}},
	volume = {11},
	issn = {2167-8359},
	doi = {10.7717/peerj.14723},
	abstract = {BACKGROUND: In the past several decades, obesity has become a major public health issue worldwide, associated with increased rates of chronic disease and death. Like many developing nations, South Africa is experiencing rapid increases in BMI, and as a result, evidence-based preventive strategies are needed to reduce the increasing burden of overweight and obesity. This study aimed to determine the prevalence and predictors of overweight and obesity among a multi-ethnic cohort from the rural Northern Cape of South Africa.
METHODS: These data were collected as part of a tuberculosis (TB) case-control study, with 395 healthy control participants included in the final analysis. Overweight and obesity were defined according to WHO classification. Multivariate linear models of BMI were generated using sex, age, education level, smoking, alcohol consumption, and diabetes as predictor variables. We also used multivariable logistic regression analysis to assess the relationship of these factors with overweight and obesity.
RESULTS: The average BMI in our study cohort was 25.2. The prevalence of overweight was 18.0\% and the prevalence of obesity was 25.0\%. We find that female sex, being older, having more years of formal education, having diabetes, and being in a rural area are all positively associated with BMI in our dataset. Women (OR = 5.6, 95\% CI [3.3-9.8]), rural individuals (OR = 3.3, 95\% CI [1.9-6.0]), older individuals (OR = 1.02, 95\% CI [1-1.04]), and those with more years of education (OR = 1.2, 95\% CI [1.09-1.32]) were all more likely to be overweight or obese. Alternatively, being a smoker is negatively associated with BMI and decreases one's odds of being overweight or obese (OR = 0.28, 95\% CI [0.16-0.46]).
CONCLUSIONS: We observed a high prevalence of overweight and obesity in this study. The odds of being overweight and obese were higher in women, those living in rural areas, and those with more education, and increases with age. Community-based interventions to control obesity in this region should pay special attention to these groups.},
	language = {eng},
	journal = {PeerJ},
	author = {Smith, Mackenzie H. and Myrick, Justin W. and Oyageshio, Oshiomah and Uren, Caitlin and Saayman, Jamie and Boolay, Sihaam and van der Westhuizen, Lena and Werely, Cedric and Möller, Marlo and Henn, Brenna M. and Reynolds, Austin W.},
	year = {2023},
	pmid = {36788809},
	pmcid = {PMC9922494},
	keywords = {Body Mass Index, Case-Control Studies, Epidemiology, Female, Global health, Humans, Obesity, Overweight, Risk Factors, South Africa},
	pages = {e14723},
}

BACKGROUND: In the past several decades, obesity has become a major public health issue worldwide, associated with increased rates of chronic disease and death. Like many developing nations, South Africa is experiencing rapid increases in BMI, and as a result, evidence-based preventive strategies are needed to reduce the increasing burden of overweight and obesity. This study aimed to determine the prevalence and predictors of overweight and obesity among a multi-ethnic cohort from the rural Northern Cape of South Africa. METHODS: These data were collected as part of a tuberculosis (TB) case-control study, with 395 healthy control participants included in the final analysis. Overweight and obesity were defined according to WHO classification. Multivariate linear models of BMI were generated using sex, age, education level, smoking, alcohol consumption, and diabetes as predictor variables. We also used multivariable logistic regression analysis to assess the relationship of these factors with overweight and obesity. RESULTS: The average BMI in our study cohort was 25.2. The prevalence of overweight was 18.0% and the prevalence of obesity was 25.0%. We find that female sex, being older, having more years of formal education, having diabetes, and being in a rural area are all positively associated with BMI in our dataset. Women (OR = 5.6, 95% CI [3.3-9.8]), rural individuals (OR = 3.3, 95% CI [1.9-6.0]), older individuals (OR = 1.02, 95% CI [1-1.04]), and those with more years of education (OR = 1.2, 95% CI [1.09-1.32]) were all more likely to be overweight or obese. Alternatively, being a smoker is negatively associated with BMI and decreases one's odds of being overweight or obese (OR = 0.28, 95% CI [0.16-0.46]). CONCLUSIONS: We observed a high prevalence of overweight and obesity in this study. The odds of being overweight and obese were higher in women, those living in rural areas, and those with more education, and increases with age. Community-based interventions to control obesity in this region should pay special attention to these groups.

@article{oelofse_pharmacogenetics_2023,
	title = {Pharmacogenetics as part of recommended precision medicine for tuberculosis treatment in {African} populations: {Could} it be a reality?},
	volume = {16},
	issn = {1752-8062},
	shorttitle = {Pharmacogenetics as part of recommended precision medicine for tuberculosis treatment in {African} populations},
	doi = {10.1111/cts.13520},
	abstract = {Globally, tuberculosis (TB) is the second most lethal infectious disease. However, in sub-Saharan Africa, TB has the largest disease burden, with drug-resistant TB increasingly becoming a concern. The social and economic impact of TB should not be overlooked, especially in areas where healthcare systems are overburdened, and resources need to be allocated judiciously. The aim of pharmacogenetics (PGx) is to improve therapeutic response and to minimize adverse drug reactions by selecting the most optimal drug and dosage for the individual patient. Implementation of PGx into routine clinical care has been slow, especially in resource-limited settings, because of perceived high costs relative to uncertain benefit. Given the impact of TB on the disease and disability burden in these regions, a better understanding and optimization of TB treatment in understudied African populations is vital. The first weeks of treatment are the most crucial for treatment success, and a point-of-care pre-emptive PGx test could start patients on the most bactericidal and least toxic drug combination. This may potentially reduce the number of patients returning to clinical care and streamline the use of limited resources across the healthcare system. This review explores the status of TB PGx in Africa, the utility of existing TB PGx testing panels, and the economic feasibility in developing a clinically valuable, cost-effective, pre-emptive PGx test to guide optimized, new dosing regimens specifically for African population groups. TB is a disease of poverty, but investment in PGx research in African populations could ensure improved treatments and long-term cost savings.},
	language = {eng},
	number = {7},
	journal = {Clinical and Translational Science},
	author = {Oelofse, Carola and Ndong Sima, Carene Anne Alene and Möller, Marlo and Uren, Caitlin},
	month = jul,
	year = {2023},
	pmid = {37291686},
	pmcid = {PMC10339705},
	keywords = {Africa, Drug-Related Side Effects and Adverse Reactions, Humans, Pharmacogenetics, Precision Medicine, Tuberculosis},
	pages = {1101--1112},
}

Globally, tuberculosis (TB) is the second most lethal infectious disease. However, in sub-Saharan Africa, TB has the largest disease burden, with drug-resistant TB increasingly becoming a concern. The social and economic impact of TB should not be overlooked, especially in areas where healthcare systems are overburdened, and resources need to be allocated judiciously. The aim of pharmacogenetics (PGx) is to improve therapeutic response and to minimize adverse drug reactions by selecting the most optimal drug and dosage for the individual patient. Implementation of PGx into routine clinical care has been slow, especially in resource-limited settings, because of perceived high costs relative to uncertain benefit. Given the impact of TB on the disease and disability burden in these regions, a better understanding and optimization of TB treatment in understudied African populations is vital. The first weeks of treatment are the most crucial for treatment success, and a point-of-care pre-emptive PGx test could start patients on the most bactericidal and least toxic drug combination. This may potentially reduce the number of patients returning to clinical care and streamline the use of limited resources across the healthcare system. This review explores the status of TB PGx in Africa, the utility of existing TB PGx testing panels, and the economic feasibility in developing a clinically valuable, cost-effective, pre-emptive PGx test to guide optimized, new dosing regimens specifically for African population groups. TB is a disease of poverty, but investment in PGx research in African populations could ensure improved treatments and long-term cost savings.

@article{ragsdale_weakly_2023,
	title = {A weakly structured stem for human origins in {Africa}},
	volume = {617},
	issn = {1476-4687},
	doi = {10.1038/s41586-023-06055-y},
	abstract = {Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent1. Progress is hampered by a shortage of fossil and genomic data, as well as variability in previous estimates of divergence times1. Here we seek to discriminate among such models by considering linkage disequilibrium and diversity-based statistics, optimized for rapid, complex demographic inference2. We infer detailed demographic models for populations across Africa, including eastern and western representatives, and newly sequenced whole genomes from 44 Nama (Khoe-San) individuals from southern Africa. We infer a reticulated African population history in which present-day population structure dates back to Marine Isotope Stage 5. The earliest population divergence among contemporary populations occurred 120,000 to 135,000 years ago and was preceded by links between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years. Such weakly structured stem models explain patterns of polymorphism that had previously been attributed to contributions from archaic hominins in Africa2-7. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be genetically and morphologically similar, and that only an inferred 1-4\% of genetic differentiation among contemporary human populations can be attributed to genetic drift between stem populations. We show that model misspecification explains the variation in previous estimates of divergence times, and argue that studying a range of models is key to making robust inferences about deep history.},
	language = {eng},
	number = {7962},
	journal = {Nature},
	author = {Ragsdale, Aaron P. and Weaver, Timothy D. and Atkinson, Elizabeth G. and Hoal, Eileen G. and Möller, Marlo and Henn, Brenna M. and Gravel, Simon},
	month = may,
	year = {2023},
	pmid = {37198480},
	pmcid = {PMC10208968},
	keywords = {Africa, Fossils, Gene Flow, Genetic Drift, Genetic Introgression, Genetics, Population, Genome, Human, History, Ancient, Human Migration, Humans, Linkage Disequilibrium, Phylogeny, Polymorphism, Genetic, Time Factors},
	pages = {755--763},
}

Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent1. Progress is hampered by a shortage of fossil and genomic data, as well as variability in previous estimates of divergence times1. Here we seek to discriminate among such models by considering linkage disequilibrium and diversity-based statistics, optimized for rapid, complex demographic inference2. We infer detailed demographic models for populations across Africa, including eastern and western representatives, and newly sequenced whole genomes from 44 Nama (Khoe-San) individuals from southern Africa. We infer a reticulated African population history in which present-day population structure dates back to Marine Isotope Stage 5. The earliest population divergence among contemporary populations occurred 120,000 to 135,000 years ago and was preceded by links between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years. Such weakly structured stem models explain patterns of polymorphism that had previously been attributed to contributions from archaic hominins in Africa2-7. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be genetically and morphologically similar, and that only an inferred 1-4% of genetic differentiation among contemporary human populations can be attributed to genetic drift between stem populations. We show that model misspecification explains the variation in previous estimates of divergence times, and argue that studying a range of models is key to making robust inferences about deep history.

@article{kroon_neutrophil_2023,
	title = {Neutrophil extracellular trap formation and gene programs distinguish {TST}/{IGRA} sensitization outcomes among {Mycobacterium} tuberculosis exposed persons living with {HIV}},
	volume = {19},
	issn = {1553-7404},
	doi = {10.1371/journal.pgen.1010888},
	abstract = {Persons living with HIV (PLWH) have an increased risk for tuberculosis (TB). After prolonged and repeated exposure, some PLWH never develop TB and show no evidence of immune sensitization to Mycobacterium tuberculosis (Mtb) as defined by persistently negative tuberculin skin tests (TST) and interferon gamma release assays (IGRA). This group has been identified and defined as HIV+ persistently TB, tuberculin and IGRA negative (HITTIN). To investigate potential innate mechanisms unique to individuals with the HITTIN phenotype we compared their neutrophil Mtb infection response to that of PLWH, with no TB history, but who test persistently IGRA positive, and tuberculin positive (HIT). Neutrophil samples from 17 HITTIN (PMNHITTIN) and 11 HIT (PMNHIT) were isolated and infected with Mtb H37Rv for 1h and 6h. RNA was extracted and used for RNAseq analysis. Since there was no significant differential transcriptional response at 1h between infected PMNHITTIN and PMNHIT, we focused on the 6h timepoint. When compared to uninfected PMN, PMNHITTIN displayed 3106 significantly upregulated and 3548 significantly downregulated differentially expressed genes (DEGs) (absolute cutoff of a log2FC of 0.2, FDR {\textless} 0.05) whereas PMNHIT demonstrated 3816 significantly upregulated and 3794 significantly downregulated DEGs following 6h Mtb infection. Contrasting the log2FC 6h infection response to Mtb from PMNHITTIN against PMNHIT, 2285 genes showed significant differential response between the two groups. Overall PMNHITTIN had a lower fold change response to Mtb infection compared to PMNHIT. According to pathway enrichment, Apoptosis and NETosis were differentially regulated between HITTIN and HIT PMN responses after 6h Mtb infection. To corroborate the blunted NETosis transcriptional response measured among HITTIN, fluorescence microscopy revealed relatively lower neutrophil extracellular trap formation and cell loss in PMNHITTIN compared to PMNHIT, showing that PMNHITTIN have a distinct response to Mtb.},
	language = {eng},
	number = {8},
	journal = {PLoS genetics},
	author = {Kroon, Elouise E. and Correa-Macedo, Wilian and Evans, Rachel and Seeger, Allison and Engelbrecht, Lize and Kriel, Jurgen A. and Loos, Ben and Okugbeni, Naomi and Orlova, Marianna and Cassart, Pauline and Kinnear, Craig J. and Tromp, Gerard C. and Möller, Marlo and Wilkinson, Robert J. and Coussens, Anna K. and Schurr, Erwin and Hoal, Eileen G.},
	month = aug,
	year = {2023},
	pmid = {37616312},
	pmcid = {PMC10470897},
	keywords = {Extracellular Traps, HIV Infections, Humans, Interferon-gamma Release Tests, Mycobacterium tuberculosis, Tuberculin},
	pages = {e1010888},
}

Persons living with HIV (PLWH) have an increased risk for tuberculosis (TB). After prolonged and repeated exposure, some PLWH never develop TB and show no evidence of immune sensitization to Mycobacterium tuberculosis (Mtb) as defined by persistently negative tuberculin skin tests (TST) and interferon gamma release assays (IGRA). This group has been identified and defined as HIV+ persistently TB, tuberculin and IGRA negative (HITTIN). To investigate potential innate mechanisms unique to individuals with the HITTIN phenotype we compared their neutrophil Mtb infection response to that of PLWH, with no TB history, but who test persistently IGRA positive, and tuberculin positive (HIT). Neutrophil samples from 17 HITTIN (PMNHITTIN) and 11 HIT (PMNHIT) were isolated and infected with Mtb H37Rv for 1h and 6h. RNA was extracted and used for RNAseq analysis. Since there was no significant differential transcriptional response at 1h between infected PMNHITTIN and PMNHIT, we focused on the 6h timepoint. When compared to uninfected PMN, PMNHITTIN displayed 3106 significantly upregulated and 3548 significantly downregulated differentially expressed genes (DEGs) (absolute cutoff of a log2FC of 0.2, FDR \textless 0.05) whereas PMNHIT demonstrated 3816 significantly upregulated and 3794 significantly downregulated DEGs following 6h Mtb infection. Contrasting the log2FC 6h infection response to Mtb from PMNHITTIN against PMNHIT, 2285 genes showed significant differential response between the two groups. Overall PMNHITTIN had a lower fold change response to Mtb infection compared to PMNHIT. According to pathway enrichment, Apoptosis and NETosis were differentially regulated between HITTIN and HIT PMN responses after 6h Mtb infection. To corroborate the blunted NETosis transcriptional response measured among HITTIN, fluorescence microscopy revealed relatively lower neutrophil extracellular trap formation and cell loss in PMNHITTIN compared to PMNHIT, showing that PMNHITTIN have a distinct response to Mtb.

@article{ochieng_feedback_2022,
	title = {Feedback of individual genetic and genomics research results: {A} qualitative study involving grassroots communities in {Uganda}},
	volume = {17},
	issn = {1932-6203},
	shorttitle = {Feedback of individual genetic and genomics research results},
	doi = {10.1371/journal.pone.0267375},
	abstract = {BACKGROUND: Genetics and genomics research (GGR) is associated with several challenges including, but not limited to, methods and implications of sharing research findings with participants and their family members, issues of confidentiality, and ownership of data obtained from samples. Additionally, GGR holds significant potential risk for social and psychological harms. Considerable research has been conducted globally, and has advanced the debate on return of genetic and genomics testing results. However, such investigations are limited in the African setting, including Uganda where research ethics guidance on return of results is deficient or suboptimal at best. The objective of this study was to assess perceptions of grassroots communities on if and how feedback of individual genetics and genomics testing results should occur in Uganda with a view to improving ethics guidance.
METHODS: This was a cross-sectional study that employed a qualitative exploratory approach. Five deliberative focus group discussions (FGDs) were conducted with 42 participants from grassroots communities representing three major ethnic groupings. These were rural settings and the majority of participants were subsistence farmers with limited or no exposure to GGR. Data were analysed through thematic analysis, with both deductive and inductive approaches applied to interrogate predetermined themes and to identify any emerging themes. NVivo software (QSR international 2020) was used to support data analysis and illustrative quotes were extracted.
RESULTS: All the respondents were willing to participate in GGR and receive feedback of results conditional upon a health benefit. The main motivation was diagnostic and therapeutic benefits as well as facilitating future health planning. Thematic analysis identified four themes and several sub-themes including 1) the need-to-know health status 2) paternity information as a benefit and risk; 3) ethical considerations for feedback of findings and 4) extending feedback of genetics findings to family and community.
CONCLUSION: Participation in hypothetical GGR as well as feedback of results is acceptable to individuals in grassroots communities. However, the strong therapeutic and/or diagnostic misconception linked to GGR is concerning given that hopes for therapeutic and/or diagnostic benefit are unfounded. Viewing GGR as an opportunity to confirm or dispute paternity was another interesting perception. These findings carry profound implications for consent processes, genetic counselling and research ethics guidance. Privacy and confidentiality, benefits, risks as well as implications for sharing need to be considered for such feedback of results to be conducted appropriately.},
	language = {eng},
	number = {11},
	journal = {PloS One},
	author = {Ochieng, Joseph and Kwagala, Betty and Barugahare, John and Möller, Marlo and Moodley, Keymanthri},
	year = {2022},
	pmid = {36399445},
	pmcid = {PMC9674126},
	keywords = {Cross-Sectional Studies, Feedback, Genomics, Humans, Qualitative Research, Uganda, United States},
	pages = {e0267375},
}

BACKGROUND: Genetics and genomics research (GGR) is associated with several challenges including, but not limited to, methods and implications of sharing research findings with participants and their family members, issues of confidentiality, and ownership of data obtained from samples. Additionally, GGR holds significant potential risk for social and psychological harms. Considerable research has been conducted globally, and has advanced the debate on return of genetic and genomics testing results. However, such investigations are limited in the African setting, including Uganda where research ethics guidance on return of results is deficient or suboptimal at best. The objective of this study was to assess perceptions of grassroots communities on if and how feedback of individual genetics and genomics testing results should occur in Uganda with a view to improving ethics guidance. METHODS: This was a cross-sectional study that employed a qualitative exploratory approach. Five deliberative focus group discussions (FGDs) were conducted with 42 participants from grassroots communities representing three major ethnic groupings. These were rural settings and the majority of participants were subsistence farmers with limited or no exposure to GGR. Data were analysed through thematic analysis, with both deductive and inductive approaches applied to interrogate predetermined themes and to identify any emerging themes. NVivo software (QSR international 2020) was used to support data analysis and illustrative quotes were extracted. RESULTS: All the respondents were willing to participate in GGR and receive feedback of results conditional upon a health benefit. The main motivation was diagnostic and therapeutic benefits as well as facilitating future health planning. Thematic analysis identified four themes and several sub-themes including 1) the need-to-know health status 2) paternity information as a benefit and risk; 3) ethical considerations for feedback of findings and 4) extending feedback of genetics findings to family and community. CONCLUSION: Participation in hypothetical GGR as well as feedback of results is acceptable to individuals in grassroots communities. However, the strong therapeutic and/or diagnostic misconception linked to GGR is concerning given that hopes for therapeutic and/or diagnostic benefit are unfounded. Viewing GGR as an opportunity to confirm or dispute paternity was another interesting perception. These findings carry profound implications for consent processes, genetic counselling and research ethics guidance. Privacy and confidentiality, benefits, risks as well as implications for sharing need to be considered for such feedback of results to be conducted appropriately.

@article{petersen_african_2022,
	title = {African {Genetic} {Representation} in the {Context} of {SARS}-{CoV}-2 {Infection} and {COVID}-19 {Severity}},
	volume = {13},
	issn = {1664-8021},
	doi = {10.3389/fgene.2022.909117},
	language = {eng},
	journal = {Frontiers in Genetics},
	author = {Petersen, Desiree C. and Steyl, Chrystal and Scholtz, Denise and Baker, Bienyameen and Abdullah, Ibtisam and Uren, Caitlin and Möller, Marlo and {and for The COVID-19 Host Genetics Project}},
	year = {2022},
	pmid = {35620464},
	pmcid = {PMC9127354},
	keywords = {African genomics, COVID-19 genetic associations, COVID-19 severity, SARS-CoV-2 infection variability, genetic susceptibility, limited African data},
	pages = {909117},
}

@article{van_eeden_recombination_2022,
	title = {The recombination landscape of the {Khoe}-{San} likely represents the upper limits of recombination divergence in humans},
	volume = {23},
	issn = {1474-760X},
	doi = {10.1186/s13059-022-02744-5},
	abstract = {BACKGROUND: Recombination maps are  important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We infer the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derive a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesise that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups.
RESULTS: We show that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we use selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans.
CONCLUSIONS: Fine-scale differences in recombination can meaningfully alter the results of a selection scan. The recombination map we infer likely represents an upper bound on the extent of divergence we expect to see for a recombination map in humans and would be of interest to any researcher that wants to test the sensitivity of population genetic or GWAS analysis to recombination map input.},
	language = {eng},
	number = {1},
	journal = {Genome Biology},
	author = {van Eeden, Gerald and Uren, Caitlin and Pless, Evlyn and Mastoras, Mira and van der Spuy, Gian D. and Tromp, Gerard and Henn, Brenna M. and Möller, Marlo},
	month = aug,
	year = {2022},
	pmid = {35945619},
	pmcid = {PMC9361568},
	keywords = {Africa, Southern, Biological Evolution, Black People, Genetic map, Genetics, Population, Haplotypes, Humans, Khoe-San, Recombination map, Recombination rate, Selection scan},
	pages = {172},
}

BACKGROUND: Recombination maps are  important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We infer the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derive a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesise that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups. RESULTS: We show that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we use selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans. CONCLUSIONS: Fine-scale differences in recombination can meaningfully alter the results of a selection scan. The recombination map we infer likely represents an upper bound on the extent of divergence we expect to see for a recombination map in humans and would be of interest to any researcher that wants to test the sensitivity of population genetic or GWAS analysis to recombination map input.

@article{swart_gwas_2022,
	title = {{GWAS} in the southern {African} context},
	volume = {17},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0264657},
	abstract = {Researchers would generally adjust for the possible confounding effect of population structure by considering global ancestry proportions or top principle components. Alternatively, researchers would conduct admixture mapping to increase the power to detect variants with an ancestry effect. This is sufficient in simple admixture scenarios, however, populations from southern Africa can be complex multi-way admixed populations. Duan et al. (2018) first described local ancestry adjusted allelic (LAAA) analysis as a robust method for discovering association signals, while producing minimal false positive hits. Their simulation study, however, was limited to a two-way admixed population. Realizing that their findings might not translate to other admixture scenarios, we simulated a three- and five-way admixed population to compare the LAAA model to other models commonly used in genome-wide association studies (GWAS). We found that, given our admixture scenarios, the LAAA model identifies the most causal variants in most of the phenotypes we tested across both the three-way and five-way admixed populations. The LAAA model also produced a high number of false positive hits which was potentially caused by the ancestry effect size that we assumed. Considering the extent to which the various models tested differed in their results and considering that the source of a given association is unknown, we recommend that researchers use multiple GWAS models when analysing populations with complex ancestry.},
	language = {eng},
	number = {9},
	journal = {PloS One},
	author = {Swart, Yolandi and van Eeden, Gerald and Uren, Caitlin and van der Spuy, Gian and Tromp, Gerard and Möller, Marlo},
	year = {2022},
	pmid = {36170230},
	pmcid = {PMC9518849},
	keywords = {Alleles, Black People, Genetics, Population, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide},
	pages = {e0264657},
}

Researchers would generally adjust for the possible confounding effect of population structure by considering global ancestry proportions or top principle components. Alternatively, researchers would conduct admixture mapping to increase the power to detect variants with an ancestry effect. This is sufficient in simple admixture scenarios, however, populations from southern Africa can be complex multi-way admixed populations. Duan et al. (2018) first described local ancestry adjusted allelic (LAAA) analysis as a robust method for discovering association signals, while producing minimal false positive hits. Their simulation study, however, was limited to a two-way admixed population. Realizing that their findings might not translate to other admixture scenarios, we simulated a three- and five-way admixed population to compare the LAAA model to other models commonly used in genome-wide association studies (GWAS). We found that, given our admixture scenarios, the LAAA model identifies the most causal variants in most of the phenotypes we tested across both the three-way and five-way admixed populations. The LAAA model also produced a high number of false positive hits which was potentially caused by the ancestry effect size that we assumed. Considering the extent to which the various models tested differed in their results and considering that the source of a given association is unknown, we recommend that researchers use multiple GWAS models when analysing populations with complex ancestry.

@article{schurz_deciphering_2022,
	title = {Deciphering {Genetic} {Susceptibility} to {Tuberculous} {Meningitis}},
	volume = {13},
	issn = {1664-2295},
	doi = {10.3389/fneur.2022.820168},
	abstract = {Tuberculous meningitis (TBM) is the most severe form of extrapulmonary tuberculosis (TB) that arises when a caseating meningeal granuloma discharges its contents into the subarachnoid space. It accounts for {\textasciitilde}1\% of all disease caused by Mycobacterium tuberculosis and the age of peak incidence is from 2-4 years. The exact pathogenesis of TBM is still not fully understood and the mechanism(s) by which the bacilli initially invade the blood-brain-barrier are still to be elucidated. This study investigated the involvement of the host genome in TBM susceptibility, by considering common variants (minor allele frequency (MAF) {\textgreater}5\%) using microarray genotyping and rare variants (MAF {\textless}1\%) via exome sequencing. A total of 123 TBM cases, 400 pulmonary TB (pTB) cases and 477 healthy controls were genotyped on the MEGA array. A genome-wide association study (GWAS) comparing 114 TBM cases to 395 healthy controls showed no association with TBM susceptibility. A second analysis comparing 114 TBM cases to 382 pTB cases was conducted to investigate variants associated with different TB phenotypes. No significant associations were found with progression from pTB to TBM. Ten TBM cases and 10 healthy controls were exome sequenced. Gene set association tests SKAT-O and SKAT Common Rare were used to assess the association of rare SNPs and the cumulative effect of both common and rare SNPs with susceptibility to TBM, respectively. Ingenuity Pathway Analysis (IPA) of the top-hits of the SKAT-O analysis showed that NOD2 and CYP4F2 are both important in TBM pathogenesis and highlighted these as targets for future study. For the SKAT Common Rare analysis Centriolar Coiled-Coil Protein 110 (CCP110) was nominally associated (p = 5.89x10-6) with TBM susceptibility. In addition, several top-hit genes ascribed to the development of the central nervous system (CNS) and innate immune system regulation were identified. Exome sequencing and GWAS of our TBM cohort has identified a single previously undescribed association of CCP110 with TBM susceptibility. These results advance our understanding of TBM in terms of both variants and genes that influence susceptibility. In addition, several candidate genes involved in innate immunity have been identified for further genotypic and functional investigation.},
	language = {eng},
	journal = {Frontiers in Neurology},
	author = {Schurz, Haiko and Glanzmann, Brigitte and Bowker, Nicholas and van Toorn, Ronald and Solomons, Regan and Schoeman, Johan and van Helden, Paul D. and Kinnear, Craig J. and Hoal, Eileen G. and Möller, Marlo},
	year = {2022},
	pmid = {35401413},
	pmcid = {PMC8993185},
	keywords = {exome sequencing, genome-wide association study, microarray, pulmonary tuberculosis, tuberculous meningitis},
	pages = {820168},
}

Tuberculous meningitis (TBM) is the most severe form of extrapulmonary tuberculosis (TB) that arises when a caseating meningeal granuloma discharges its contents into the subarachnoid space. It accounts for ~1% of all disease caused by Mycobacterium tuberculosis and the age of peak incidence is from 2-4 years. The exact pathogenesis of TBM is still not fully understood and the mechanism(s) by which the bacilli initially invade the blood-brain-barrier are still to be elucidated. This study investigated the involvement of the host genome in TBM susceptibility, by considering common variants (minor allele frequency (MAF) \textgreater5%) using microarray genotyping and rare variants (MAF \textless1%) via exome sequencing. A total of 123 TBM cases, 400 pulmonary TB (pTB) cases and 477 healthy controls were genotyped on the MEGA array. A genome-wide association study (GWAS) comparing 114 TBM cases to 395 healthy controls showed no association with TBM susceptibility. A second analysis comparing 114 TBM cases to 382 pTB cases was conducted to investigate variants associated with different TB phenotypes. No significant associations were found with progression from pTB to TBM. Ten TBM cases and 10 healthy controls were exome sequenced. Gene set association tests SKAT-O and SKAT Common Rare were used to assess the association of rare SNPs and the cumulative effect of both common and rare SNPs with susceptibility to TBM, respectively. Ingenuity Pathway Analysis (IPA) of the top-hits of the SKAT-O analysis showed that NOD2 and CYP4F2 are both important in TBM pathogenesis and highlighted these as targets for future study. For the SKAT Common Rare analysis Centriolar Coiled-Coil Protein 110 (CCP110) was nominally associated (p = 5.89x10-6) with TBM susceptibility. In addition, several top-hit genes ascribed to the development of the central nervous system (CNS) and innate immune system regulation were identified. Exome sequencing and GWAS of our TBM cohort has identified a single previously undescribed association of CCP110 with TBM susceptibility. These results advance our understanding of TBM in terms of both variants and genes that influence susceptibility. In addition, several candidate genes involved in innate immunity have been identified for further genotypic and functional investigation.

@article{meiring_african_2022,
	title = {African wild dogs ({Lycaon} pictus) from the {Kruger} {National} {Park}, {South} {Africa} are currently not inbred but have low genomic diversity},
	volume = {12},
	issn = {2045-2322},
	doi = {10.1038/s41598-022-19025-7},
	abstract = {African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.},
	language = {eng},
	number = {1},
	journal = {Scientific Reports},
	author = {Meiring, Christina and Schurz, Haiko and van Helden, Paul and Hoal, Eileen and Tromp, Gerard and Kinnear, Craig and Kleynhans, Léanie and Glanzmann, Brigitte and van Schalkwyk, Louis and Miller, Michele and Möller, Marlo},
	month = sep,
	year = {2022},
	pmid = {36056068},
	pmcid = {PMC9440078},
	keywords = {Animals, Canidae, Endangered Species, Genomics, Humans, Parks, Recreational, South Africa},
	pages = {14979},
}

African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.

@article{engelbrecht_clinical_2021,
	title = {Clinical {Utility} of {Whole} {Exome} {Sequencing} and {Targeted} {Panels} for the {Identification} of {Inborn} {Errors} of {Immunity} in a {Resource}-{Constrained} {Setting}},
	volume = {12},
	issn = {1664-3224},
	doi = {10.3389/fimmu.2021.665621},
	abstract = {Primary immunodeficiency disorders (PIDs) are inborn errors of immunity (IEI) that cause immune system impairment. To date, more than 400 single-gene IEI have been well defined. The advent of next generation sequencing (NGS) technologies has improved clinical diagnosis and allowed for discovery of novel genes and variants associated with IEI. Molecular diagnosis provides clear clinical benefits for patients by altering management, enabling access to certain treatments and facilitates genetic counselling. Here we report on an 8-year experience using two different NGS technologies, namely research-based WES and targeted gene panels, in patients with suspected IEI in the South African healthcare system. A total of 52 patients' had WES only, 26 had a targeted gene panel only, and 2 had both panel and WES. Overall, a molecular diagnosis was achieved in 30\% (24/80) of patients. Clinical management was significantly altered in 67\% of patients following molecular results. All 24 families with a molecular diagnosis received more accurate genetic counselling and family cascade testing. Results highlight the clinical value of expanded genetic testing in IEI and its relevance to understanding the genetic and clinical spectrum of the IEI-related disorders in Africa. Detection rates under 40\% illustrate the complexity and heterogeneity of these disorders, especially in an African population, thus highlighting the need for expanded genomic testing and research to further elucidate this.},
	language = {eng},
	journal = {Frontiers in Immunology},
	author = {Engelbrecht, Clair and Urban, Michael and Schoeman, Mardelle and Paarwater, Brandon and van Coller, Ansia and Abraham, Deepthi Raju and Cornelissen, Helena and Glashoff, Richard and Esser, Monika and Möller, Marlo and Kinnear, Craig and Glanzmann, Brigitte},
	year = {2021},
	pmid = {34093558},
	pmcid = {PMC8176954},
	keywords = {Adolescent, Child, Child, Preschool, Exome Sequencing, Family Health, Female, Genetic Diseases, Inborn, High-Throughput Nucleotide Sequencing, Humans, Immunity, Infant, Infant, Newborn, Male, Primary Immunodeficiency Diseases, South Africa, genetic variants, inborn errors of immunity, targeted sequencing, whole exome sequencing},
	pages = {665621},
}

Primary immunodeficiency disorders (PIDs) are inborn errors of immunity (IEI) that cause immune system impairment. To date, more than 400 single-gene IEI have been well defined. The advent of next generation sequencing (NGS) technologies has improved clinical diagnosis and allowed for discovery of novel genes and variants associated with IEI. Molecular diagnosis provides clear clinical benefits for patients by altering management, enabling access to certain treatments and facilitates genetic counselling. Here we report on an 8-year experience using two different NGS technologies, namely research-based WES and targeted gene panels, in patients with suspected IEI in the South African healthcare system. A total of 52 patients' had WES only, 26 had a targeted gene panel only, and 2 had both panel and WES. Overall, a molecular diagnosis was achieved in 30% (24/80) of patients. Clinical management was significantly altered in 67% of patients following molecular results. All 24 families with a molecular diagnosis received more accurate genetic counselling and family cascade testing. Results highlight the clinical value of expanded genetic testing in IEI and its relevance to understanding the genetic and clinical spectrum of the IEI-related disorders in Africa. Detection rates under 40% illustrate the complexity and heterogeneity of these disorders, especially in an African population, thus highlighting the need for expanded genomic testing and research to further elucidate this.

@article{van_coller_phenotypic_2021,
	title = {Phenotypic and immune functional profiling of patients with suspected {Mendelian} {Susceptibility} to {Mycobacterial} {Disease} in {South} {Africa}},
	volume = {22},
	issn = {1471-2172},
	doi = {10.1186/s12865-021-00452-6},
	abstract = {BACKGROUND: Mendelian Susceptibility to Mycobacterial Disease (MSMD) is a primary immunodeficiency (PID) characterised by a predisposition to infection by weakly-pathogenic mycobacteria. In countries with a high prevalence of tuberculosis (TB), individuals with MSMD are also prone to infections by Mycobacterium tuberculosis. Several MSMD-associated genes have been described, all resulting in a disruption of IL-12 and IFN-γ cytokine axis, which is essential for control of mycobacterial infections. An accurate molecular diagnosis, confirmed by phenotypic and functional immune investigations, is essential to ensure that the patient receives optimal treatment and prophylaxis for infections. The aim of this study was to implement a set of functional assays to assess the integrity of the IL-12-IFN-γ cytokine pathways in patients presenting with severe, persistent, unusual and/or recurrent TB, mycobacterial infections or other clinical MSMD-defining infections such as Salmonella.
METHODS: Blood was collected for subsequent PBMC isolation from 16 participants with MSMD-like clinical phenotypes. A set of flow cytometry (phenotype and signalling integrity) and ELISA-based (cytokine production) functional assays were implemented to assess the integrity of the IL-12-IFN-γ pathway.
RESULTS: The combination of the three assays for the assessment of the integrity of the IL-12-IFN-γ pathway was successful in identifying immune deficits in the IL-12-IFN-γ pathway in all of the participants included in this study.
CONCLUSIONS: The data presented here emphasise the importance of investigating PID and TB susceptibility in TB endemic regions such as South Africa as MSMD and other previously described PIDs relating to TB susceptibility may present differently in such regions. It is therefore important to have access to in vitro functional investigations to better understand the immune function of these individuals. Although functional assays alone are unlikely to always provide a clear diagnosis, they do give an overview of the integrity of the IL-12-IFN-γ pathway. It would be beneficial to apply these assays routinely to patients with suspected PID relating to mycobacterial susceptibility. A molecular diagnosis with confirmed functional impairment paves the way for targeted treatment and improved disease management options for these patients.},
	language = {eng},
	number = {1},
	journal = {BMC immunology},
	author = {van Coller, Ansia and Glanzmann, Brigitte and Cornelissen, Helena and Möller, Marlo and Kinnear, Craig and Esser, Monika and Glashoff, Richard},
	month = sep,
	year = {2021},
	pmid = {34517836},
	pmcid = {PMC8436520},
	keywords = {Child, Child, Preschool, Disease Susceptibility, Female, Humans, IFN-γ-IL-12 cytokine pathways, Immune profiling, Infant, Interferon-gamma, Interleukin-12, Male, Mendelian Randomization Analysis, Mendelian Susceptibility to Mycobacterial Disease, Mycobacterium Infections, Mycobacterium tuberculosis, Phenotype, Signal Transduction, South Africa, Tuberculosis, Young Adult},
	pages = {62},
}

BACKGROUND: Mendelian Susceptibility to Mycobacterial Disease (MSMD) is a primary immunodeficiency (PID) characterised by a predisposition to infection by weakly-pathogenic mycobacteria. In countries with a high prevalence of tuberculosis (TB), individuals with MSMD are also prone to infections by Mycobacterium tuberculosis. Several MSMD-associated genes have been described, all resulting in a disruption of IL-12 and IFN-γ cytokine axis, which is essential for control of mycobacterial infections. An accurate molecular diagnosis, confirmed by phenotypic and functional immune investigations, is essential to ensure that the patient receives optimal treatment and prophylaxis for infections. The aim of this study was to implement a set of functional assays to assess the integrity of the IL-12-IFN-γ cytokine pathways in patients presenting with severe, persistent, unusual and/or recurrent TB, mycobacterial infections or other clinical MSMD-defining infections such as Salmonella. METHODS: Blood was collected for subsequent PBMC isolation from 16 participants with MSMD-like clinical phenotypes. A set of flow cytometry (phenotype and signalling integrity) and ELISA-based (cytokine production) functional assays were implemented to assess the integrity of the IL-12-IFN-γ pathway. RESULTS: The combination of the three assays for the assessment of the integrity of the IL-12-IFN-γ pathway was successful in identifying immune deficits in the IL-12-IFN-γ pathway in all of the participants included in this study. CONCLUSIONS: The data presented here emphasise the importance of investigating PID and TB susceptibility in TB endemic regions such as South Africa as MSMD and other previously described PIDs relating to TB susceptibility may present differently in such regions. It is therefore important to have access to in vitro functional investigations to better understand the immune function of these individuals. Although functional assays alone are unlikely to always provide a clear diagnosis, they do give an overview of the integrity of the IL-12-IFN-γ pathway. It would be beneficial to apply these assays routinely to patients with suspected PID relating to mycobacterial susceptibility. A molecular diagnosis with confirmed functional impairment paves the way for targeted treatment and improved disease management options for these patients.

@article{cornelissen_mendelian_2021,
	title = {Mendelian susceptibility to mycobacterial disease in tuberculosis-hyperendemic {South} {Africa}},
	volume = {111},
	issn = {2078-5135},
	doi = {10.7196/SAMJ.2021.v111i10.15341},
	abstract = {BACKGROUND: Severe infections in the absence of secondary immunodeficiency can alert clinicians to single-gene inborn errors of immunity/primary immunodeficiency disorders (PIDDs). Mendelian susceptibility to mycobacterial disease (MSMD) is characterised by selective susceptibility to mycobacterial infections due to inborn errors in the interleukin 12-interferon gamma pathway. The South African (SA) burden of hyperendemic tuberculosis (TB) infection provides an interesting context for the study of MSMD.
OBJECTIVES: To evaluate whether severe, persistent, unusual or recurrent (SPUR) definitions of TB can be applied in the context of MSMD in SA.
METHODS: This study is a retrospective review of an SA PIDD cohort. Patients aged 0 - 15 years with SPUR TB infections, assessed between 2013 and 2018, were identified using a proposed algorithm. HIV infection or other secondary causes for immunodeficiency were excluded. Basic investigations, then focused immunophenotyping and next-generation sequencing, were performed.
RESULTS: A total of 20 patients with a clinical diagnosis of MSMD were identified. A further two, forming part of a family cohort, had pathogenic variants but remain asymptomatic. Infection with Mycobacterium tuberculosis complex predominated (64\%), while 27\% had BCG infection or non-tuberculous mycobacteria (NTM) infection. Molecular analysis revealed pathogenic variants in 41\% of patients with SPUR mycobacterial infection, mainly in those with BCG/NTM infection.
CONCLUSIONS: In the SA paediatric population, SPUR TB infections, particularly BCG/NTM, in the absence of secondary immunodeficiency, can alert to possible MSMD. The molecular diagnosis is pivotal, guiding disease classification and influencing clinical approach and management. The diagnosis is complex and requires a multidisciplinary approach with close collaboration between clinical immunologists, bioinformaticians, immunologists, clinical geneticists and genetic counsellors.},
	language = {eng},
	number = {10},
	journal = {South African Medical Journal = Suid-Afrikaanse Tydskrif Vir Geneeskunde},
	author = {Cornelissen, H. M. and Glanzmann, B. and Van Coller, A. and Engelbrecht, C. and Abraham, D. R. and Reddy, K. and Möller, M. and Kinnear, C. and Glashoff, R. H. and Esser, M.},
	month = oct,
	year = {2021},
	pmid = {34949297},
	keywords = {Adolescent, Algorithms, Child, Child, Preschool, Female, Genetic Predisposition to Disease, High-Throughput Nucleotide Sequencing, Humans, Immunophenotyping, Infant, Infant, Newborn, Interleukin-12, Male, Mycobacterium Infections, Retrospective Studies, South Africa},
	pages = {998--1005},
}

BACKGROUND: Severe infections in the absence of secondary immunodeficiency can alert clinicians to single-gene inborn errors of immunity/primary immunodeficiency disorders (PIDDs). Mendelian susceptibility to mycobacterial disease (MSMD) is characterised by selective susceptibility to mycobacterial infections due to inborn errors in the interleukin 12-interferon gamma pathway. The South African (SA) burden of hyperendemic tuberculosis (TB) infection provides an interesting context for the study of MSMD. OBJECTIVES: To evaluate whether severe, persistent, unusual or recurrent (SPUR) definitions of TB can be applied in the context of MSMD in SA. METHODS: This study is a retrospective review of an SA PIDD cohort. Patients aged 0 - 15 years with SPUR TB infections, assessed between 2013 and 2018, were identified using a proposed algorithm. HIV infection or other secondary causes for immunodeficiency were excluded. Basic investigations, then focused immunophenotyping and next-generation sequencing, were performed. RESULTS: A total of 20 patients with a clinical diagnosis of MSMD were identified. A further two, forming part of a family cohort, had pathogenic variants but remain asymptomatic. Infection with Mycobacterium tuberculosis complex predominated (64%), while 27% had BCG infection or non-tuberculous mycobacteria (NTM) infection. Molecular analysis revealed pathogenic variants in 41% of patients with SPUR mycobacterial infection, mainly in those with BCG/NTM infection. CONCLUSIONS: In the SA paediatric population, SPUR TB infections, particularly BCG/NTM, in the absence of secondary immunodeficiency, can alert to possible MSMD. The molecular diagnosis is pivotal, guiding disease classification and influencing clinical approach and management. The diagnosis is complex and requires a multidisciplinary approach with close collaboration between clinical immunologists, bioinformaticians, immunologists, clinical geneticists and genetic counsellors.

@article{van_eeden_local_2021,
	title = {Local ancestry inference in heterogeneous populations-{Are} recent recombination events more relevant?},
	volume = {22},
	issn = {1477-4054},
	doi = {10.1093/bib/bbab300},
	abstract = {To date, numerous software tools have been developed to infer recombination maps. Many of these software tools infer the recombination rate from linkage disequilibrium, and therefore they infer recombination many generations into the past. Other recently developed methods rely on the inference of recent recombination events to determine the recombination rate, such as identity by descent- and local ancestry inference (LAI)-based tools. Methods that mainly use recent recombination events to infer the recombination rate might be more relevant for certain analyses like LAI. We therefore describe a protocol for creating high-resolution, population-specific recombination maps using methods that mainly use recent recombination events and a method that uses recent and distant recombination events for recombination rate inference. Subsequently, we compared the effect of using maps inferred by these two paradigms on LAI accuracy.},
	language = {eng},
	number = {6},
	journal = {Briefings in Bioinformatics},
	author = {van Eeden, Gerald and Uren, Caitlin and van der Spuy, Gian and Tromp, Gerard and Möller, Marlo},
	month = nov,
	year = {2021},
	pmid = {34343255},
	keywords = {Genetics, Population, Humans, Recombination, Genetic, Software, complex ancestry, genetic map, recombination, recombination inference methods},
	pages = {bbab300},
}

To date, numerous software tools have been developed to infer recombination maps. Many of these software tools infer the recombination rate from linkage disequilibrium, and therefore they infer recombination many generations into the past. Other recently developed methods rely on the inference of recent recombination events to determine the recombination rate, such as identity by descent- and local ancestry inference (LAI)-based tools. Methods that mainly use recent recombination events to infer the recombination rate might be more relevant for certain analyses like LAI. We therefore describe a protocol for creating high-resolution, population-specific recombination maps using methods that mainly use recent recombination events and a method that uses recent and distant recombination events for recombination rate inference. Subsequently, we compared the effect of using maps inferred by these two paradigms on LAI accuracy.

@article{muller_multi-phenotype_2021,
	title = {A multi-phenotype genome-wide association study of clades causing tuberculosis in a {Ghanaian}- and {South} {African} cohort},
	volume = {113},
	issn = {1089-8646},
	doi = {10.1016/j.ygeno.2021.04.024},
	abstract = {Despite decades of research and advancements in diagnostics and treatment, tuberculosis remains a major public health concern. New computational methods are needed to interrogate the intersection of host- and bacterial genomes. Paired host genotype datum and infecting bacterial isolate information were analysed for associations using a multinomial logistic regression framework implemented in SNPTest. A cohort of 853 admixed South African participants and a Ghanaian cohort of 1359 participants were included. Two directly genotyped variants, namely rs529920 and rs41472447, were identified in the Ghanaian cohort as being statistically significantly associated with risk for infection with strains of different members of the MTBC. Thus, a multinomial logistic regression using paired host-pathogen data may prove valuable for investigating the complex relationships driving infectious disease.},
	language = {eng},
	number = {4},
	journal = {Genomics},
	author = {Müller, Stephanie J. and Schurz, Haiko and Tromp, Gerard and van der Spuy, Gian D. and Hoal, Eileen G. and van Helden, Paul D. and Owusu-Dabo, Ellis and Meyer, Christian G. and Muntau, Birgit and Thye, Thorsten and Niemann, Stefan and Warren, Robin M. and Streicher, Elizabeth and Möller, Marlo and Kinnear, Craig},
	month = jul,
	year = {2021},
	pmid = {33862184},
	keywords = {Genome-Wide Association Study, Genotype, Ghana, Humans, Imputation, Multi-phenotype GWAS, Mycobacterium tuberculosis, Mycobacterium tuberculosis complex, Phenotype, South Africa, Tuberculosis},
	pages = {1802--1815},
}

Despite decades of research and advancements in diagnostics and treatment, tuberculosis remains a major public health concern. New computational methods are needed to interrogate the intersection of host- and bacterial genomes. Paired host genotype datum and infecting bacterial isolate information were analysed for associations using a multinomial logistic regression framework implemented in SNPTest. A cohort of 853 admixed South African participants and a Ghanaian cohort of 1359 participants were included. Two directly genotyped variants, namely rs529920 and rs41472447, were identified in the Ghanaian cohort as being statistically significantly associated with risk for infection with strains of different members of the MTBC. Thus, a multinomial logistic regression using paired host-pathogen data may prove valuable for investigating the complex relationships driving infectious disease.

@article{swart_local_2021,
	title = {Local {Ancestry} {Adjusted} {Allelic} {Association} {Analysis} {Robustly} {Captures} {Tuberculosis} {Susceptibility} {Loci}},
	volume = {12},
	issn = {1664-8021},
	doi = {10.3389/fgene.2021.716558},
	abstract = {Pulmonary tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease. The risk of developing active TB is in part determined by host genetic factors. Most genetic studies investigating TB susceptibility fail to replicate association signals particularly across diverse populations. South African populations arose because of multi-wave genetic admixture from the indigenous KhoeSan, Bantu-speaking Africans, Europeans, Southeast Asian-and East Asian populations. This has led to complex genetic admixture with heterogenous patterns of linkage disequilibrium and associated traits. As a result, precise estimation of both global and local ancestry is required to prevent both false positive and false-negative associations. Here, 820 individuals from South Africa were genotyped on the SNP-dense Illumina Multi-Ethnic Genotyping Array (∼1.7M SNPs) followed by local and global ancestry inference using RFMix. Local ancestry adjusted allelic association (LAAA) models were utilized owing to the extensive genetic heterogeneity present in this population. Hence, an interaction term, comprising the identification of the minor allele that corresponds to the ancestry present at the specific locus under investigation, was included as a covariate. One SNP (rs28647531) located on chromosome 4q22 was significantly associated with TB susceptibility and displayed a SNP minor allelic effect (G allele, frequency = 0.204) whilst correcting for local ancestry for Bantu-speaking African ancestry (p-value = 5.518 × 10-7; OR = 3.065; SE = 0.224). Although no other variants passed the significant threshold, clear differences were observed between the lead variants identified for each ancestry. Furthermore, the LAAA model robustly captured the source of association signals in multi-way admixed individuals from South Africa and allowed the identification of ancestry-specific disease risk alleles associated with TB susceptibility that have previously been missed.},
	language = {eng},
	journal = {Frontiers in Genetics},
	author = {Swart, Yolandi and Uren, Caitlin and van Helden, Paul D. and Hoal, Eileen G. and Möller, Marlo},
	year = {2021},
	pmid = {34721521},
	pmcid = {PMC8554120},
	keywords = {South Africa, TB susceptibility, admixture mapping, ancestry-specific risk alleles, host genetics, local ancestry adjustments, population genetics},
	pages = {716558},
}

Pulmonary tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease. The risk of developing active TB is in part determined by host genetic factors. Most genetic studies investigating TB susceptibility fail to replicate association signals particularly across diverse populations. South African populations arose because of multi-wave genetic admixture from the indigenous KhoeSan, Bantu-speaking Africans, Europeans, Southeast Asian-and East Asian populations. This has led to complex genetic admixture with heterogenous patterns of linkage disequilibrium and associated traits. As a result, precise estimation of both global and local ancestry is required to prevent both false positive and false-negative associations. Here, 820 individuals from South Africa were genotyped on the SNP-dense Illumina Multi-Ethnic Genotyping Array (∼1.7M SNPs) followed by local and global ancestry inference using RFMix. Local ancestry adjusted allelic association (LAAA) models were utilized owing to the extensive genetic heterogeneity present in this population. Hence, an interaction term, comprising the identification of the minor allele that corresponds to the ancestry present at the specific locus under investigation, was included as a covariate. One SNP (rs28647531) located on chromosome 4q22 was significantly associated with TB susceptibility and displayed a SNP minor allelic effect (G allele, frequency = 0.204) whilst correcting for local ancestry for Bantu-speaking African ancestry (p-value = 5.518 × 10-7; OR = 3.065; SE = 0.224). Although no other variants passed the significant threshold, clear differences were observed between the lead variants identified for each ancestry. Furthermore, the LAAA model robustly captured the source of association signals in multi-way admixed individuals from South Africa and allowed the identification of ancestry-specific disease risk alleles associated with TB susceptibility that have previously been missed.

@article{chileshe_cytokine_2021,
	title = {Cytokine biomarker discovery in the white rhinoceros ({Ceratotherium} simum)},
	volume = {232},
	issn = {1873-2534},
	doi = {10.1016/j.vetimm.2020.110168},
	abstract = {Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis) infection, disrupts conservation programs of threatened species such as the white rhinoceros (Ceratotherium simum). Interferon gamma release assays have been developed for the diagnosis of M. bovis infection in rhinoceros, however, the discovery of additional diagnostic biomarkers might improve the accuracy of case detection. The aim of this pilot study was therefore to evaluate a novel unbiased approach to candidate biomarker discovery and preliminary validation. Whole blood samples from twelve white rhinoceros were incubated in Nil and TB antigen tubes of the QuantiFERON® TB Gold (In-Tube) system after which RNA was extracted and reverse transcribed. Using the equine RT2 profiler PCR array, relative gene expression analysis of samples from two immune sensitized rhinoceros identified CCL4, CCL8, IL23A, LTA, NODAL, TNF, CSF3, CXCL10 and GPI as upregulated in response to antigen stimulation. Novel gene expression assays (GEAs) were designed for selected candidates, i.e. CCL4, CXCL10 and IFNG, and analysis of QFT-processed samples showed the CXCL10 GEA could distinguish between five M. bovis-infected and five uninfected rhinoceros. These findings confirm the value of the equine RT2 profiler PCR array as a useful tool for screening biomarkers for the diagnosis of M. bovis infection in rhinoceros.},
	language = {eng},
	journal = {Veterinary Immunology and Immunopathology},
	author = {Chileshe, Josephine and Kerr, Tanya J. and Kinnear, Craig and Buss, Peter E. and van Helden, Paul D. and Warren, Robin M. and Miller, Michele A. and Parsons, Sven D. C.},
	month = feb,
	year = {2021},
	pmid = {33373875},
	keywords = {CCL4, CXCL10, Cytokines, Gene expression, Mycobacterium bovis, White rhinoceros (Ceratotherium simum)},
	pages = {110168},
}

Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis) infection, disrupts conservation programs of threatened species such as the white rhinoceros (Ceratotherium simum). Interferon gamma release assays have been developed for the diagnosis of M. bovis infection in rhinoceros, however, the discovery of additional diagnostic biomarkers might improve the accuracy of case detection. The aim of this pilot study was therefore to evaluate a novel unbiased approach to candidate biomarker discovery and preliminary validation. Whole blood samples from twelve white rhinoceros were incubated in Nil and TB antigen tubes of the QuantiFERON® TB Gold (In-Tube) system after which RNA was extracted and reverse transcribed. Using the equine RT2 profiler PCR array, relative gene expression analysis of samples from two immune sensitized rhinoceros identified CCL4, CCL8, IL23A, LTA, NODAL, TNF, CSF3, CXCL10 and GPI as upregulated in response to antigen stimulation. Novel gene expression assays (GEAs) were designed for selected candidates, i.e. CCL4, CXCL10 and IFNG, and analysis of QFT-processed samples showed the CXCL10 GEA could distinguish between five M. bovis-infected and five uninfected rhinoceros. These findings confirm the value of the equine RT2 profiler PCR array as a useful tool for screening biomarkers for the diagnosis of M. bovis infection in rhinoceros.

@article{quistrebert_genome-wide_2021,
	title = {Genome-wide association study of resistance to {Mycobacterium} tuberculosis infection identifies a locus at 10q26.2 in three distinct populations},
	volume = {17},
	issn = {1553-7404},
	doi = {10.1371/journal.pgen.1009392},
	abstract = {The natural history of tuberculosis (TB) is characterized by a large inter-individual outcome variability after exposure to Mycobacterium tuberculosis. Specifically, some highly exposed individuals remain resistant to M. tuberculosis infection, as inferred by tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). We performed a genome-wide association study of resistance to M. tuberculosis infection in an endemic region of Southern Vietnam. We enrolled household contacts (HHC) of pulmonary TB cases and compared subjects who were negative for both TST and IGRA (n = 185) with infected individuals (n = 353) who were either positive for both TST and IGRA or had a diagnosis of TB. We found a genome-wide significant locus on chromosome 10q26.2 with a cluster of variants associated with strong protection against M. tuberculosis infection (OR = 0.42, 95\%CI 0.35-0.49, P = 3.71×10-8, for the genotyped variant rs17155120). The locus was replicated in a French multi-ethnic HHC cohort and a familial admixed cohort from a hyper-endemic area of South Africa, with an overall OR for rs17155120 estimated at 0.50 (95\%CI 0.45-0.55, P = 1.26×10-9). The variants are located in intronic regions and upstream of C10orf90, a tumor suppressor gene which encodes an ubiquitin ligase activating the transcription factor p53. In silico analysis showed that the protective alleles were associated with a decreased expression in monocytes of the nearby gene ADAM12 which could lead to an enhanced response of Th17 lymphocytes. Our results reveal a novel locus controlling resistance to M. tuberculosis infection across different populations.},
	language = {eng},
	number = {3},
	journal = {PLoS genetics},
	author = {Quistrebert, Jocelyn and Orlova, Marianna and Kerner, Gaspard and Ton, Le Thi and Luong, Nguyễn Trong and Danh, Nguyễn Thanh and Vincent, Quentin B. and Jabot-Hanin, Fabienne and Seeleuthner, Yoann and Bustamante, Jacinta and Boisson-Dupuis, Stéphanie and Huong, Nguyen Thu and Ba, Nguyen Ngoc and Casanova, Jean-Laurent and Delacourt, Christophe and Hoal, Eileen G. and Alcaïs, Alexandre and Thai, Vu Hong and Thành, Lai The and Abel, Laurent and Schurr, Erwin and Cobat, Aurélie},
	month = mar,
	year = {2021},
	pmid = {33661925},
	pages = {e1009392},
}

The natural history of tuberculosis (TB) is characterized by a large inter-individual outcome variability after exposure to Mycobacterium tuberculosis. Specifically, some highly exposed individuals remain resistant to M. tuberculosis infection, as inferred by tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). We performed a genome-wide association study of resistance to M. tuberculosis infection in an endemic region of Southern Vietnam. We enrolled household contacts (HHC) of pulmonary TB cases and compared subjects who were negative for both TST and IGRA (n = 185) with infected individuals (n = 353) who were either positive for both TST and IGRA or had a diagnosis of TB. We found a genome-wide significant locus on chromosome 10q26.2 with a cluster of variants associated with strong protection against M. tuberculosis infection (OR = 0.42, 95%CI 0.35-0.49, P = 3.71×10-8, for the genotyped variant rs17155120). The locus was replicated in a French multi-ethnic HHC cohort and a familial admixed cohort from a hyper-endemic area of South Africa, with an overall OR for rs17155120 estimated at 0.50 (95%CI 0.45-0.55, P = 1.26×10-9). The variants are located in intronic regions and upstream of C10orf90, a tumor suppressor gene which encodes an ubiquitin ligase activating the transcription factor p53. In silico analysis showed that the protective alleles were associated with a decreased expression in monocytes of the nearby gene ADAM12 which could lead to an enhanced response of Th17 lymphocytes. Our results reveal a novel locus controlling resistance to M. tuberculosis infection across different populations.

@article{glanzmann_human_2021,
	title = {Human whole genome sequencing in {South} {Africa}},
	volume = {11},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-79794-x},
	abstract = {The advent and evolution of next generation sequencing has considerably impacted genomic research. Until recently, South African researchers were unable to access affordable platforms capable of human whole genome sequencing locally and DNA samples had to be exported. Here we report the whole genome sequences of the first six human DNA samples sequenced and analysed at the South African Medical Research Council's Genomics Centre. We demonstrate that the data obtained is of high quality, with an average sequencing depth of 36.41, and that the output is comparable to data generated internationally on a similar platform. The Genomics Centre creates an environment where African researchers are able to access world class facilities, increasing local capacity to sequence whole genomes as well as store and analyse the data.},
	language = {eng},
	number = {1},
	journal = {Scientific Reports},
	author = {Glanzmann, Brigitte and Jooste, Tracey and Ghoor, Samira and Gordon, Richard and Mia, Rizwana and Mao, Jun and Li, Hao and Charls, Patrick and Douman, Craig and Kotze, Maritha J. and Peeters, Armand V. and Loots, Glaudina and Esser, Monika and Tiemessen, Caroline T. and Wilkinson, Robert J. and Louw, Johan and Gray, Glenda and Warren, Robin M. and Möller, Marlo and Kinnear, Craig},
	month = jan,
	year = {2021},
	pmid = {33436733},
	pmcid = {PMC7803990},
	pages = {606},
}

The advent and evolution of next generation sequencing has considerably impacted genomic research. Until recently, South African researchers were unable to access affordable platforms capable of human whole genome sequencing locally and DNA samples had to be exported. Here we report the whole genome sequences of the first six human DNA samples sequenced and analysed at the South African Medical Research Council's Genomics Centre. We demonstrate that the data obtained is of high quality, with an average sequencing depth of 36.41, and that the output is comparable to data generated internationally on a similar platform. The Genomics Centre creates an environment where African researchers are able to access world class facilities, increasing local capacity to sequence whole genomes as well as store and analyse the data.

@article{eeden_inferring_2021,
	title = {Inferring {Recombination} {Patterns} {In} {African} {Populations}},
	issn = {1460-2083},
	doi = {10.1093/hmg/ddab020},
	abstract = {While several high-resolution recombination maps exist for European-descent populations, the recombination landscape of African populations remains relatively understudied. Given that there is high genetic divergence among groups in Africa, it is possible that recombination hotspots also diverge significantly. Both limitations and opportunities exist for developing recombination maps for these populations. In this review, we discuss various recombination inference methods, and the strengths and weaknesses of these methods in analysing recombination in African-descent populations. Furthermore, we provide a decision tree and recommendations for which inference method to use in various research contexts. Establishing an appropriate methodology for recombination rate inference in a particular study will improve the accuracy of various downstream analyses including but not limited to local ancestry inference, haplotype phasing, fine-mapping of GWAS loci and genome assemblies.},
	language = {eng},
	journal = {Human Molecular Genetics},
	author = {Eeden, Gerald and Uren, Caitlin and Möller, Marlo and Henn, Brenna M.},
	month = jan,
	year = {2021},
	pmid = {33445180},
}

While several high-resolution recombination maps exist for European-descent populations, the recombination landscape of African populations remains relatively understudied. Given that there is high genetic divergence among groups in Africa, it is possible that recombination hotspots also diverge significantly. Both limitations and opportunities exist for developing recombination maps for these populations. In this review, we discuss various recombination inference methods, and the strengths and weaknesses of these methods in analysing recombination in African-descent populations. Furthermore, we provide a decision tree and recommendations for which inference method to use in various research contexts. Establishing an appropriate methodology for recombination rate inference in a particular study will improve the accuracy of various downstream analyses including but not limited to local ancestry inference, haplotype phasing, fine-mapping of GWAS loci and genome assemblies.

@article{de_jager_high_2021,
	title = {High diversity, inbreeding and a dynamic {Pleistocene} demographic history revealed by {African} buffalo genomes},
	volume = {11},
	issn = {2045-2322},
	doi = {10.1038/s41598-021-83823-8},
	abstract = {Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.},
	language = {eng},
	number = {1},
	journal = {Scientific Reports},
	author = {de Jager, Deon and Glanzmann, Brigitte and Möller, Marlo and Hoal, Eileen and van Helden, Paul and Harper, Cindy and Bloomer, Paulette},
	month = feb,
	year = {2021},
	pmid = {33633171},
	pmcid = {PMC7907399},
	pages = {4540},
}

Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.

@article{kroon_observational_2020,
	title = {An observational study identifying highly tuberculosis-exposed, {HIV}-1-positive but persistently {TB}, tuberculin and {IGRA} negative persons with {M}. tuberculosis specific antibodies in {Cape} {Town}, {South} {Africa}},
	volume = {61},
	issn = {2352-3964},
	doi = {10.1016/j.ebiom.2020.103053},
	abstract = {BACKGROUND: Mycobacterium tuberculosis (Mtb) infection is inferred from positive results of T-cell immune conversion assays measuring Mtb-specific interferon gamma production or tuberculin skin test (TST) reactivity. Certain exposed individuals do not display T-cell immune conversion in these assays and do not develop TB. Here we report a hitherto unknown form of this phenotype: HIV-1-positive persistently TB, tuberculin and IGRA negative (HITTIN).
METHODS: A community-based case-control design was used to systematically screen and identify adults living with HIV (HIV+), aged 35-60 years, who met stringent study criteria, and then longitudinally followed up for repeat IGRA and TST testing. Participants had no history of TB despite living in TB hyper-endemic environments in Cape Town, South Africa with a provincial incidence of 681/100,000. Mtb-specific antibodies were measured using ELISA and Luminex.
FINDINGS: We identified 48/286 (17\%) individuals who tested persistently negative for Mtb-specific T-cell immunoreactivity (three negative Quantiferon results and one TST = 0mm) over 206±154 days on average. Of these, 97·2\% had documented CD4 counts{\textless}200 prior to antiretroviral therapy (ART). They had received ART for 7·0±3·0 years with a latest CD4 count of 505·8±191·4 cells/mm3. All HITTIN sent for further antibody testing (n=38) displayed  Mtb-specific antibody titres.
INTERPRETATION: Immune reconstituted HIV+ persons can be persistently non-immunoreactive to TST and interferon-γ T-cell responses to Mtb, yet develop species-specific antibody responses. Exposure is evidenced by Mtb-specific antibody titres. Our identification of HIV+ individuals displaying a persisting lack of response to TST and IGRA T-cell immune conversion paves the way for future studies to investigate this phenotype in the context of HIV-infection that so far have received only scant attention.},
	language = {eng},
	journal = {EBioMedicine},
	author = {Kroon, Elouise E. and Kinnear, Craig J. and Orlova, Marianna and Fischinger, Stephanie and Shin, Sally and Boolay, Sihaam and Walzl, Gerhard and Jacobs, Ashley and Wilkinson, Robert J. and Alter, Galit and Schurr, Erwin and Hoal, Eileen G. and Möller, Marlo},
	month = nov,
	year = {2020},
	pmid = {33038764},
	pmcid = {PMC7648124},
	keywords = {Antibodies, Early clearance, Interferon gamma release assay, Resister, Tuberculin skin test},
	pages = {103053},
}

BACKGROUND: Mycobacterium tuberculosis (Mtb) infection is inferred from positive results of T-cell immune conversion assays measuring Mtb-specific interferon gamma production or tuberculin skin test (TST) reactivity. Certain exposed individuals do not display T-cell immune conversion in these assays and do not develop TB. Here we report a hitherto unknown form of this phenotype: HIV-1-positive persistently TB, tuberculin and IGRA negative (HITTIN). METHODS: A community-based case-control design was used to systematically screen and identify adults living with HIV (HIV+), aged 35-60 years, who met stringent study criteria, and then longitudinally followed up for repeat IGRA and TST testing. Participants had no history of TB despite living in TB hyper-endemic environments in Cape Town, South Africa with a provincial incidence of 681/100,000. Mtb-specific antibodies were measured using ELISA and Luminex. FINDINGS: We identified 48/286 (17%) individuals who tested persistently negative for Mtb-specific T-cell immunoreactivity (three negative Quantiferon results and one TST = 0mm) over 206±154 days on average. Of these, 97·2% had documented CD4 counts\textless200 prior to antiretroviral therapy (ART). They had received ART for 7·0±3·0 years with a latest CD4 count of 505·8±191·4 cells/mm3. All HITTIN sent for further antibody testing (n=38) displayed  Mtb-specific antibody titres. INTERPRETATION: Immune reconstituted HIV+ persons can be persistently non-immunoreactive to TST and interferon-γ T-cell responses to Mtb, yet develop species-specific antibody responses. Exposure is evidenced by Mtb-specific antibody titres. Our identification of HIV+ individuals displaying a persisting lack of response to TST and IGRA T-cell immune conversion paves the way for future studies to investigate this phenotype in the context of HIV-infection that so far have received only scant attention.

@article{bezuidenhout_hyperphosphatasia_2020,
	title = {Hyperphosphatasia with mental retardation syndrome type 4 in three unrelated {South} {African} patients},
	volume = {182},
	issn = {1552-4833},
	doi = {10.1002/ajmg.a.61797},
	abstract = {Hyperphosphatasia with mental retardation syndrome (HPMRS) is a rare autosomal recessive disorder caused by pathogenic variants in genes involved in glycosylphosphatidylinositol metabolism that result in a similar phenotype. We describe the first three patients with HPMRS from sub-Saharan Africa. Detection was assisted by Face2Gene phenotype matching and confirmed by the presence of elevated serum alkaline phosphatase. All three patients had severe intellectual disability, absent speech, hypotonia and palatal abnormality (cleft palate in two, very high-arched palate in one), no or minimal brachytelephalangy, and high serum alkaline phosphatase levels. Additional findings included seizures in two, and brain imaging abnormalities in two. In all three patients HPMRS was a top-20 gestalt match using Face2Gene. The overall phenotype is consistent with descriptions in the literature of HPMRS type 4, although not specific to it. Whole exome sequencing in the index patient and his mother detected a candidate variant in a homozygous state in the index patient (PGAP3:c.557G{\textgreater}C, p.Arg186Thr) and heterozygous in the mother. Further variant interpretation indicated pathogenicity. Sanger sequencing of another two patients identified the same homozygous, pathogenic variant, confirming a diagnosis of HPMRS type 4. The shared homozygous variant in apparently unrelated families, and in the absence of consanguinity, suggests the possibility of genetic drift due to a population bottleneck effect, and further research is recommended.},
	language = {eng},
	number = {10},
	journal = {American Journal of Medical Genetics. Part A},
	author = {Bezuidenhout, Heidre and Bayley, Samantha and Smit, Liani and Kinnear, Craig and Möller, Marlo and Uren, Caitlin and Urban, Michael F.},
	month = oct,
	year = {2020},
	pmid = {32845056},
	keywords = {Face2Gene, HPMRS4, PGAP3, hyperphosphatasia},
	pages = {2230--2235},
}

Hyperphosphatasia with mental retardation syndrome (HPMRS) is a rare autosomal recessive disorder caused by pathogenic variants in genes involved in glycosylphosphatidylinositol metabolism that result in a similar phenotype. We describe the first three patients with HPMRS from sub-Saharan Africa. Detection was assisted by Face2Gene phenotype matching and confirmed by the presence of elevated serum alkaline phosphatase. All three patients had severe intellectual disability, absent speech, hypotonia and palatal abnormality (cleft palate in two, very high-arched palate in one), no or minimal brachytelephalangy, and high serum alkaline phosphatase levels. Additional findings included seizures in two, and brain imaging abnormalities in two. In all three patients HPMRS was a top-20 gestalt match using Face2Gene. The overall phenotype is consistent with descriptions in the literature of HPMRS type 4, although not specific to it. Whole exome sequencing in the index patient and his mother detected a candidate variant in a homozygous state in the index patient (PGAP3:c.557G\textgreaterC, p.Arg186Thr) and heterozygous in the mother. Further variant interpretation indicated pathogenicity. Sanger sequencing of another two patients identified the same homozygous, pathogenic variant, confirming a diagnosis of HPMRS type 4. The shared homozygous variant in apparently unrelated families, and in the absence of consanguinity, suggests the possibility of genetic drift due to a population bottleneck effect, and further research is recommended.

@article{uren_mycobacterium_2020,
	title = {Mycobacterium tuberculosis complex and human co-adaptation: a two-way street complicating host susceptibility to {TB}},
	issn = {1460-2083},
	shorttitle = {Mycobacterium tuberculosis complex and human co-adaptation},
	doi = {10.1093/hmg/ddaa254},
	abstract = {For centuries, the Mycobacterium tuberculosis complex (MTBC) has infected numerous populations, both human and non-human, causing symptomatic tuberculosis in some hosts. Research investigating the MTBC and how it has evolved with its host over time is sparse and has not resulted in many significant findings. There are even fewer studies investigating adaptation of the human host susceptibility to tuberculosis and these have largely focused on genome wide association and candidate gene association studies. However, results emanating from these association studies are rarely replicated and appear to be population specific. It is therefore necessary to relook at the approach taken to investigate the relationship between the MTBC and the human host. Understanding that the evolution of the pathogen is coupled to the evolution of the host might be the missing link needed to effectively investigate their relationship. We hypothesize that this knowledge will bolster future efforts in combating the disease.},
	language = {eng},
	journal = {Human Molecular Genetics},
	author = {Uren, Caitlin and Hoal, Eileen G. and Möller, Marlo},
	month = dec,
	year = {2020},
	pmid = {33258469},
}

For centuries, the Mycobacterium tuberculosis complex (MTBC) has infected numerous populations, both human and non-human, causing symptomatic tuberculosis in some hosts. Research investigating the MTBC and how it has evolved with its host over time is sparse and has not resulted in many significant findings. There are even fewer studies investigating adaptation of the human host susceptibility to tuberculosis and these have largely focused on genome wide association and candidate gene association studies. However, results emanating from these association studies are rarely replicated and appear to be population specific. It is therefore necessary to relook at the approach taken to investigate the relationship between the MTBC and the human host. Understanding that the evolution of the pathogen is coupled to the evolution of the host might be the missing link needed to effectively investigate their relationship. We hypothesize that this knowledge will bolster future efforts in combating the disease.

@article{bruiners_regulatory_2020,
	title = {A regulatory variant in the {C1Q} gene cluster is associated with tuberculosis susceptibility and {C1qA} plasma levels in a {South} {African} population},
	volume = {72},
	issn = {1432-1211},
	doi = {10.1007/s00251-020-01167-5},
	abstract = {Several genetic studies have implicated genes that encode for components of the innate immune response in tuberculosis (TB) susceptibility. The complement system is an early player in the innate immune response and provides the host with initial protection by promoting phagocytosis of apoptotic or necrotic cells. The C1q molecule is the first component of the classical pathway that leads to the activation of complement by binding to immune complexes and is encoded by the C1Q gene cluster. We investigated variants in this region to determine its association with TB susceptibility. Five single nucleotide polymorphisms (SNPs) (rs12033074, rs631090, rs172378, rs587585, and rs665691) were genotyped using TaqMan® SNP assays in 456 TB cases and 448 healthy controls and analysed by logistic regression models. The rs587585 variant showed a significant additive allelic association where the minor G allele was found more frequently in TB cases than in controls in both the discovery (p = 0.023; OR = 1.30; 95\% CI, 1.04-1.64) and validation cohort (p = 0.038; OR = 1.31; 95\% CI, 1.22-1.40). In addition, we detected increased C1qA expression when comparing cases and controls (p = 0.037) and linked this to a dosage effect of the G allele, which increased C1qA expression in TB cases. This is the first study to report the association of C1Q gene polymorphisms with progression to tuberculosis.},
	language = {eng},
	number = {5},
	journal = {Immunogenetics},
	author = {Bruiners, Natalie and Schurz, Haiko and Daya, Michelle and Salie, Muneeb and van Helden, Paul D. and Kinnear, Craig J. and Hoal, Eileen G. and Möller, Marlo and Gey van Pittius, Nicolaas C.},
	month = jul,
	year = {2020},
	pmid = {32556499},
	keywords = {Association, C1q, Dosage, Susceptibility, Tuberculosis},
	pages = {305--314},
}

Several genetic studies have implicated genes that encode for components of the innate immune response in tuberculosis (TB) susceptibility. The complement system is an early player in the innate immune response and provides the host with initial protection by promoting phagocytosis of apoptotic or necrotic cells. The C1q molecule is the first component of the classical pathway that leads to the activation of complement by binding to immune complexes and is encoded by the C1Q gene cluster. We investigated variants in this region to determine its association with TB susceptibility. Five single nucleotide polymorphisms (SNPs) (rs12033074, rs631090, rs172378, rs587585, and rs665691) were genotyped using TaqMan® SNP assays in 456 TB cases and 448 healthy controls and analysed by logistic regression models. The rs587585 variant showed a significant additive allelic association where the minor G allele was found more frequently in TB cases than in controls in both the discovery (p = 0.023; OR = 1.30; 95% CI, 1.04-1.64) and validation cohort (p = 0.038; OR = 1.31; 95% CI, 1.22-1.40). In addition, we detected increased C1qA expression when comparing cases and controls (p = 0.037) and linked this to a dosage effect of the G allele, which increased C1qA expression in TB cases. This is the first study to report the association of C1Q gene polymorphisms with progression to tuberculosis.

@article{uren_putting_2020,
	title = {Putting {RFMix} and {ADMIXTURE} to the test in a complex admixed population},
	volume = {21},
	issn = {1471-2156},
	doi = {10.1186/s12863-020-00845-3},
	abstract = {BACKGROUND: Global and local ancestry inference in admixed human populations can be performed using computational tools implementing distinct algorithms. The development and resulting accuracy of these tools has been tested largely on populations with relatively straightforward admixture histories but little is known about how well they perform in more complex admixture scenarios.
RESULTS: Using simulations, we show that RFMix outperforms ADMIXTURE in determining global ancestry proportions even in a complex 5-way admixed population, in addition to assigning local ancestry with an accuracy of 89\%. The ability of RFMix to determine global and local ancestry to a high degree of accuracy, particularly in admixed populations provides the opportunity for more accurate association analyses.
CONCLUSION: This study highlights the utility of the extension of computational tools to become more compatible to genetically structured populations, as well as the need to expand the sampling of diverse world-wide populations. This is particularly noteworthy as modern-day societies are becoming increasingly genetically complex and some genetic tools and commonly used ancestral populations are less appropriate. Based on these caveats and the results presented here, we suggest that RFMix be used for both global and local ancestry estimation in world-wide complex admixture scenarios particularly when including these estimates in association studies.},
	language = {eng},
	number = {1},
	journal = {BMC genetics},
	author = {Uren, Caitlin and Hoal, Eileen G. and Möller, Marlo},
	year = {2020},
	pmid = {32264823},
	pmcid = {PMC7140372},
	keywords = {ADMIXTURE, Local ancestry inference, Population genetics, RFMix, South Africa},
	pages = {40},
}

BACKGROUND: Global and local ancestry inference in admixed human populations can be performed using computational tools implementing distinct algorithms. The development and resulting accuracy of these tools has been tested largely on populations with relatively straightforward admixture histories but little is known about how well they perform in more complex admixture scenarios. RESULTS: Using simulations, we show that RFMix outperforms ADMIXTURE in determining global ancestry proportions even in a complex 5-way admixed population, in addition to assigning local ancestry with an accuracy of 89%. The ability of RFMix to determine global and local ancestry to a high degree of accuracy, particularly in admixed populations provides the opportunity for more accurate association analyses. CONCLUSION: This study highlights the utility of the extension of computational tools to become more compatible to genetically structured populations, as well as the need to expand the sampling of diverse world-wide populations. This is particularly noteworthy as modern-day societies are becoming increasingly genetically complex and some genetic tools and commonly used ancestral populations are less appropriate. Based on these caveats and the results presented here, we suggest that RFMix be used for both global and local ancestry estimation in world-wide complex admixture scenarios particularly when including these estimates in association studies.

@article{moller_human_2020,
	title = {Human global and population-specific genetic susceptibility to {Mycobacterium} tuberculosis infection and disease},
	volume = {26},
	issn = {1531-6971},
	doi = {10.1097/MCP.0000000000000672},
	abstract = {PURPOSE OF REVIEW: Multiple lines of evidence support a role of the host genetic component in Mycobacterium tuberculosis infection and disease progression. However, genomic studies of tuberculosis susceptibility have been disappointing compared with that of other complex disorders. Recently the field has explored alternative strategies to facilitate locus discovery. Results emanating from these efforts during the last 18 months are addressed in this review.
RECENT FINDINGS: There has been a renewed focus on the refinement of phenotypic definitions of infection and disease as well as on age-related, sex-specific and population-specific effects. Genome-wide association studies have yielded candidate genes but the findings have not always been transferable to all population groups. Candidate gene association studies remain popular as it is used for GWAS replication and is affordable, particularly in lower and middle-income countries. Pharmacogenetic studies involving tuberculosis drugs may locate variants that can be cost-effectively genotyped to identify individuals at risk of developing adverse events during treatment.
SUMMARY: Additional GWAS and candidate gene association studies of crudely defined study participants are unlikely to make further important contributions to the TB susceptibility field. Instead refined phenotyping will allow the elucidation of genetic mechanisms contributing to infection and disease in distinct populations and the calculation of polygenic risk scores.},
	language = {eng},
	number = {3},
	journal = {Current Opinion in Pulmonary Medicine},
	author = {Möller, Marlo and Kinnear, Craig J.},
	month = may,
	year = {2020},
	pmid = {32101905},
	pages = {302--310},
}

PURPOSE OF REVIEW: Multiple lines of evidence support a role of the host genetic component in Mycobacterium tuberculosis infection and disease progression. However, genomic studies of tuberculosis susceptibility have been disappointing compared with that of other complex disorders. Recently the field has explored alternative strategies to facilitate locus discovery. Results emanating from these efforts during the last 18 months are addressed in this review. RECENT FINDINGS: There has been a renewed focus on the refinement of phenotypic definitions of infection and disease as well as on age-related, sex-specific and population-specific effects. Genome-wide association studies have yielded candidate genes but the findings have not always been transferable to all population groups. Candidate gene association studies remain popular as it is used for GWAS replication and is affordable, particularly in lower and middle-income countries. Pharmacogenetic studies involving tuberculosis drugs may locate variants that can be cost-effectively genotyped to identify individuals at risk of developing adverse events during treatment. SUMMARY: Additional GWAS and candidate gene association studies of crudely defined study participants are unlikely to make further important contributions to the TB susceptibility field. Instead refined phenotyping will allow the elucidation of genetic mechanisms contributing to infection and disease in distinct populations and the calculation of polygenic risk scores.

@article{swart_prospective_2020,
	title = {Prospective avenues for human population genomics and disease mapping in southern {Africa}},
	issn = {1617-4623},
	doi = {10.1007/s00438-020-01684-8},
	abstract = {Population substructure within human populations is globally evident and a well-known confounding factor in many genetic studies. In contrast, admixture mapping exploits population stratification to detect genotype-phenotype correlations in admixed populations. Southern Africa has untapped potential for disease mapping of ancestry-specific disease risk alleles due to the distinct genetic diversity in its populations compared to other populations worldwide. This diversity contributes to a number of phenotypes, including ancestry-specific disease risk and response to pathogens. Although the 1000 Genomes Project significantly improved our understanding of genetic variation globally, southern African populations are still severely underrepresented in biomedical and human genetic studies due to insufficient large-scale publicly available data. In addition to a lack of genetic data in public repositories, existing software, algorithms and resources used for imputation and phasing of genotypic data (amongst others) are largely ineffective for populations with a complex genetic architecture such as that seen in southern Africa. This review article, therefore, aims to summarise the current limitations of conducting genetic studies on populations with a complex genetic architecture to identify potential areas for further research and development.},
	language = {eng},
	journal = {Molecular genetics and genomics: MGG},
	author = {Swart, Yolandi and van Eeden, Gerald and Sparks, Anel and Uren, Caitlin and Möller, Marlo},
	month = may,
	year = {2020},
	pmid = {32440765},
	pmcid = {PMC7240165},
	keywords = {Admixture mapping, Disease risk alleles, Population genetics, Southern Africa},
}

Population substructure within human populations is globally evident and a well-known confounding factor in many genetic studies. In contrast, admixture mapping exploits population stratification to detect genotype-phenotype correlations in admixed populations. Southern Africa has untapped potential for disease mapping of ancestry-specific disease risk alleles due to the distinct genetic diversity in its populations compared to other populations worldwide. This diversity contributes to a number of phenotypes, including ancestry-specific disease risk and response to pathogens. Although the 1000 Genomes Project significantly improved our understanding of genetic variation globally, southern African populations are still severely underrepresented in biomedical and human genetic studies due to insufficient large-scale publicly available data. In addition to a lack of genetic data in public repositories, existing software, algorithms and resources used for imputation and phasing of genotypic data (amongst others) are largely ineffective for populations with a complex genetic architecture such as that seen in southern Africa. This review article, therefore, aims to summarise the current limitations of conducting genetic studies on populations with a complex genetic architecture to identify potential areas for further research and development.

@article{glanzmann_identification_2020,
	title = {Identification of a novel {WAS} mutation in a {South} {African} patient presenting with atypical {Wiskott}-{Aldrich} syndrome: a case report},
	volume = {21},
	issn = {1471-2350},
	shorttitle = {Identification of a novel {WAS} mutation in a {South} {African} patient presenting with atypical {Wiskott}-{Aldrich} syndrome},
	doi = {10.1186/s12881-020-01054-6},
	abstract = {BACKGROUND: The X-linked recessive primary immunodeficiency disease (PIDD) Wiskott-Aldrich syndrome (WAS) is identified by an extreme susceptibility to infections, eczema and thrombocytopenia with microplatelets. The syndrome, the result of mutations in the WAS gene which encodes the Wiskott-Aldrich protein (WASp), has wide clinical phenotype variation, ranging from classical WAS to X-linked thrombocytopaenia and X-linked neutropaenia. In many cases, the diagnosis of WAS in first affected males is delayed, because patients may not present with the classic signs and symptoms, which may intersect with other thrombocytopenia causes.
CASE PRESENTATION: Here, we describe a three-year-old HIV negative boy presenting with recurrent infections, skin rashes, features of autoimmunity and atopy. However, platelets were initially reported as normal in numbers and morphology as were baseline immune investigations. An older male sibling had died in infancy from suspected immunodeficiency. Uncertainty of diagnosis and suspected severe PIDD prompted urgent further molecular investigation. Whole exome sequencing identified c. 397 G {\textgreater} A as a novel hemizygous missense mutation located in exon 4 of WAS.
CONCLUSION: With definitive molecular diagnosis, we could target treatment and offer genetic counselling and prenatal diagnostic testing to the family. The identification of novel variants is important to confirm phenotype variations of a syndrome.},
	language = {eng},
	number = {1},
	journal = {BMC medical genetics},
	author = {Glanzmann, Brigitte and Möller, Marlo and Schoeman, Mardelle and Urban, Michael and van Helden, Paul D. and Frigati, Lisa and Grewal, Ravnit and Pieters, Hermanus and Loos, Ben and Hoal, Eileen G. and Glashoff, Richard H. and Cornelissen, Helena and Rabie, Helena and Esser, Monika M. and Kinnear, Craig J.},
	month = jun,
	year = {2020},
	pmid = {32503528},
	pmcid = {PMC7275612},
	keywords = {Exome sequencing, Primary immunodeficiency diseases, Wiskott-Aldrich syndrome},
	pages = {124},
}

BACKGROUND: The X-linked recessive primary immunodeficiency disease (PIDD) Wiskott-Aldrich syndrome (WAS) is identified by an extreme susceptibility to infections, eczema and thrombocytopenia with microplatelets. The syndrome, the result of mutations in the WAS gene which encodes the Wiskott-Aldrich protein (WASp), has wide clinical phenotype variation, ranging from classical WAS to X-linked thrombocytopaenia and X-linked neutropaenia. In many cases, the diagnosis of WAS in first affected males is delayed, because patients may not present with the classic signs and symptoms, which may intersect with other thrombocytopenia causes. CASE PRESENTATION: Here, we describe a three-year-old HIV negative boy presenting with recurrent infections, skin rashes, features of autoimmunity and atopy. However, platelets were initially reported as normal in numbers and morphology as were baseline immune investigations. An older male sibling had died in infancy from suspected immunodeficiency. Uncertainty of diagnosis and suspected severe PIDD prompted urgent further molecular investigation. Whole exome sequencing identified c. 397 G \textgreater A as a novel hemizygous missense mutation located in exon 4 of WAS. CONCLUSION: With definitive molecular diagnosis, we could target treatment and offer genetic counselling and prenatal diagnostic testing to the family. The identification of novel variants is important to confirm phenotype variations of a syndrome.

@article{van_helden_mycobacterium_2019,
	title = {Mycobacterium tuberculosis: concentrate resources on recent infections},
	volume = {367},
	issn = {1756-1833},
	shorttitle = {Mycobacterium tuberculosis},
	doi = {10.1136/bmj.l6485},
	language = {eng},
	journal = {BMJ (Clinical research ed.)},
	author = {van Helden, Paul D. and Hoal, Eileen G.},
	month = nov,
	year = {2019},
	pmid = {31732487},
	keywords = {Diagnostic Tests, Routine, Health Resources, Humans, Mycobacterium tuberculosis, Tuberculosis, Tuberculosis, Pulmonary},
	pages = {l6485},
}

@article{tavalire_risk_2019,
	title = {Risk alleles for tuberculosis infection associate with reduced immune reactivity in a wild mammalian host},
	volume = {286},
	issn = {1471-2954},
	doi = {10.1098/rspb.2019.0914},
	abstract = {Integrating biological processes across scales remains a central challenge in disease ecology. Genetic variation drives differences in host immune responses, which, along with environmental factors, generates temporal and spatial infection patterns in natural populations that epidemiologists seek to predict and control. However, genetics and immunology are typically studied in model systems, whereas population-level patterns of infection status and susceptibility are uniquely observable in nature. Despite obvious causal connections, organizational scales from genes to host outcomes to population patterns are rarely linked explicitly. Here we identify two loci near genes involved in macrophage (phagocyte) activation and pathogen degradation that additively increase risk of bovine tuberculosis infection by up to ninefold in wild African buffalo. Furthermore, we observe genotype-specific variation in IL-12 production indicative of variation in macrophage activation. Here, we provide measurable differences in infection resistance at multiple scales by characterizing the genetic and inflammatory variation driving patterns of infection in a wild mammal.},
	language = {eng},
	number = {1907},
	journal = {Proceedings. Biological Sciences},
	author = {Tavalire, Hannah F. and Hoal, Eileen G. and le Roex, Nikki and van Helden, Paul D. and Ezenwa, Vanessa O. and Jolles, Anna E.},
	year = {2019},
	pmid = {31311473},
	pmcid = {PMC6661349},
	keywords = {Alleles, Animals, Buffaloes, Female, Genotype, Mycobacterium bovis, South Africa, Syncerus caffer, Tuberculosis, ecoimmunology, ecological genetics},
	pages = {20190914},
}

Integrating biological processes across scales remains a central challenge in disease ecology. Genetic variation drives differences in host immune responses, which, along with environmental factors, generates temporal and spatial infection patterns in natural populations that epidemiologists seek to predict and control. However, genetics and immunology are typically studied in model systems, whereas population-level patterns of infection status and susceptibility are uniquely observable in nature. Despite obvious causal connections, organizational scales from genes to host outcomes to population patterns are rarely linked explicitly. Here we identify two loci near genes involved in macrophage (phagocyte) activation and pathogen degradation that additively increase risk of bovine tuberculosis infection by up to ninefold in wild African buffalo. Furthermore, we observe genotype-specific variation in IL-12 production indicative of variation in macrophage activation. Here, we provide measurable differences in infection resistance at multiple scales by characterizing the genetic and inflammatory variation driving patterns of infection in a wild mammal.

@article{warren_tuberculosis_2019,
	title = {Tuberculosis research in {South} {Africa} over the past 30 years: {From} bench to bedside},
	volume = {109},
	issn = {2078-5135},
	shorttitle = {Tuberculosis research in {South} {Africa} over the past 30 years},
	doi = {10.7196/SAMJ.2019.v109i11b.14249},
	abstract = {The South African Medical Research Council Centre for Tuberculosis Research has a rich history of high-impact research that has influenced our understating of this hyper-epidemic which is further exacerbated by the emergence and spread of drug-resistant forms of the disease. This review aims to summarise the past 30 years of research conducted in the Centre which has influenced the way that tuberculosis (TB) is diagnosed and treated. The review includes the development of new technologies for rapid screening of people with probable TB and the repurposing of human diagnostics for wildlife conservation.},
	language = {eng},
	number = {11b},
	journal = {South African Medical Journal = Suid-Afrikaanse Tydskrif Vir Geneeskunde},
	author = {Warren, R. and Ismail, N. and Chegou, N. N. and Theron, G. and Walzl, G. and Malherbe, S. T. and Kinnear, C. J. and Van der Spuy, G. D. and Goosen, W. and Miller, M. A. and Diacon, A. H. and Van Helden, P. D.},
	month = dec,
	year = {2019},
	pmid = {32252868},
	keywords = {Academies and Institutes, Animals, Animals, Wild, Antitubercular Agents, Biomedical Research, Cattle, Extensively Drug-Resistant Tuberculosis, Humans, Interferon-gamma Release Tests, Latent Tuberculosis, Livestock, Mass Screening, Polymerase Chain Reaction, Positron Emission Tomography Computed Tomography, South Africa, Tuberculosis, Tuberculosis, Bovine, Tuberculosis, Multidrug-Resistant},
	pages = {45--52},
}

The South African Medical Research Council Centre for Tuberculosis Research has a rich history of high-impact research that has influenced our understating of this hyper-epidemic which is further exacerbated by the emergence and spread of drug-resistant forms of the disease. This review aims to summarise the past 30 years of research conducted in the Centre which has influenced the way that tuberculosis (TB) is diagnosed and treated. The review includes the development of new technologies for rapid screening of people with probable TB and the repurposing of human diagnostics for wildlife conservation.

@article{erjaee_primary_2019,
	title = {Primary immunodeficiency in {Africa} - a review},
	volume = {109},
	issn = {2078-5135},
	doi = {10.7196/SAMJ.2019.v109i8b.13820},
	abstract = {BACKGROUND: Efforts have been made worldwide to improve awareness and treatment of primary immunodeficiency (PID). This has also gained momentum on the African continent albeit at a slower pace. Objective. This review reports on the current status of PID on the African continent regarding its prevalence, distribution, genetic mutations and challenges in diagnosis and treatment of affected patients. Method. We evaluated all studies published from the African continent in the field of PID dealing with prevalence, epidemiology, case reports and genetic findings. Results. The prevalence of PID on the African continent has been estimated to be as high as 902 631 individuals. PID still is mostly underdiagnosed in Africa and although progress has been made in parts of the continent many challenges still remain regarding awareness, diagnosis, registration and care of these patients. Conclusion. Given the unique genetic mutations reported in PID patients on the African continent and the feasibility of hematopoietic stem cell transplantation and gene therapy, increased awareness should be encouraged and new therapeutic options considered.},
	language = {eng},
	number = {8b},
	journal = {South African Medical Journal = Suid-Afrikaanse Tydskrif Vir Geneeskunde},
	author = {Erjaee, A. and Bagherpour, M. and Van Rooyen, C. and Van den Berg, S. and Kinnear, C. J. and Green, R. J. and Pepper, M.},
	month = sep,
	year = {2019},
	pmid = {31662142},
	keywords = {Africa, Genetic Therapy, Hematopoietic Stem Cell Transplantation, Humans, Mutation, Prevalence, Primary Immunodeficiency Diseases},
	pages = {3--11},
}

BACKGROUND: Efforts have been made worldwide to improve awareness and treatment of primary immunodeficiency (PID). This has also gained momentum on the African continent albeit at a slower pace. Objective. This review reports on the current status of PID on the African continent regarding its prevalence, distribution, genetic mutations and challenges in diagnosis and treatment of affected patients. Method. We evaluated all studies published from the African continent in the field of PID dealing with prevalence, epidemiology, case reports and genetic findings. Results. The prevalence of PID on the African continent has been estimated to be as high as 902 631 individuals. PID still is mostly underdiagnosed in Africa and although progress has been made in parts of the continent many challenges still remain regarding awareness, diagnosis, registration and care of these patients. Conclusion. Given the unique genetic mutations reported in PID patients on the African continent and the feasibility of hematopoietic stem cell transplantation and gene therapy, increased awareness should be encouraged and new therapeutic options considered.

@article{glanzmann_primary_2019,
	title = {Primary immunodeficiency diseases in a tuberculosis endemic region: challenges and opportunities},
	volume = {20},
	issn = {1476-5470},
	shorttitle = {Primary immunodeficiency diseases in a tuberculosis endemic region},
	doi = {10.1038/s41435-018-0041-0},
	abstract = {While individual primary immunodeficiency diseases (PIDs) are rare, collectively they represent a significant burden of disease. Recent estimates show that about one million people in Africa suffer from a PID. However, data from African PID registries reflect only a small percentage of the estimated prevalence. This disparity is partly due to the lack of PID awareness and the masking of PIDs by the endemic pathogens. Over three million tuberculosis (TB) cases were reported in Africa in 2016, with many of these from southern Africa. Despite concerted efforts to address this high burden of disease, the underlying genetic correlates of susceptibility to TB remain poorly understood. High penetrance mutations in immune system genes can cause PIDs that selectively predispose individuals to TB and other mycobacterial diseases. Additionally, the identification of individuals at a heightened risk of developing TB or of presenting with severe or disseminated TB due to their genetic ancestry is crucial to promote a positive treatment outcome. The screening for and identification of PID mutations in TB-endemic regions by next-generation sequencing (NGS) represents a promising approach to improve the understanding of what constitutes an effective immune response to TB, as well as the range of associated PIDs and phenotypes.},
	language = {eng},
	number = {6},
	journal = {Genes and Immunity},
	author = {Glanzmann, Brigitte and Uren, Caitlin and de Villiers, Nikola and van Coller, Ansia and Glashoff, Richard H. and Urban, Michael and Hoal, Eileen G. and Esser, Monika M. and Möller, Marlo and Kinnear, Craig J.},
	year = {2019},
	pmid = {30185814},
	keywords = {Africa, Southern, High-Throughput Nucleotide Sequencing, Humans, Mutation, Primary Immunodeficiency Diseases, Tuberculosis},
	pages = {447--454},
}

While individual primary immunodeficiency diseases (PIDs) are rare, collectively they represent a significant burden of disease. Recent estimates show that about one million people in Africa suffer from a PID. However, data from African PID registries reflect only a small percentage of the estimated prevalence. This disparity is partly due to the lack of PID awareness and the masking of PIDs by the endemic pathogens. Over three million tuberculosis (TB) cases were reported in Africa in 2016, with many of these from southern Africa. Despite concerted efforts to address this high burden of disease, the underlying genetic correlates of susceptibility to TB remain poorly understood. High penetrance mutations in immune system genes can cause PIDs that selectively predispose individuals to TB and other mycobacterial diseases. Additionally, the identification of individuals at a heightened risk of developing TB or of presenting with severe or disseminated TB due to their genetic ancestry is crucial to promote a positive treatment outcome. The screening for and identification of PID mutations in TB-endemic regions by next-generation sequencing (NGS) represents a promising approach to improve the understanding of what constitutes an effective immune response to TB, as well as the range of associated PIDs and phenotypes.

@article{schurz_evaluating_2019,
	title = {Evaluating the {Accuracy} of {Imputation} {Methods} in a {Five}-{Way} {Admixed} {Population}},
	volume = {10},
	issn = {1664-8021},
	doi = {10.3389/fgene.2019.00034},
	abstract = {Genotype imputation is a powerful tool for increasing statistical power in an association analysis. Meta-analysis of multiple study datasets also requires a substantial overlap of SNPs for a successful association analysis, which can be achieved by imputation. Quality of imputed datasets is largely dependent on the software used, as well as the reference populations chosen. The accuracy of imputation of available reference populations has not been tested for the five-way admixed South African Colored (SAC) population. In this study, imputation results obtained using three freely-accessible methods were evaluated for accuracy and quality. We show that the African Genome Resource is the best reference panel for imputation of missing genotypes in samples from the SAC population, implemented via the freely accessible Sanger Imputation Server.},
	language = {eng},
	journal = {Frontiers in Genetics},
	author = {Schurz, Haiko and Müller, Stephanie J. and van Helden, Paul David and Tromp, Gerard and Hoal, Eileen G. and Kinnear, Craig J. and Möller, Marlo},
	year = {2019},
	pmid = {30804980},
	pmcid = {PMC6370942},
	keywords = {1000 Genomes, AGR, African, CAAPA, accuracy, admixture, imputation, quality},
	pages = {34},
}

Genotype imputation is a powerful tool for increasing statistical power in an association analysis. Meta-analysis of multiple study datasets also requires a substantial overlap of SNPs for a successful association analysis, which can be achieved by imputation. Quality of imputed datasets is largely dependent on the software used, as well as the reference populations chosen. The accuracy of imputation of available reference populations has not been tested for the five-way admixed South African Colored (SAC) population. In this study, imputation results obtained using three freely-accessible methods were evaluated for accuracy and quality. We show that the African Genome Resource is the best reference panel for imputation of missing genotypes in samples from the SAC population, implemented via the freely accessible Sanger Imputation Server.

@article{schurz_x_2019,
	title = {The {X} chromosome and sex-specific effects in infectious disease susceptibility},
	volume = {13},
	issn = {1479-7364},
	doi = {10.1186/s40246-018-0185-z},
	abstract = {The X chromosome and X-linked variants have largely been ignored in genome-wide and candidate association studies of infectious diseases due to the complexity of statistical analysis of the X chromosome. This exclusion is significant, since the X chromosome contains a high density of immune-related genes and regulatory elements that are extensively involved in both the innate and adaptive immune responses. Many diseases present with a clear sex bias, and apart from the influence of sex hormones and socioeconomic and behavioural factors, the X chromosome, X-linked genes and X chromosome inactivation mechanisms contribute to this difference. Females are functional mosaics for X-linked genes due to X chromosome inactivation and this, combined with other X chromosome inactivation mechanisms such as genes that escape silencing and skewed inactivation, could contribute to an immunological advantage for females in many infections. In this review, we discuss the involvement of the X chromosome and X inactivation in immunity and address its role in sexual dimorphism of infectious diseases using tuberculosis susceptibility as an example, in which male sex bias is clear, yet not fully explored.},
	language = {eng},
	number = {1},
	journal = {Human Genomics},
	author = {Schurz, Haiko and Salie, Muneeb and Tromp, Gerard and Hoal, Eileen G. and Kinnear, Craig J. and Möller, Marlo},
	month = jan,
	year = {2019},
	pmid = {30621780},
	keywords = {Host genetics, Sex bias, Susceptibility, Tuberculosis, X chromosome},
	pages = {2},
}

The X chromosome and X-linked variants have largely been ignored in genome-wide and candidate association studies of infectious diseases due to the complexity of statistical analysis of the X chromosome. This exclusion is significant, since the X chromosome contains a high density of immune-related genes and regulatory elements that are extensively involved in both the innate and adaptive immune responses. Many diseases present with a clear sex bias, and apart from the influence of sex hormones and socioeconomic and behavioural factors, the X chromosome, X-linked genes and X chromosome inactivation mechanisms contribute to this difference. Females are functional mosaics for X-linked genes due to X chromosome inactivation and this, combined with other X chromosome inactivation mechanisms such as genes that escape silencing and skewed inactivation, could contribute to an immunological advantage for females in many infections. In this review, we discuss the involvement of the X chromosome and X inactivation in immunity and address its role in sexual dimorphism of infectious diseases using tuberculosis susceptibility as an example, in which male sex bias is clear, yet not fully explored.

@article{schurz_sex-stratified_2018,
	title = {A {Sex}-{Stratified} {Genome}-{Wide} {Association} {Study} of {Tuberculosis} {Using} a {Multi}-{Ethnic} {Genotyping} {Array}},
	volume = {9},
	issn = {1664-8021},
	doi = {10.3389/fgene.2018.00678},
	abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease with a known human genetic component. Males seem to be more affected than females and in most countries the TB notification rate is twice as high in males than in females. While socio-economic status, behavior and sex hormones influence the male bias they do not fully account for it. Males have only one copy of the X chromosome, while diploid females are subject to X chromosome inactivation. In addition, the X chromosome codes for many immune-related genes, supporting the hypothesis that X-linked genes could contribute to TB susceptibility in a sex-biased manner. We report the first TB susceptibility genome-wide association study (GWAS) with a specific focus on sex-stratified autosomal analysis and the X chromosome. A total of 810 individuals (410 cases and 405 controls) from an admixed South African population were genotyped using the Illumina Multi Ethnic Genotyping Array, specifically designed as a suitable platform for diverse and admixed populations. Association testing was done on the autosome (8,27,386 variants) and X chromosome (20,939 variants) in a sex stratified and combined manner. SNP association testing was not statistically significant using a stringent cut-off for significance but revealed likely candidate genes that warrant further investigation. A genome wide interaction analysis detected 16 significant interactions. Finally, the results highlight the importance of sex-stratified analysis as strong sex-specific effects were identified on both the autosome and X chromosome.},
	language = {eng},
	journal = {Frontiers in Genetics},
	author = {Schurz, Haiko and Kinnear, Craig J. and Gignoux, Chris and Wojcik, Genevieve and van Helden, Paul D. and Tromp, Gerard and Henn, Brenna and Hoal, Eileen G. and Möller, Marlo},
	year = {2018},
	pmid = {30713548},
	pmcid = {PMC6346682},
	keywords = {GWAS, X chromosome, host genetics, sex-bias, sex-stratified, susceptibility, tuberculosis},
	pages = {678},
}

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease with a known human genetic component. Males seem to be more affected than females and in most countries the TB notification rate is twice as high in males than in females. While socio-economic status, behavior and sex hormones influence the male bias they do not fully account for it. Males have only one copy of the X chromosome, while diploid females are subject to X chromosome inactivation. In addition, the X chromosome codes for many immune-related genes, supporting the hypothesis that X-linked genes could contribute to TB susceptibility in a sex-biased manner. We report the first TB susceptibility genome-wide association study (GWAS) with a specific focus on sex-stratified autosomal analysis and the X chromosome. A total of 810 individuals (410 cases and 405 controls) from an admixed South African population were genotyped using the Illumina Multi Ethnic Genotyping Array, specifically designed as a suitable platform for diverse and admixed populations. Association testing was done on the autosome (8,27,386 variants) and X chromosome (20,939 variants) in a sex stratified and combined manner. SNP association testing was not statistically significant using a stringent cut-off for significance but revealed likely candidate genes that warrant further investigation. A genome wide interaction analysis detected 16 significant interactions. Finally, the results highlight the importance of sex-stratified analysis as strong sex-specific effects were identified on both the autosome and X chromosome.

@article{neethling_wild-type_2018,
	title = {Wild-type and mutant ({G2019S}) leucine-rich repeat kinase 2 ({LRRK2}) associate with subunits of the translocase of outer mitochondrial membrane ({TOM}) complex},
	issn = {1090-2422},
	doi = {10.1016/j.yexcr.2018.12.022},
	abstract = {Leucine-rich repeat kinase 2 (LRRK2) is important in various cellular processes including mitochondrial homeostasis and mutations in this gene lead to Parkinson's disease (PD). However, the full spectrum of LRRK2's functions remain to be elucidated. The translocase of outer mitochondrial membrane (TOM) complex is essential for the import of almost all nuclear-encoded mitochondrial proteins and is fundamental for cellular survival. Using co-immunoprecipitation, super-resolution structured illumination microscopy (SR-SIM), and 3D virtual reality (VR) assisted co-localization analysis techniques we show that wild-type and mutant (G2019S) LRRK2 associate and co-localize with subunits of the TOM complex, either under basal (dimethyl sulfoxide, DMSO) or stress-induced (carbonyl cyanide m-chlorophenyl hydrazine, CCCP) conditions. Interestingly, LRRK2 interacted with TOM40 under both DMSO and CCCP conditions, and when the PD causing mutation, G2019S was introduced, the association was not altered. Moreover, overexpression of G2019S LRRK2 resulted in the formation of large, perinuclear aggregates that co-localized with the TOM complex. Taken together, this is the first study to show that both WT and mutant LRRK2 associate with the TOM complex subunits. These findings provide additional evidence for LRRK2's role in mitochondrial function which has important implications for its role in PD pathogenesis.},
	language = {eng},
	journal = {Experimental Cell Research},
	author = {Neethling, Annika and Engelbrecht, Lize and Loos, Ben and Kinnear, Craig and Theart, Rensu and Abrahams, Shameemah and Niesler, Thomas and Mellick, George D. and Williams, Monique and Bardien, Soraya},
	month = dec,
	year = {2018},
	pmid = {30597143},
	keywords = {LRRK2, Parkinson's disease, TOM complex, TOM40, co-immunoprecipitation, co-localization},
}

Leucine-rich repeat kinase 2 (LRRK2) is important in various cellular processes including mitochondrial homeostasis and mutations in this gene lead to Parkinson's disease (PD). However, the full spectrum of LRRK2's functions remain to be elucidated. The translocase of outer mitochondrial membrane (TOM) complex is essential for the import of almost all nuclear-encoded mitochondrial proteins and is fundamental for cellular survival. Using co-immunoprecipitation, super-resolution structured illumination microscopy (SR-SIM), and 3D virtual reality (VR) assisted co-localization analysis techniques we show that wild-type and mutant (G2019S) LRRK2 associate and co-localize with subunits of the TOM complex, either under basal (dimethyl sulfoxide, DMSO) or stress-induced (carbonyl cyanide m-chlorophenyl hydrazine, CCCP) conditions. Interestingly, LRRK2 interacted with TOM40 under both DMSO and CCCP conditions, and when the PD causing mutation, G2019S was introduced, the association was not altered. Moreover, overexpression of G2019S LRRK2 resulted in the formation of large, perinuclear aggregates that co-localized with the TOM complex. Taken together, this is the first study to show that both WT and mutant LRRK2 associate with the TOM complex subunits. These findings provide additional evidence for LRRK2's role in mitochondrial function which has important implications for its role in PD pathogenesis.

@article{lin_rapid_2018,
	title = {Rapid evolution of a skin-lightening allele in southern {African} {KhoeSan}},
	volume = {115},
	issn = {1091-6490},
	doi = {10.1073/pnas.1801948115},
	abstract = {Skin pigmentation is under strong directional selection in northern European and Asian populations. The indigenous KhoeSan populations of far southern Africa have lighter skin than other sub-Saharan African populations, potentially reflecting local adaptation to a region of Africa with reduced UV radiation. Here, we demonstrate that a canonical Eurasian skin pigmentation gene, SLC24A5, was introduced to southern Africa via recent migration and experienced strong adaptive evolution in the KhoeSan. To reconstruct the evolution of skin pigmentation, we collected phenotypes from over 400 ≠Khomani San and Nama individuals and high-throughput sequenced candidate pigmentation genes. The derived causal allele in SLC24A5, p.Ala111Thr, significantly lightens basal skin pigmentation in the KhoeSan and explains 8 to 15\% of phenotypic variance in these populations. The frequency of this allele (33 to 53\%) is far greater than expected from colonial period European gene flow; however, the most common derived haplotype is identical among European, eastern African, and KhoeSan individuals. Using four-population demographic simulations with selection, we show that the allele was introduced into the KhoeSan only 2,000 y ago via a back-to-Africa migration and then experienced a selective sweep (s = 0.04 to 0.05 in ≠Khomani and Nama). The SLC24A5 locus is both a rare example of intense, ongoing adaptation in very recent human history, as well as an adaptive gene flow at a pigmentation locus in humans.},
	language = {eng},
	number = {52},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Lin, Meng and Siford, Rebecca L. and Martin, Alicia R. and Nakagome, Shigeki and Möller, Marlo and Hoal, Eileen G. and Bustamante, Carlos D. and Gignoux, Christopher R. and Henn, Brenna M.},
	month = dec,
	year = {2018},
	pmid = {30530665},
	pmcid = {PMC6310813},
	keywords = {Africa, KhoeSan, SLC24A5, adaptation, pigmentation},
	pages = {13324--13329},
}

Skin pigmentation is under strong directional selection in northern European and Asian populations. The indigenous KhoeSan populations of far southern Africa have lighter skin than other sub-Saharan African populations, potentially reflecting local adaptation to a region of Africa with reduced UV radiation. Here, we demonstrate that a canonical Eurasian skin pigmentation gene, SLC24A5, was introduced to southern Africa via recent migration and experienced strong adaptive evolution in the KhoeSan. To reconstruct the evolution of skin pigmentation, we collected phenotypes from over 400 ≠Khomani San and Nama individuals and high-throughput sequenced candidate pigmentation genes. The derived causal allele in SLC24A5, p.Ala111Thr, significantly lightens basal skin pigmentation in the KhoeSan and explains 8 to 15% of phenotypic variance in these populations. The frequency of this allele (33 to 53%) is far greater than expected from colonial period European gene flow; however, the most common derived haplotype is identical among European, eastern African, and KhoeSan individuals. Using four-population demographic simulations with selection, we show that the allele was introduced into the KhoeSan only 2,000 y ago via a back-to-Africa migration and then experienced a selective sweep (s = 0.04 to 0.05 in ≠Khomani and Nama). The SLC24A5 locus is both a rare example of intense, ongoing adaptation in very recent human history, as well as an adaptive gene flow at a pigmentation locus in humans.

@article{moller_genetic_2018,
	title = {Genetic {Resistance} to {Mycobacterium} tuberculosis {Infection} and {Disease}},
	volume = {9},
	issn = {1664-3224},
	doi = {10.3389/fimmu.2018.02219},
	abstract = {Natural history studies of tuberculosis (TB) have revealed a spectrum of clinical outcomes after exposure to Mycobacterium tuberculosis, the cause of TB. Not all individuals exposed to the bacterium will become diseased and depending on the infection pressure, many will remain infection-free. Intriguingly, complete resistance to infection is observed in some individuals (termed resisters) after intense, continuing M. tuberculosis exposure. After successful infection, the majority of individuals will develop latent TB infection (LTBI). This infection state is currently (and perhaps imperfectly) defined by the presence of a positive tuberculin skin test (TST) and/or interferon gamma release assay (IGRA), but no detectable clinical disease symptoms. The majority of healthy individuals with LTBI are resistant to clinical TB, indicating that infection is remarkably well-contained in these non-progressors. The remaining 5-15\% of LTBI positive individuals will progress to active TB. Epidemiological investigations have indicated that the host genetic component contributes to these infection and disease phenotypes, influencing both susceptibility and resistance. Elucidating these genetic correlates is therefore a priority as it may translate to new interventions to prevent, diagnose or treat TB. The most successful approaches in resistance/susceptibility investigation have focused on specific infection and disease phenotypes and the resister phenotype may hold the key to the discovery of actionable genetic variants in TB infection and disease. This review will not only discuss lessons from epidemiological studies, but will also focus on the contribution of epidemiology and functional genetics to human genetic resistance to M. tuberculosis infection and disease.},
	language = {eng},
	journal = {Frontiers in Immunology},
	author = {Möller, Marlo and Kinnear, Craig J. and Orlova, Marianna and Kroon, Elouise E. and van Helden, Paul D. and Schurr, Erwin and Hoal, Eileen G.},
	year = {2018},
	pmid = {30319657},
	pmcid = {PMC6170664},
	keywords = {host genetics, resistance, resisters, susceptibility, tuberculosis},
	pages = {2219},
}

Natural history studies of tuberculosis (TB) have revealed a spectrum of clinical outcomes after exposure to Mycobacterium tuberculosis, the cause of TB. Not all individuals exposed to the bacterium will become diseased and depending on the infection pressure, many will remain infection-free. Intriguingly, complete resistance to infection is observed in some individuals (termed resisters) after intense, continuing M. tuberculosis exposure. After successful infection, the majority of individuals will develop latent TB infection (LTBI). This infection state is currently (and perhaps imperfectly) defined by the presence of a positive tuberculin skin test (TST) and/or interferon gamma release assay (IGRA), but no detectable clinical disease symptoms. The majority of healthy individuals with LTBI are resistant to clinical TB, indicating that infection is remarkably well-contained in these non-progressors. The remaining 5-15% of LTBI positive individuals will progress to active TB. Epidemiological investigations have indicated that the host genetic component contributes to these infection and disease phenotypes, influencing both susceptibility and resistance. Elucidating these genetic correlates is therefore a priority as it may translate to new interventions to prevent, diagnose or treat TB. The most successful approaches in resistance/susceptibility investigation have focused on specific infection and disease phenotypes and the resister phenotype may hold the key to the discovery of actionable genetic variants in TB infection and disease. This review will not only discuss lessons from epidemiological studies, but will also focus on the contribution of epidemiology and functional genetics to human genetic resistance to M. tuberculosis infection and disease.

@article{kroon_neutrophils:_2018,
	title = {Neutrophils: {Innate} {Effectors} of {TB} {Resistance}?},
	volume = {9},
	issn = {1664-3224},
	shorttitle = {Neutrophils},
	doi = {10.3389/fimmu.2018.02637},
	abstract = {Certain individuals are able to resist Mycobacterium tuberculosis infection despite persistent and intense exposure. These persons do not exhibit adaptive immune priming as measured by tuberculin skin test (TST) and interferon-γ (IFN-γ) release assay (IGRA) responses, nor do they develop active tuberculosis (TB). Genetic investigation of individuals who are able to resist M. tuberculosis infection shows there are likely a combination of genetic variants that contribute to the phenotype. The contribution of the innate immune system and the exact cells involved in this phenotype remain incompletely elucidated. Neutrophils are prominent candidates for possible involvement as primers for microbial clearance. Significant variability is observed in neutrophil gene expression and DNA methylation. Furthermore, inter-individual variability is seen between the mycobactericidal capacities of donor neutrophils. Clearance of M. tuberculosis infection is favored by the mycobactericidal activity of neutrophils, apoptosis, effective clearance of cells by macrophages, and resolution of inflammation. In this review we will discuss the different mechanisms neutrophils utilize to clear M. tuberculosis infection. We discuss the duality between neutrophils' ability to clear infection and how increasing numbers of neutrophils contribute to active TB severity and mortality. Further investigation into the potential role of neutrophils in innate immune-mediated M. tuberculosis infection resistance is warranted since it may reveal clinically important activities for prevention as well as vaccine and treatment development.},
	language = {eng},
	journal = {Frontiers in Immunology},
	author = {Kroon, Elouise E. and Coussens, Anna K. and Kinnear, Craig and Orlova, Marianna and Möller, Marlo and Seeger, Allison and Wilkinson, Robert J. and Hoal, Eileen G. and Schurr, Erwin},
	year = {2018},
	pmid = {30487797},
	pmcid = {PMC6246713},
	keywords = {Mycobacterium, NETs, antimicrobial, inflammation, necrosis, protection, tuberculosis},
	pages = {2637},
}

Certain individuals are able to resist Mycobacterium tuberculosis infection despite persistent and intense exposure. These persons do not exhibit adaptive immune priming as measured by tuberculin skin test (TST) and interferon-γ (IFN-γ) release assay (IGRA) responses, nor do they develop active tuberculosis (TB). Genetic investigation of individuals who are able to resist M. tuberculosis infection shows there are likely a combination of genetic variants that contribute to the phenotype. The contribution of the innate immune system and the exact cells involved in this phenotype remain incompletely elucidated. Neutrophils are prominent candidates for possible involvement as primers for microbial clearance. Significant variability is observed in neutrophil gene expression and DNA methylation. Furthermore, inter-individual variability is seen between the mycobactericidal capacities of donor neutrophils. Clearance of M. tuberculosis infection is favored by the mycobactericidal activity of neutrophils, apoptosis, effective clearance of cells by macrophages, and resolution of inflammation. In this review we will discuss the different mechanisms neutrophils utilize to clear M. tuberculosis infection. We discuss the duality between neutrophils' ability to clear infection and how increasing numbers of neutrophils contribute to active TB severity and mortality. Further investigation into the potential role of neutrophils in innate immune-mediated M. tuberculosis infection resistance is warranted since it may reveal clinically important activities for prevention as well as vaccine and treatment development.

@article{tavalire_context-dependent_2018,
	title = {Context-dependent costs and benefits of tuberculosis resistance traits in a wild mammalian host},
	volume = {8},
	issn = {2045-7758},
	doi = {10.1002/ece3.4699},
	abstract = {Disease acts as a powerful driver of evolution in natural host populations, yet individuals in a population often vary in their susceptibility to infection. Energetic trade-offs between immune and reproductive investment lead to the evolution of distinct life history strategies, driven by the relative fitness costs and benefits of resisting infection. However, examples quantifying the cost of resistance outside of the laboratory are rare. Here, we observe two distinct forms of resistance to bovine tuberculosis (bTB), an important zoonotic pathogen, in a free-ranging African buffalo (Syncerus caffer) population. We characterize these phenotypes as "infection resistance," in which hosts delay or prevent infection, and "proliferation resistance," in which the host limits the spread of lesions caused by the pathogen after infection has occurred. We found weak evidence that infection resistance to bTB may be heritable in this buffalo population (h2 = 0.10) and comes at the cost of reduced body condition and marginally reduced survival once infected, but also associates with an overall higher reproductive rate. Infection-resistant animals thus appear to follow a "fast" pace-of-life syndrome, in that they reproduce more quickly but die upon infection. In contrast, proliferation resistance had no apparent costs and was associated with measures of positive host health-such as having a higher body condition and reproductive rate. This study quantifies striking phenotypic variation in pathogen resistance and provides evidence for a link between life history variation and a disease resistance trait in a wild mammalian host population.},
	language = {eng},
	number = {24},
	journal = {Ecology and Evolution},
	author = {Tavalire, Hannah F. and Beechler, Brianna R. and Buss, Peter E. and Gorsich, Erin E. and Hoal, Eileen G. and le Roex, Nikki and Spaan, Johannie M. and Spaan, Robert S. and van Helden, Paul D. and Ezenwa, Vanessa O. and Jolles, Anna E.},
	month = dec,
	year = {2018},
	pmid = {30619576},
	pmcid = {PMC6308860},
	keywords = {African buffalo, coevolution, heritability, host‐pathogen, pace‐of‐life},
	pages = {12712--12726},
}

Disease acts as a powerful driver of evolution in natural host populations, yet individuals in a population often vary in their susceptibility to infection. Energetic trade-offs between immune and reproductive investment lead to the evolution of distinct life history strategies, driven by the relative fitness costs and benefits of resisting infection. However, examples quantifying the cost of resistance outside of the laboratory are rare. Here, we observe two distinct forms of resistance to bovine tuberculosis (bTB), an important zoonotic pathogen, in a free-ranging African buffalo (Syncerus caffer) population. We characterize these phenotypes as "infection resistance," in which hosts delay or prevent infection, and "proliferation resistance," in which the host limits the spread of lesions caused by the pathogen after infection has occurred. We found weak evidence that infection resistance to bTB may be heritable in this buffalo population (h2 = 0.10) and comes at the cost of reduced body condition and marginally reduced survival once infected, but also associates with an overall higher reproductive rate. Infection-resistant animals thus appear to follow a "fast" pace-of-life syndrome, in that they reproduce more quickly but die upon infection. In contrast, proliferation resistance had no apparent costs and was associated with measures of positive host health-such as having a higher body condition and reproductive rate. This study quantifies striking phenotypic variation in pathogen resistance and provides evidence for a link between life history variation and a disease resistance trait in a wild mammalian host population.

@article{martin_critical_2018,
	title = {The critical needs and challenges for genetic architecture studies in {Africa}},
	volume = {53},
	issn = {1879-0380},
	doi = {10.1016/j.gde.2018.08.005},
	abstract = {Human genetic studies have long been vastly Eurocentric, raising a key question about the generalizability of these study findings to other populations. Because humans originated in Africa, these populations retain more genetic diversity, and yet individuals of African descent have been tremendously underrepresented in genetic studies. The diversity in Africa affords ample opportunities to improve fine-mapping resolution for associated loci, discover novel genetic associations with phenotypes, build more generalizable genetic risk prediction models, and better understand the genetic architecture of complex traits and diseases subject to varying environmental pressures. Thus, it is both ethically and scientifically imperative that geneticists globally surmount challenges that have limited progress in African genetic studies to date. Additionally, African investigators need to be meaningfully included, as greater inclusivity and enhanced research capacity afford enormous opportunities to accelerate genomic discoveries that translate more effectively to all populations. We review the advantages, challenges, and examples of genetic architecture studies of complex traits and diseases in Africa. For example, with greater genetic diversity comes greater ancestral heterogeneity; this higher level of understudied diversity can yield novel genetic findings, but some methods that assume homogeneous population structure and work well in European populations may work less well in the presence of greater heterogeneity in African populations. Consequently, we advocate for methodological development that will accelerate studies important for all populations, especially those currently underrepresented in genetics.},
	language = {eng},
	journal = {Current Opinion in Genetics \& Development},
	author = {Martin, Alicia R. and Teferra, Solomon and Möller, Marlo and Hoal, Eileen G. and Daly, Mark J.},
	month = sep,
	year = {2018},
	pmid = {30240950},
	pages = {113--120},
}

Human genetic studies have long been vastly Eurocentric, raising a key question about the generalizability of these study findings to other populations. Because humans originated in Africa, these populations retain more genetic diversity, and yet individuals of African descent have been tremendously underrepresented in genetic studies. The diversity in Africa affords ample opportunities to improve fine-mapping resolution for associated loci, discover novel genetic associations with phenotypes, build more generalizable genetic risk prediction models, and better understand the genetic architecture of complex traits and diseases subject to varying environmental pressures. Thus, it is both ethically and scientifically imperative that geneticists globally surmount challenges that have limited progress in African genetic studies to date. Additionally, African investigators need to be meaningfully included, as greater inclusivity and enhanced research capacity afford enormous opportunities to accelerate genomic discoveries that translate more effectively to all populations. We review the advantages, challenges, and examples of genetic architecture studies of complex traits and diseases in Africa. For example, with greater genetic diversity comes greater ancestral heterogeneity; this higher level of understudied diversity can yield novel genetic findings, but some methods that assume homogeneous population structure and work well in European populations may work less well in the presence of greater heterogeneity in African populations. Consequently, we advocate for methodological development that will accelerate studies important for all populations, especially those currently underrepresented in genetics.

@article{glanzmann_primary_2018,
	title = {Primary immunodeficiency diseases in a tuberculosis endemic region: challenges and opportunities},
	issn = {1476-5470},
	shorttitle = {Primary immunodeficiency diseases in a tuberculosis endemic region},
	doi = {10.1038/s41435-018-0041-0},
	abstract = {While individual primary immunodeficiency diseases (PIDs) are rare, collectively they represent a significant burden of disease. Recent estimates show that about one million people in Africa suffer from a PID. However, data from African PID registries reflect only a small percentage of the estimated prevalence. This disparity is partly due to the lack of PID awareness and the masking of PIDs by the endemic pathogens. Over three million tuberculosis (TB) cases were reported in Africa in 2016, with many of these from southern Africa. Despite concerted efforts to address this high burden of disease, the underlying genetic correlates of susceptibility to TB remain poorly understood. High penetrance mutations in immune system genes can cause PIDs that selectively predispose individuals to TB and other mycobacterial diseases. Additionally, the identification of individuals at a heightened risk of developing TB or of presenting with severe or disseminated TB due to their genetic ancestry is crucial to promote a positive treatment outcome. The screening for and identification of PID mutations in TB-endemic regions by next-generation sequencing (NGS) represents a promising approach to improve the understanding of what constitutes an effective immune response to TB, as well as the range of associated PIDs and phenotypes.},
	language = {eng},
	journal = {Genes and Immunity},
	author = {Glanzmann, Brigitte and Uren, Caitlin and de Villiers, Nikola and van Coller, Ansia and Glashoff, Richard H. and Urban, Michael and Hoal, Eileen G. and Esser, Monika M. and Möller, Marlo and Kinnear, Craig J.},
	month = sep,
	year = {2018},
	pmid = {30185814},
}

While individual primary immunodeficiency diseases (PIDs) are rare, collectively they represent a significant burden of disease. Recent estimates show that about one million people in Africa suffer from a PID. However, data from African PID registries reflect only a small percentage of the estimated prevalence. This disparity is partly due to the lack of PID awareness and the masking of PIDs by the endemic pathogens. Over three million tuberculosis (TB) cases were reported in Africa in 2016, with many of these from southern Africa. Despite concerted efforts to address this high burden of disease, the underlying genetic correlates of susceptibility to TB remain poorly understood. High penetrance mutations in immune system genes can cause PIDs that selectively predispose individuals to TB and other mycobacterial diseases. Additionally, the identification of individuals at a heightened risk of developing TB or of presenting with severe or disseminated TB due to their genetic ancestry is crucial to promote a positive treatment outcome. The screening for and identification of PID mutations in TB-endemic regions by next-generation sequencing (NGS) represents a promising approach to improve the understanding of what constitutes an effective immune response to TB, as well as the range of associated PIDs and phenotypes.

@article{nemat-gorgani_different_2018,
	title = {Different {Selected} {Mechanisms} {Attenuated} the {Inhibitory} {Interaction} of {KIR2DL1} with {C2}+ {HLA}-{C} in {Two} {Indigenous} {Human} {Populations} in {Southern} {Africa}},
	volume = {200},
	issn = {1550-6606},
	doi = {10.4049/jimmunol.1701780},
	abstract = {The functions of human NK cells in defense against pathogens and placental development during reproduction are modulated by interactions of killer cell Ig-like receptors (KIRs) with HLA-A, -B and -C class I ligands. Both receptors and ligands are highly polymorphic and exhibit extensive differences between human populations. Indigenous to southern Africa are the KhoeSan, the most ancient group of modern human populations, who have highest genomic diversity worldwide. We studied two KhoeSan populations, the Nama pastoralists and the ≠Khomani San hunter-gatherers. Comprehensive next-generation sequence analysis of HLA-A, -B, and -C and all KIR genes identified 248 different KIR and 137 HLA class I, which assort into ∼200 haplotypes for each gene family. All 74 Nama and 78 ≠Khomani San studied have different genotypes. Numerous novel KIR alleles were identified, including three arising by intergenic recombination. On average, KhoeSan individuals have seven to eight pairs of interacting KIR and HLA class I ligands, the highest diversity and divergence of polymorphic NK cell receptors and ligands observed to date. In this context of high genetic diversity, both the Nama and the ≠Khomani San have an unusually conserved, centromeric KIR haplotype that has arisen to high frequency and is different in the two KhoeSan populations. Distinguishing these haplotypes are independent mutations in KIR2DL1, which both prevent KIR2DL1 from functioning as an inhibitory receptor for C2+ HLA-C. The relatively high frequency of C2+ HLA-C in the Nama and the ≠Khomani San appears to have led to natural selection against strong inhibitory C2-specific KIR.},
	language = {eng},
	number = {8},
	journal = {Journal of Immunology (Baltimore, Md.: 1950)},
	author = {Nemat-Gorgani, Neda and Hilton, Hugo G. and Henn, Brenna M. and Lin, Meng and Gignoux, Christopher R. and Myrick, Justin W. and Werely, Cedric J. and Granka, Julie M. and Möller, Marlo and Hoal, Eileen G. and Yawata, Makoto and Yawata, Nobuyo and Boelen, Lies and Asquith, Becca and Parham, Peter and Norman, Paul J.},
	month = apr,
	year = {2018},
	pmid = {29549179},
	pages = {2640--2655},
}

The functions of human NK cells in defense against pathogens and placental development during reproduction are modulated by interactions of killer cell Ig-like receptors (KIRs) with HLA-A, -B and -C class I ligands. Both receptors and ligands are highly polymorphic and exhibit extensive differences between human populations. Indigenous to southern Africa are the KhoeSan, the most ancient group of modern human populations, who have highest genomic diversity worldwide. We studied two KhoeSan populations, the Nama pastoralists and the ≠Khomani San hunter-gatherers. Comprehensive next-generation sequence analysis of HLA-A, -B, and -C and all KIR genes identified 248 different KIR and 137 HLA class I, which assort into ∼200 haplotypes for each gene family. All 74 Nama and 78 ≠Khomani San studied have different genotypes. Numerous novel KIR alleles were identified, including three arising by intergenic recombination. On average, KhoeSan individuals have seven to eight pairs of interacting KIR and HLA class I ligands, the highest diversity and divergence of polymorphic NK cell receptors and ligands observed to date. In this context of high genetic diversity, both the Nama and the ≠Khomani San have an unusually conserved, centromeric KIR haplotype that has arisen to high frequency and is different in the two KhoeSan populations. Distinguishing these haplotypes are independent mutations in KIR2DL1, which both prevent KIR2DL1 from functioning as an inhibitory receptor for C2+ HLA-C. The relatively high frequency of C2+ HLA-C in the Nama and the ≠Khomani San appears to have led to natural selection against strong inhibitory C2-specific KIR.

@article{colli_new_2018,
	title = {New {Insights} on {Water} {Buffalo} {Genomic} {Diversity} and {Post}-{Domestication} {Migration} {Routes} {From} {Medium} {Density} {SNP} {Chip} {Data}},
	volume = {9},
	issn = {1664-8021},
	doi = {10.3389/fgene.2018.00053},
	abstract = {The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.},
	language = {eng},
	journal = {Frontiers in Genetics},
	author = {Colli, Licia and Milanesi, Marco and Vajana, Elia and Iamartino, Daniela and Bomba, Lorenzo and Puglisi, Francesco and Del Corvo, Marcello and Nicolazzi, Ezequiel L. and Ahmed, Sahar S. E. and Herrera, Jesus R. V. and Cruz, Libertado and Zhang, Shujun and Liang, Aixin and Hua, Guohua and Yang, Liguo and Hao, Xingjie and Zuo, Fuyuan and Lai, Song-Jia and Wang, Shuilian and Liu, Ruyu and Gong, Yundeng and Mokhber, Mahdi and Mao, Yongjiang and Guan, Feng and Vlaic, Augustin and Vlaic, Bogdan and Ramunno, Luigi and Cosenza, Gianfranco and Ahmad, Ali and Soysal, Ihsan and Ünal, Emel Ö and Ketudat-Cairns, Mariena and Garcia, José F. and Utsunomiya, Yuri T. and Baruselli, Pietro S. and Amaral, Maria E. J. and Parnpai, Rangsun and Drummond, Marcela G. and Galbusera, Peter and Burton, James and Hoal, Eileen and Yusnizar, Yulnawati and Sumantri, Cece and Moioli, Bianca and Valentini, Alessio and Stella, Alessandra and Williams, John L. and Ajmone-Marsan, Paolo},
	year = {2018},
	pmid = {29552025},
	pmcid = {PMC5841121},
	keywords = {Bubalus bubalis, SNP, domestication, evolutionary history, genomic diversity, river buffalo, swamp buffalo},
	pages = {53},
}

The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.

@article{glanzmann_autosomal_2018,
	title = {Autosomal {Dominant} {IFN}-γ{R1} {Deficiency} {Presenting} with both {Atypical} {Mycobacteriosis} and {Tuberculosis} in a {BCG}-{Vaccinated} {South} {African} {Patient}},
	issn = {1573-2592},
	doi = {10.1007/s10875-018-0509-8},
	language = {eng},
	journal = {Journal of Clinical Immunology},
	author = {Glanzmann, Brigitte and Möller, Marlo and Moncada-Velez, Marcela and Peter, Jonny and Urban, Michael and van Helden, Paul D. and Hoal, Eileen G. and de Villiers, Nikola and Glashoff, Richard H. and Nortje, Rina and Bustamante, Jacinta and Abel, Laurent and Casanova, Jean-Laurent and Boisson-Dupuis, Stephanie and Esser, Monika and Kinnear, Craig J.},
	month = may,
	year = {2018},
	pmid = {29777412},
	keywords = {IFN-γ immunity, IFNGR1, Mendelian susceptibility to mycobacterial disease, Mycobacterium other than tuberculosis, South Africa, Ttuberculosis},
}

@article{mcgregor_translational_2018,
	title = {A translational approach to the genetics of anxiety disorders},
	volume = {341},
	issn = {1872-7549},
	doi = {10.1016/j.bbr.2017.12.030},
	abstract = {There have been important advances in our understanding of the genetic architecture of anxiety disorders. At the same time, relatively few genes have reached genome wide significance in anxiety disorders, and there is relatively little work on how exposure to an adverse environment impacts on gene expression in either animal models or human clinical populations. Here we assessed differential expression of genes of the dorsal striatum involved in synaptic transmission in an animal models of early adversity (maternal separation followed by restraint stress), and investigated whether variants in these genes were associated with risk for anxiety disorders, particularly in the presence of environmental stressors. Fifty-two male Sprague Dawley rats underwent maternal separation, and gene expression was studied using array technology. The human homologues of the differentially expressed genes were screened and analysed in a DSM-IV anxiety disorders cohort, and healthy controls (patients, n = 92; controls, n = 194), using blood. Two candidate genes (Mmp9 and Bdnf) were aberrantly expressed in the experimental rodent group relative to controls. Four single nucleotide polymorphisms (SNPs) in the human homologues of these genes were significantly associated with susceptibility for anxiety disorders (MMP9: rs3918242 and BDNF: rs6265, rs10835210 and rs11030107). Three of these (BDNF: rs6265, rs10835210, rs11030107) were found to interact significantly with childhood trauma severity resulting in increased likelihood of an anxiety disorder diagnosis. This study provides insights into the utility of rat models for identifying molecular candidates for anxiety disorders in humans.},
	language = {eng},
	journal = {Behavioural Brain Research},
	author = {McGregor, N. W. and Dimatelis, J. J. and Van Zyl, P. J. and Hemmings, S. M. J. and Kinnear, C. and Russell, V. A. and Stein, D. J. and Lochner, C.},
	month = apr,
	year = {2018},
	pmid = {29288745},
	keywords = {Animal model, Anxiety, Childhood trauma, Epigenetics, Genetics},
	pages = {91--97},
}

There have been important advances in our understanding of the genetic architecture of anxiety disorders. At the same time, relatively few genes have reached genome wide significance in anxiety disorders, and there is relatively little work on how exposure to an adverse environment impacts on gene expression in either animal models or human clinical populations. Here we assessed differential expression of genes of the dorsal striatum involved in synaptic transmission in an animal models of early adversity (maternal separation followed by restraint stress), and investigated whether variants in these genes were associated with risk for anxiety disorders, particularly in the presence of environmental stressors. Fifty-two male Sprague Dawley rats underwent maternal separation, and gene expression was studied using array technology. The human homologues of the differentially expressed genes were screened and analysed in a DSM-IV anxiety disorders cohort, and healthy controls (patients, n = 92; controls, n = 194), using blood. Two candidate genes (Mmp9 and Bdnf) were aberrantly expressed in the experimental rodent group relative to controls. Four single nucleotide polymorphisms (SNPs) in the human homologues of these genes were significantly associated with susceptibility for anxiety disorders (MMP9: rs3918242 and BDNF: rs6265, rs10835210 and rs11030107). Three of these (BDNF: rs6265, rs10835210, rs11030107) were found to interact significantly with childhood trauma severity resulting in increased likelihood of an anxiety disorder diagnosis. This study provides insights into the utility of rat models for identifying molecular candidates for anxiety disorders in humans.

@article{de_wet_pyoderma_2017,
	title = {Pyoderma gangrenosum, acne, and suppurative hidradenitis syndrome in end-stage renal disease successfully treated with adalimumab},
	volume = {23},
	issn = {1087-2108},
	abstract = {PASH syndrome (pyoderma gangrenosum, acne, and suppurative hidradenitis) forms part of the spectrum of autoinflammatory diseases. We report an unusual case of PASH syndrome in a patient with end-stagerenal disease (ESRD) who was successfully treated with the tumor necrosis factor inhibitor, adalimumab. The case underscores the challenges associatedwith the treatment of PASH syndrome as well as the ongoing search to establish a genetic basis for the syndrome. Renal impairment has been reported in association with pyoderma gangrenosum but has notbeen described in PASH syndrome. We believe this to be the first reported case of a patient who developed PASH syndrome in the setting of ESRD.},
	language = {eng},
	number = {12},
	journal = {Dermatology Online Journal},
	author = {De Wet, J. and Jordaan, H. F. and Kannenberg, S. M. and Tod, B. and Glanzmann, B. and Visser, W. I.},
	month = dec,
	year = {2017},
	pmid = {29447652},
	keywords = {Acne Vulgaris, Adalimumab, Adult, Anti-Inflammatory Agents, Hidradenitis Suppurativa, Humans, Kidney Failure, Chronic, Male, Pyoderma Gangrenosum, Syndrome, Tumor Necrosis Factor-alpha},
}

PASH syndrome (pyoderma gangrenosum, acne, and suppurative hidradenitis) forms part of the spectrum of autoinflammatory diseases. We report an unusual case of PASH syndrome in a patient with end-stagerenal disease (ESRD) who was successfully treated with the tumor necrosis factor inhibitor, adalimumab. The case underscores the challenges associatedwith the treatment of PASH syndrome as well as the ongoing search to establish a genetic basis for the syndrome. Renal impairment has been reported in association with pyoderma gangrenosum but has notbeen described in PASH syndrome. We believe this to be the first reported case of a patient who developed PASH syndrome in the setting of ESRD.

@article{kannan_wd40-repeat_2017,
	title = {{WD40}-repeat 47, a microtubule-associated protein, is essential for brain development and autophagy},
	volume = {114},
	issn = {1091-6490},
	doi = {10.1073/pnas.1713625114},
	abstract = {The family of WD40-repeat (WDR) proteins is one of the largest in eukaryotes, but little is known about their function in brain development. Among 26 WDR genes assessed, we found 7 displaying a major impact in neuronal morphology when inactivated in mice. Remarkably, all seven genes showed corpus callosum defects, including thicker (Atg16l1,Coro1c,Dmxl2, andHerc1), thinner (Kif21bandWdr89), or absent corpus callosum (Wdr47), revealing a common role for WDR genes in brain connectivity. We focused on the poorly studied WDR47 protein sharing structural homology with LIS1, which causes lissencephaly. In a dosage-dependent manner, mice lackingWdr47showed lethality, extensive fiber defects, microcephaly, thinner cortices, and sensory motor gating abnormalities. We showed that WDR47 shares functional characteristics with LIS1 and participates in key microtubule-mediated processes, including neural stem cell proliferation, radial migration, and growth cone dynamics. In absence of WDR47, the exhaustion of late cortical progenitors and the consequent decrease of neurogenesis together with the impaired survival of late-born neurons are likely yielding to the worsening of the microcephaly phenotype postnatally. Interestingly, the WDR47-specific C-terminal to LisH (CTLH) domain was associated with functions in autophagy described in mammals. Silencing WDR47 in hypothalamic GT1-7 neuronal cells and yeast models independently recapitulated these findings, showing conserved mechanisms. Finally, our data identified superior cervical ganglion-10 (SCG10) as an interacting partner of WDR47. Taken together, these results provide a starting point for studying the implications of WDR proteins in neuronal regulation of microtubules and autophagy.},
	language = {eng},
	number = {44},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Kannan, Meghna and Bayam, Efil and Wagner, Christel and Rinaldi, Bruno and Kretz, Perrine F. and Tilly, Peggy and Roos, Marna and McGillewie, Lara and Bär, Séverine and Minocha, Shilpi and Chevalier, Claire and Po, Chrystelle and {Sanger Mouse Genetics Project} and Chelly, Jamel and Mandel, Jean-Louis and Borgatti, Renato and Piton, Amélie and Kinnear, Craig and Loos, Ben and Adams, David J. and Hérault, Yann and Collins, Stephan C. and Friant, Sylvie and Godin, Juliette D. and Yalcin, Binnaz},
	month = oct,
	year = {2017},
	pmid = {29078390},
	pmcid = {PMC5676932},
	keywords = {WD40-repeat proteins, autophagy, corpus callosum agenesis, microcephaly, neurogenesis},
	pages = {E9308--E9317},
}

The family of WD40-repeat (WDR) proteins is one of the largest in eukaryotes, but little is known about their function in brain development. Among 26 WDR genes assessed, we found 7 displaying a major impact in neuronal morphology when inactivated in mice. Remarkably, all seven genes showed corpus callosum defects, including thicker (Atg16l1,Coro1c,Dmxl2, andHerc1), thinner (Kif21bandWdr89), or absent corpus callosum (Wdr47), revealing a common role for WDR genes in brain connectivity. We focused on the poorly studied WDR47 protein sharing structural homology with LIS1, which causes lissencephaly. In a dosage-dependent manner, mice lackingWdr47showed lethality, extensive fiber defects, microcephaly, thinner cortices, and sensory motor gating abnormalities. We showed that WDR47 shares functional characteristics with LIS1 and participates in key microtubule-mediated processes, including neural stem cell proliferation, radial migration, and growth cone dynamics. In absence of WDR47, the exhaustion of late cortical progenitors and the consequent decrease of neurogenesis together with the impaired survival of late-born neurons are likely yielding to the worsening of the microcephaly phenotype postnatally. Interestingly, the WDR47-specific C-terminal to LisH (CTLH) domain was associated with functions in autophagy described in mammals. Silencing WDR47 in hypothalamic GT1-7 neuronal cells and yeast models independently recapitulated these findings, showing conserved mechanisms. Finally, our data identified superior cervical ganglion-10 (SCG10) as an interacting partner of WDR47. Taken together, these results provide a starting point for studying the implications of WDR proteins in neuronal regulation of microtubules and autophagy.

@article{kinnear_role_2017,
	title = {The role of human host genetics in tuberculosis resistance},
	volume = {11},
	issn = {1747-6356},
	doi = {10.1080/17476348.2017.1354700},
	abstract = {INTRODUCTION: Tuberculosis (TB) remains a public health problem: the latest estimate of new incident cases per year is a staggering 10.4 million. Despite this overwhelming number, the majority of the immunocompetent population can control infection with Mycobacterium tuberculosis. The human genome underlies the immune response and contributes to the outcome of TB infection. Areas covered: Investigations of TB resistance in the general population have closely mirrored those of other infectious diseases and initially involved epidemiological observations. Linkage and association studies, including studies of VDR, SLC11A1 and HLA-DRB1 followed. Genome-wide association studies of common variants, not necessarily sufficient for disease, became possible after technological advancements. Other approaches involved the identification of those individuals with rare disease-causing mutations that strongly predispose to TB, epistasis and the role of ethnicity in disease. Despite these efforts, infection outcome, on an individual basis, cannot yet be predicted. Expert commentary: The early identification of future disease progressors is necessary to stem the TB epidemic. Human genetics may contribute to this endeavour and could in future suggest pathways to target for disease prevention. This will however require concerted efforts to establish large, well-phenotyped cohorts from different ethnicities, improved genomic resources and a better understanding of the human genome architecture.},
	language = {eng},
	number = {9},
	journal = {Expert Review of Respiratory Medicine},
	author = {Kinnear, Craig and Hoal, Eileen G. and Schurz, Haiko and van Helden, Paul D. and Möller, Marlo},
	month = sep,
	year = {2017},
	pmid = {28703045},
	keywords = {GWAS, Tuberculosis, association, host genetics, linkage, resistance, susceptibility},
	pages = {721--737},
}

INTRODUCTION: Tuberculosis (TB) remains a public health problem: the latest estimate of new incident cases per year is a staggering 10.4 million. Despite this overwhelming number, the majority of the immunocompetent population can control infection with Mycobacterium tuberculosis. The human genome underlies the immune response and contributes to the outcome of TB infection. Areas covered: Investigations of TB resistance in the general population have closely mirrored those of other infectious diseases and initially involved epidemiological observations. Linkage and association studies, including studies of VDR, SLC11A1 and HLA-DRB1 followed. Genome-wide association studies of common variants, not necessarily sufficient for disease, became possible after technological advancements. Other approaches involved the identification of those individuals with rare disease-causing mutations that strongly predispose to TB, epistasis and the role of ethnicity in disease. Despite these efforts, infection outcome, on an individual basis, cannot yet be predicted. Expert commentary: The early identification of future disease progressors is necessary to stem the TB epidemic. Human genetics may contribute to this endeavour and could in future suggest pathways to target for disease prevention. This will however require concerted efforts to establish large, well-phenotyped cohorts from different ethnicities, improved genomic resources and a better understanding of the human genome architecture.

@article{hoal_arms_2017,
	title = {The arms race between man and {Mycobacterium} tuberculosis: {Time} to regroup},
	issn = {1567-7257},
	shorttitle = {The arms race between man and {Mycobacterium} tuberculosis},
	doi = {10.1016/j.meegid.2017.08.021},
	abstract = {An arms race is an appropriate metaphor to use for the interaction of man and Mycobacterium tuberculosis (M.tb) through the millennia. Estimates of the time of infection of modern humans with M.tb often pre-date the Out-of-Africa migration. Humans have adapted to the changing environment during the migration with respect to climate, food sources and encounters with local pathogens. More recently, there has been adaptation to the demographic changes brought about in the majority of the human population by the Neolithic revolution. By chance and/or selection, specific variants in immune defence have arisen in different population groups. These select for M.tb strains more fit to cause disease and be transmitted, sometimes by exploiting defence systems effective on other bacteria. The different selection pressures on the M.tb lineages carried by specific human groups have resulted in a worldwide M.tb population that is geographically structured according to the humans historically found there. A similar structure is seen with pathogens such as M. leprae and Helicobacter pylori. Modern M.tb strains have emerged which may be more fit, such as the Beijing lineage, leading to their rapid spread both in the areas where they arose, and into new areas after recent introduction. The speed at which this is occurring is outpacing coevolution for the time being. By using the results of genome wide and other association studies, as well as admixture mapping and 'natural experiments' in areas where both a number of populations, admixed populations, and a variety of M.tb strains occur, we can investigate the forces that have driven the coevolution of man and M.tb. The diversity of human and bacterial genetic background may be used in the future to discover and target the specific host-pathogen interactions leading to tuberculosis diseases, which suggests the potential for rational design of vaccines and host-directed therapies.},
	language = {eng},
	journal = {Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases},
	author = {Hoal, Eileen G. and Dippenaar, Anzaan and Kinnear, Craig and van Helden, Paul D. and Möller, Marlo},
	month = aug,
	year = {2017},
	pmid = {28843547},
	keywords = {Admixture, Coevolution, Human evolution, Mycobacterium tuberculosis, Strain lineages},
}

An arms race is an appropriate metaphor to use for the interaction of man and Mycobacterium tuberculosis (M.tb) through the millennia. Estimates of the time of infection of modern humans with M.tb often pre-date the Out-of-Africa migration. Humans have adapted to the changing environment during the migration with respect to climate, food sources and encounters with local pathogens. More recently, there has been adaptation to the demographic changes brought about in the majority of the human population by the Neolithic revolution. By chance and/or selection, specific variants in immune defence have arisen in different population groups. These select for M.tb strains more fit to cause disease and be transmitted, sometimes by exploiting defence systems effective on other bacteria. The different selection pressures on the M.tb lineages carried by specific human groups have resulted in a worldwide M.tb population that is geographically structured according to the humans historically found there. A similar structure is seen with pathogens such as M. leprae and Helicobacter pylori. Modern M.tb strains have emerged which may be more fit, such as the Beijing lineage, leading to their rapid spread both in the areas where they arose, and into new areas after recent introduction. The speed at which this is occurring is outpacing coevolution for the time being. By using the results of genome wide and other association studies, as well as admixture mapping and 'natural experiments' in areas where both a number of populations, admixed populations, and a variety of M.tb strains occur, we can investigate the forces that have driven the coevolution of man and M.tb. The diversity of human and bacterial genetic background may be used in the future to discover and target the specific host-pathogen interactions leading to tuberculosis diseases, which suggests the potential for rational design of vaccines and host-directed therapies.

@article{jabot-hanin_eqtl_2017,
	title = {An {eQTL} variant of {ZXDC} is associated with {IFN}-γ production following {Mycobacterium} tuberculosis antigen-specific stimulation},
	volume = {7},
	issn = {2045-2322},
	doi = {10.1038/s41598-017-13017-8},
	abstract = {There is a large inter-individual variability in the response to Mycobacterium tuberculosis infection. In previous linkage analyses, we identified a major locus on chromosome region 8q controlling IFN-γ production after stimulation with live BCG (Bacillus Calmette-Guérin), and a second locus on chromosome region 3q affecting IFN-γ production triggered by the 6-kDa early secretory antigen target (ESAT-6), taking into account the IFN-γ production induced by BCG (IFNγ-ESAT6BCG). High-density genotyping and imputation identified {\textasciitilde}100,000 variants within each linkage region, which we tested for association with the corresponding IFN-γ phenotype in families from a tuberculosis household contact study in France. Significant associations were replicated in a South African familial sample. The most convincing association observed was that between the IFNγ-ESAT6BCGphenotype and rs9828868 on chromosome 3q (p = 9.8 × 10-6in the French sample). This variant made a significant contribution to the linkage signal (p {\textless} 0.001), and a trend towards the same association was observed in the South African sample. This variant was reported to be an eQTL of the ZXDC gene, biologically linked to monocyte IL-12 production through CCL2/MCP1. The identification of rs9828868 as a genetic driver of IFNγ production in response to mycobacterial antigens provides new insights into human anti-tuberculosis immunity.},
	language = {eng},
	number = {1},
	journal = {Scientific Reports},
	author = {Jabot-Hanin, Fabienne and Cobat, Aurélie and Feinberg, Jacqueline and Orlova, Marianna and Niay, Jonathan and Deswarte, Caroline and Poirier, Christine and Theodorou, Ioannis and Bustamante, Jacinta and Boisson-Dupuis, Stéphanie and Casanova, Jean-Laurent and Alcaïs, Alexandre and Hoal, Eileen G. and Delacourt, Christophe and Schurr, Erwin and Abel, Laurent},
	month = oct,
	year = {2017},
	pmid = {28993696},
	pmcid = {PMC5634485},
	pages = {12800},
}

There is a large inter-individual variability in the response to Mycobacterium tuberculosis infection. In previous linkage analyses, we identified a major locus on chromosome region 8q controlling IFN-γ production after stimulation with live BCG (Bacillus Calmette-Guérin), and a second locus on chromosome region 3q affecting IFN-γ production triggered by the 6-kDa early secretory antigen target (ESAT-6), taking into account the IFN-γ production induced by BCG (IFNγ-ESAT6BCG). High-density genotyping and imputation identified ~100,000 variants within each linkage region, which we tested for association with the corresponding IFN-γ phenotype in families from a tuberculosis household contact study in France. Significant associations were replicated in a South African familial sample. The most convincing association observed was that between the IFNγ-ESAT6BCGphenotype and rs9828868 on chromosome 3q (p = 9.8 × 10-6in the French sample). This variant made a significant contribution to the linkage signal (p \textless 0.001), and a trend towards the same association was observed in the South African sample. This variant was reported to be an eQTL of the ZXDC gene, biologically linked to monocyte IL-12 production through CCL2/MCP1. The identification of rs9828868 as a genetic driver of IFNγ production in response to mycobacterial antigens provides new insights into human anti-tuberculosis immunity.

@article{martin_unexpectedly_2017,
	title = {An {Unexpectedly} {Complex} {Architecture} for {Skin} {Pigmentation} in {Africans}},
	volume = {171},
	issn = {1097-4172},
	doi = {10.1016/j.cell.2017.11.015},
	abstract = {Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.},
	language = {eng},
	number = {6},
	journal = {Cell},
	author = {Martin, Alicia R. and Lin, Meng and Granka, Julie M. and Myrick, Justin W. and Liu, Xiaomin and Sockell, Alexandra and Atkinson, Elizabeth G. and Werely, Cedric J. and Möller, Marlo and Sandhu, Manjinder S. and Kingsley, David M. and Hoal, Eileen G. and Liu, Xiao and Daly, Mark J. and Feldman, Marcus W. and Gignoux, Christopher R. and Bustamante, Carlos D. and Henn, Brenna M.},
	month = nov,
	year = {2017},
	pmid = {29195075},
	keywords = {Africa, African Continental Ancestry Group, Humans, Polymorphism, Single Nucleotide, Skin Pigmentation, heritability, human evolution, pigmentation, population genetics},
	pages = {1340--1353.e14},
}

Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.

@article{schlechter_exome_2017,
	title = {Exome {Sequencing} {Identifies} a {NovelMAP3K14Mutation} in {Recessive} {Atypical} {Combined} {Immunodeficiency}},
	volume = {8},
	issn = {1664-3224},
	doi = {10.3389/fimmu.2017.01624},
	abstract = {Primary immunodeficiency disorders (PIDs) render patients vulnerable to infection with a wide range of microorganisms and thus provide goodin vivomodels for the assessment of immune responses during infectious challenges. Priming of the immune system, especially in infancy, depends on different environmental exposures and medical practices. This may determine the timing and phenotype of clinical appearance of immune deficits as exemplified with early exposure to Bacillus Calmette-Guérin (BCG) vaccination and dissemination in combined immunodeficiencies. Varied phenotype expression poses a challenge to identification of the putative immune deficit. Without the availability of genomic diagnosis and data analysis resources and with limited capacity for functional definition of immune pathways, it is difficult to establish a definitive diagnosis and to decide on appropriate treatment. This study describes the use of exome sequencing to identify a homozygous recessive variant inMAP3K14, NIKVal345Met, in a patient with combined immunodeficiency, disseminated BCG-osis, and paradoxically elevated lymphocytes. Laboratory testing confirmed hypogammaglobulinemia with normal CD19, but failed to confirm a definitive diagnosis for targeted treatment decisions. NIKVal345Metis predicted to be deleterious and pathogenic by twoin silicoprediction tools and is situated in a gene crucial for effective functioning of the non-canonical nuclear factor-kappa B signaling pathway. Functional analysis of NIKVal345Met- versus NIKWT-transfected human embryonic kidney-293T cells showed that this mutation significantly affects the kinase activity of NIK leading to decreased levels of phosphorylated IkappaB kinase-alpha (IKKα), the target of NIK. BCG-stimulated RAW264.7 cells transfected with NIKVal345Met also presented with reduced levels of phosphorylated IKKα, significantly increased p100 levels and significantly decreased p52 levels compared to cells transfected with NIKWT. Ideally, these experiments would have been conducted in patient-derived immune cells, but we were unable to source these cells from the patient. The functional analysis described in this paper supports previous illustrations of the importance of NIK in human immune responses and demonstrates the involvement of function-altering mutations inMAP3K14in PIDs. The genomic approach used for this patient demonstrates its value in the diagnosis of an unusual PID and as a tool for detecting rarer mutations to help guide treatment approaches.},
	language = {eng},
	journal = {Frontiers in Immunology},
	author = {Schlechter, Nikola and Glanzmann, Brigitte and Hoal, Eileen Garner and Schoeman, Mardelle and Petersen, Britt-Sabina and Franke, Andre and Lau, Yu-Lung and Urban, Michael and van Helden, Paul David and Esser, Monika Maria and Möller, Marlo and Kinnear, Craig},
	year = {2017},
	pmid = {29230214},
	pmcid = {PMC5712007},
	keywords = {BCG dissemination, nuclear factor-kappa B-inducing kinase, primary immunodeficiency, tuberculosis, whole exome sequencing},
	pages = {1624},
}

Primary immunodeficiency disorders (PIDs) render patients vulnerable to infection with a wide range of microorganisms and thus provide goodin vivomodels for the assessment of immune responses during infectious challenges. Priming of the immune system, especially in infancy, depends on different environmental exposures and medical practices. This may determine the timing and phenotype of clinical appearance of immune deficits as exemplified with early exposure to Bacillus Calmette-Guérin (BCG) vaccination and dissemination in combined immunodeficiencies. Varied phenotype expression poses a challenge to identification of the putative immune deficit. Without the availability of genomic diagnosis and data analysis resources and with limited capacity for functional definition of immune pathways, it is difficult to establish a definitive diagnosis and to decide on appropriate treatment. This study describes the use of exome sequencing to identify a homozygous recessive variant inMAP3K14, NIKVal345Met, in a patient with combined immunodeficiency, disseminated BCG-osis, and paradoxically elevated lymphocytes. Laboratory testing confirmed hypogammaglobulinemia with normal CD19, but failed to confirm a definitive diagnosis for targeted treatment decisions. NIKVal345Metis predicted to be deleterious and pathogenic by twoin silicoprediction tools and is situated in a gene crucial for effective functioning of the non-canonical nuclear factor-kappa B signaling pathway. Functional analysis of NIKVal345Met- versus NIKWT-transfected human embryonic kidney-293T cells showed that this mutation significantly affects the kinase activity of NIK leading to decreased levels of phosphorylated IkappaB kinase-alpha (IKKα), the target of NIK. BCG-stimulated RAW264.7 cells transfected with NIKVal345Met also presented with reduced levels of phosphorylated IKKα, significantly increased p100 levels and significantly decreased p52 levels compared to cells transfected with NIKWT. Ideally, these experiments would have been conducted in patient-derived immune cells, but we were unable to source these cells from the patient. The functional analysis described in this paper supports previous illustrations of the importance of NIK in human immune responses and demonstrates the involvement of function-altering mutations inMAP3K14in PIDs. The genomic approach used for this patient demonstrates its value in the diagnosis of an unusual PID and as a tool for detecting rarer mutations to help guide treatment approaches.

@article{uren_population_2017,
	title = {Population structure and infectious disease risk in southern {Africa}},
	volume = {292},
	issn = {1617-4623},
	doi = {10.1007/s00438-017-1296-2},
	abstract = {The KhoeSan populations are the earliest known indigenous inhabitants of southern Africa. The relatively recent expansion of Bantu-speaking agropastoralists, as well as European colonial settlement along the south-west coast, dramatically changed patterns of genetic diversity in a region which had been largely isolated for thousands of years. Owing to this unique history, population structure in southern Africa reflects both the underlying KhoeSan genetic diversity as well as differential recent admixture. This population structure has a wide range of biomedical and sociocultural implications; such as changes in disease risk profiles. Here, we consolidate information from various population genetic studies that characterize admixture patterns in southern Africa with an aim to better understand differences in adverse disease phenotypes observed among groups. Our review confirms that ancestry has a direct impact on an individual's immune response to infectious diseases. In addition, we emphasize the importance of collaborative research, especially for populations in southern Africa that have a high incidence of potentially fatal infectious diseases such as HIV and tuberculosis.},
	language = {eng},
	number = {3},
	journal = {Molecular genetics and genomics: MGG},
	author = {Uren, Caitlin and Möller, Marlo and van Helden, Paul D. and Henn, Brenna M. and Hoal, Eileen G.},
	month = jun,
	year = {2017},
	pmid = {28229227},
	note = {00000 },
	keywords = {Disease Susceptibility, Southern Africa, population structure},
	pages = {499--509},
}

The KhoeSan populations are the earliest known indigenous inhabitants of southern Africa. The relatively recent expansion of Bantu-speaking agropastoralists, as well as European colonial settlement along the south-west coast, dramatically changed patterns of genetic diversity in a region which had been largely isolated for thousands of years. Owing to this unique history, population structure in southern Africa reflects both the underlying KhoeSan genetic diversity as well as differential recent admixture. This population structure has a wide range of biomedical and sociocultural implications; such as changes in disease risk profiles. Here, we consolidate information from various population genetic studies that characterize admixture patterns in southern Africa with an aim to better understand differences in adverse disease phenotypes observed among groups. Our review confirms that ancestry has a direct impact on an individual's immune response to infectious diseases. In addition, we emphasize the importance of collaborative research, especially for populations in southern Africa that have a high incidence of potentially fatal infectious diseases such as HIV and tuberculosis.

@article{kinnear_exome_2017,
	title = {Exome sequencing identifies a novel {TTC37} mutation in the first reported case of {Trichohepatoenteric} syndrome ({THE}-{S}) in {South} {Africa}},
	volume = {18},
	issn = {1471-2350},
	doi = {10.1186/s12881-017-0388-5},
	abstract = {BACKGROUND: Trichohepatoenteric syndrome (THE-S) or phenotypic diarrhoea of infancy is a rare autosomal recessive disorder characterised by severe infantile diarrhoea, facial dysmorphism, immunodeficiency and woolly hair. It was first described in 1982 in two infants with intractable diarrhoea, liver cirrhosis and abnormal hair structure on microscopy. We report on two siblings from a consanguineous family of Somali descent who, despite extensive clinical investigation, remained undiagnosed until their demise. The index patient died of fulminant cytomegalovirus pneumonitis at 3 months of age.
METHODS: Whole exome sequencing (WES) was performed on a premortem DNA sample from the index case. Variants in a homozygous recessive state or compound heterozygous state were prioritized as potential candidate variants using TAPER™. Sanger sequencing was done to genotype the parents, unaffected sibling and a deceased sibling for the variant of interest.
RESULTS: Exome sequencing identified a novel homozygous mutation (c.4507C {\textgreater} T, rs200067423) in TTC37 which was confirmed by Sanger sequencing in the index case. The identification of this mutation led to the diagnosis of THE-S in the proband and the same homozygous variant was confirmed in a male sibling who died 4 years earlier with severe chronic diarrhoea of infancy. The unaffected parents and sister were heterozygous for the identified variant.
CONCLUSIONS: WES permitted definitive genetic diagnosis despite an atypical presentation in the index case and suggests that severe infection, likely secondary to immunodeficiency, may be a presenting feature. In addition definitive molecular diagnosis allows for genetic counseling and future prenatal diagnosis, and demonstrates the value of WES for post-mortem diagnosis of disorders with a non-specific clinical presentation in which a Mendelian cause is suspected.},
	language = {eng},
	number = {1},
	journal = {BMC medical genetics},
	author = {Kinnear, Craig and Glanzmann, Brigitte and Banda, Eric and Schlechter, Nikola and Durrheim, Glenda and Neethling, Annika and Nel, Etienne and Schoeman, Mardelle and Johnson, Glynis and van Helden, Paul D. and Hoal, Eileen G. and Esser, Monika and Urban, Michael and Möller, Marlo},
	month = mar,
	year = {2017},
	pmid = {28292286},
	pmcid = {PMC5351214},
	note = {00000 },
	keywords = {Consanguineous, Exome, Next generation sequencing, Primary immunodeficiency diseases, Sanger sequencing, Trichohepatoenteric syndrome},
	pages = {26},
}

BACKGROUND: Trichohepatoenteric syndrome (THE-S) or phenotypic diarrhoea of infancy is a rare autosomal recessive disorder characterised by severe infantile diarrhoea, facial dysmorphism, immunodeficiency and woolly hair. It was first described in 1982 in two infants with intractable diarrhoea, liver cirrhosis and abnormal hair structure on microscopy. We report on two siblings from a consanguineous family of Somali descent who, despite extensive clinical investigation, remained undiagnosed until their demise. The index patient died of fulminant cytomegalovirus pneumonitis at 3 months of age. METHODS: Whole exome sequencing (WES) was performed on a premortem DNA sample from the index case. Variants in a homozygous recessive state or compound heterozygous state were prioritized as potential candidate variants using TAPER™. Sanger sequencing was done to genotype the parents, unaffected sibling and a deceased sibling for the variant of interest. RESULTS: Exome sequencing identified a novel homozygous mutation (c.4507C \textgreater T, rs200067423) in TTC37 which was confirmed by Sanger sequencing in the index case. The identification of this mutation led to the diagnosis of THE-S in the proband and the same homozygous variant was confirmed in a male sibling who died 4 years earlier with severe chronic diarrhoea of infancy. The unaffected parents and sister were heterozygous for the identified variant. CONCLUSIONS: WES permitted definitive genetic diagnosis despite an atypical presentation in the index case and suggests that severe infection, likely secondary to immunodeficiency, may be a presenting feature. In addition definitive molecular diagnosis allows for genetic counseling and future prenatal diagnosis, and demonstrates the value of WES for post-mortem diagnosis of disorders with a non-specific clinical presentation in which a Mendelian cause is suspected.

@article{uren_post-gwas_2017,
	title = {A post-{GWAS} analysis of predicted regulatory variants and tuberculosis susceptibility},
	volume = {12},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0174738},
	abstract = {Utilizing data from published tuberculosis (TB) genome-wide association studies (GWAS), we use a bioinformatics pipeline to detect all polymorphisms in linkage disequilibrium (LD) with variants previously implicated in TB disease susceptibility. The probability that these variants had a predicted regulatory function was estimated using RegulomeDB and Ensembl's Variant Effect Predictor. Subsequent genotyping of these 133 predicted regulatory polymorphisms was performed in 400 admixed South African TB cases and 366 healthy controls in a population-based case-control association study to fine-map the causal variant. We detected associations between tuberculosis susceptibility and six intronic polymorphisms located in MARCO, IFNGR2, ASHAS2, ACACA, NISCH and TLR10. Our post-GWAS approach demonstrates the feasibility of combining multiple TB GWAS datasets with linkage information to identify regulatory variants associated with this infectious disease.},
	language = {eng},
	number = {4},
	journal = {PloS One},
	author = {Uren, Caitlin and Henn, Brenna M. and Franke, Andre and Wittig, Michael and van Helden, Paul D. and Hoal, Eileen G. and Möller, Marlo},
	year = {2017},
	pmid = {28384278},
	pmcid = {PMC5383035},
	note = {00000 },
	pages = {e0174738},
}

Utilizing data from published tuberculosis (TB) genome-wide association studies (GWAS), we use a bioinformatics pipeline to detect all polymorphisms in linkage disequilibrium (LD) with variants previously implicated in TB disease susceptibility. The probability that these variants had a predicted regulatory function was estimated using RegulomeDB and Ensembl's Variant Effect Predictor. Subsequent genotyping of these 133 predicted regulatory polymorphisms was performed in 400 admixed South African TB cases and 366 healthy controls in a population-based case-control association study to fine-map the causal variant. We detected associations between tuberculosis susceptibility and six intronic polymorphisms located in MARCO, IFNGR2, ASHAS2, ACACA, NISCH and TLR10. Our post-GWAS approach demonstrates the feasibility of combining multiple TB GWAS datasets with linkage information to identify regulatory variants associated with this infectious disease.

@article{le_roex_toll-like_2017,
	title = {Toll-like receptor ({TLR}) diversity influences mycobacterial growth in {African} buffalo},
	volume = {104},
	issn = {1873-281X},
	doi = {10.1016/j.tube.2017.03.009},
	abstract = {Understanding the role of wildlife in the maintenance or spread of emerging infectious diseases is a growing priority across the world. Bovine tuberculosis (BTB) is a chronic, infectious disease caused by Mycobacterium bovis (M. bovis). BTB is widespread within game reserves in southern Africa, and within these ecosystems the primary wildlife host of this disease is the African buffalo. We used a modified bacterial killing assay for mycobacteria to investigate the effect of Toll-like receptor (TLR) genetic diversity and demographic parameters on the ability of African buffalo to restrict mycobacterial growth. Eosinophil count, time delay, bovine PPD response and avian PPD response were negatively correlated with mycobacterial growth. TLR6 diversity and the interaction of age group and sex were positively correlated with mycobacterial growth. Our results suggest that both demographic and individual immune parameters influence the ability to control mycobacterial infection in African buffalo. TLR6 diversity is particularly interesting as this locus has also shown associations with BTB in cattle, suggesting that further research into the effects, selection and role of TLR6 variants in bovine tuberculosis will be productive.},
	language = {eng},
	journal = {Tuberculosis (Edinburgh, Scotland)},
	author = {le Roex, Nikki and Jolles, Anna and Beechler, Brianna and van Helden, Paul and Hoal, Eileen},
	month = may,
	year = {2017},
	pmid = {28454655},
	note = {00000 },
	keywords = {Bacterial killing, Bovine tuberculosis, Buffalo, Genetic, Immunity, Toll-like receptor},
	pages = {87--94},
}

Understanding the role of wildlife in the maintenance or spread of emerging infectious diseases is a growing priority across the world. Bovine tuberculosis (BTB) is a chronic, infectious disease caused by Mycobacterium bovis (M. bovis). BTB is widespread within game reserves in southern Africa, and within these ecosystems the primary wildlife host of this disease is the African buffalo. We used a modified bacterial killing assay for mycobacteria to investigate the effect of Toll-like receptor (TLR) genetic diversity and demographic parameters on the ability of African buffalo to restrict mycobacterial growth. Eosinophil count, time delay, bovine PPD response and avian PPD response were negatively correlated with mycobacterial growth. TLR6 diversity and the interaction of age group and sex were positively correlated with mycobacterial growth. Our results suggest that both demographic and individual immune parameters influence the ability to control mycobacterial infection in African buffalo. TLR6 diversity is particularly interesting as this locus has also shown associations with BTB in cattle, suggesting that further research into the effects, selection and role of TLR6 variants in bovine tuberculosis will be productive.

@article{shah_functional_2017,
	title = {A {Functional} {TOLLIP} {Variant} is {Associated} with {BCG}-{Specific} {Immune} {Responses} and {Tuberculosis}},
	issn = {1535-4970},
	doi = {10.1164/rccm.201611-2346OC},
	abstract = {RATIONALE: The molecular mechanisms that regulate tuberculosis susceptibility and BCG-induced immunity are mostly unknown. However, induction of the adaptive immune response is a critical step in host control of M. tuberculosis. TOLLIP is a ubiquitin-binding protein that regulates innate immune responses, including TLR signaling, which initiate adaptive immunity. TOLLIP variation is associated with susceptibility to tuberculosis, but the mechanism by which it regulates tuberculosis immunity is poorly understood.
OBJECTIVES: To identify functional TOLLIP variants and evaluate the role of TOLLIP variation on innate and adaptive immune responses to mycobacteria and susceptibility to tuberculosis.
METHODS: We used human cellular immunology approaches to characterize the role of a functional TOLLIP variant on monocyte mRNA expression and M. tuberculosis-induced monocyte immune functions. We also examined the association of TOLLIP variation with BCG-induced T-cell responses and susceptibility to latent TB infection.
MEASUREMENTS AND MAIN RESULTS: We identified a functional TOLLIP promoter region SNP, rs5743854, which was associated with decreased TOLLIP mRNA expression in infant monocytes. After M. tuberculosis infection, TOLLIP-deficient monocytes demonstrated increased IL-6, increased nitrite, and decreased bacterial replication. The TOLLIP-deficiency G/G genotype was associated with decreased BCG-specific IL-2+ CD4+ T-cell frequency and proliferation. This genotype was also associated with increased susceptibility to latent tuberculosis infection.
CONCLUSIONS: TOLLIP deficiency is associated with decreased BCG-specific T-cell responses and increased susceptibility to tuberculosis. We hypothesize that the heightened antibacterial monocyte responses following vaccination of TOLLIP-deficient infants are responsible for decreased BCG-specific T cell responses. Activating TOLLIP may provide a novel adjuvant strategy for BCG vaccination.},
	language = {eng},
	journal = {American Journal of Respiratory and Critical Care Medicine},
	author = {Shah, Javeed A. and Musvosvi, Munyaradzi and Shey, Muki and Horne, David J. and Wells, Richard D. and Peterson, Glenna J. and Cox, Jeffery S. and Daya, Michelle and Hoal, Eileen G. and Lin, Lin and Gottardo, Raphael and Hanekom, Willem A. and Scriba, Thomas J. and Hatherill, Mark and Hawn, Thomas R.},
	month = may,
	year = {2017},
	pmid = {28463648},
	note = {00000 },
	keywords = {BCG, Genetics, Innate Immunity, TOLLIP, Tuberculosis},
}

RATIONALE: The molecular mechanisms that regulate tuberculosis susceptibility and BCG-induced immunity are mostly unknown. However, induction of the adaptive immune response is a critical step in host control of M. tuberculosis. TOLLIP is a ubiquitin-binding protein that regulates innate immune responses, including TLR signaling, which initiate adaptive immunity. TOLLIP variation is associated with susceptibility to tuberculosis, but the mechanism by which it regulates tuberculosis immunity is poorly understood. OBJECTIVES: To identify functional TOLLIP variants and evaluate the role of TOLLIP variation on innate and adaptive immune responses to mycobacteria and susceptibility to tuberculosis. METHODS: We used human cellular immunology approaches to characterize the role of a functional TOLLIP variant on monocyte mRNA expression and M. tuberculosis-induced monocyte immune functions. We also examined the association of TOLLIP variation with BCG-induced T-cell responses and susceptibility to latent TB infection. MEASUREMENTS AND MAIN RESULTS: We identified a functional TOLLIP promoter region SNP, rs5743854, which was associated with decreased TOLLIP mRNA expression in infant monocytes. After M. tuberculosis infection, TOLLIP-deficient monocytes demonstrated increased IL-6, increased nitrite, and decreased bacterial replication. The TOLLIP-deficiency G/G genotype was associated with decreased BCG-specific IL-2+ CD4+ T-cell frequency and proliferation. This genotype was also associated with increased susceptibility to latent tuberculosis infection. CONCLUSIONS: TOLLIP deficiency is associated with decreased BCG-specific T-cell responses and increased susceptibility to tuberculosis. We hypothesize that the heightened antibacterial monocyte responses following vaccination of TOLLIP-deficient infants are responsible for decreased BCG-specific T cell responses. Activating TOLLIP may provide a novel adjuvant strategy for BCG vaccination.

@article{van_der_merwe_curcumin_2017,
	title = {Curcumin {Rescues} a {PINK1} {Knock} {Down} {SH}-{SY5Y} {Cellular} {Model} of {Parkinson}'s {Disease} from {Mitochondrial} {Dysfunction} and {Cell} {Death}},
	volume = {54},
	issn = {1559-1182},
	doi = {10.1007/s12035-016-9843-0},
	abstract = {Parkinson's disease (PD) is a neurodegenerative disorder characterised by the loss of dopaminergic neurons in the substantia nigra. Mutations in the PINK1 gene result in an autosomal recessive form of early-onset PD. PINK1 plays a vital role in mitochondrial quality control via the removal of dysfunctional mitochondria. The aim of the present study was to create a cellular model of PD using siRNA-mediated knock down of PINK1 in SH-SY5Y neuroblastoma cells The possible protective effects of curcumin, known for its many beneficial properties including antioxidant and anti-inflammatory effects, was tested on this model in the presence and absence of paraquat, an additional stressor. PINK1 siRNA and control cells were separated into four treatment groups: (i) untreated, (ii) treated with paraquat, (iii) pre-treated with curcumin then treated with paraquat, or (iv) treated with curcumin. Various parameters of cellular and mitochondrial function were then measured. The PINK1 siRNA cells exhibited significantly decreased cell viability, mitochondrial membrane potential (MMP), mitochondrial respiration and ATP production, and increased apoptosis. Paraquat-treated cells exhibited decreased cell viability, increased apoptosis, a more fragmented mitochondrial network and decreased MMP. Curcumin pre-treatment followed by paraquat exposure rescued cell viability and increased MMP and mitochondrial respiration in control cells, and significantly decreased apoptosis and increased MMP and maximal respiration in PINK1 siRNA cells. These results highlight a protective effect of curcumin against mitochondrial dysfunction and apoptosis in PINK1-deficient and paraquat-exposed cells. More studies are warranted to further elucidate the potential neuroprotective properties of curcumin.},
	language = {eng},
	number = {4},
	journal = {Molecular Neurobiology},
	author = {van der Merwe, Celia and van Dyk, Hayley Christy and Engelbrecht, Lize and van der Westhuizen, Francois Hendrikus and Kinnear, Craig and Loos, Ben and Bardien, Soraya},
	month = may,
	year = {2017},
	pmid = {27003823},
	note = {00006 },
	keywords = {Apoptosis, Curcumin, Mitochondrial dysfunction, PINK1, Parkinson’s disease},
	pages = {2752--2762},
}

Parkinson's disease (PD) is a neurodegenerative disorder characterised by the loss of dopaminergic neurons in the substantia nigra. Mutations in the PINK1 gene result in an autosomal recessive form of early-onset PD. PINK1 plays a vital role in mitochondrial quality control via the removal of dysfunctional mitochondria. The aim of the present study was to create a cellular model of PD using siRNA-mediated knock down of PINK1 in SH-SY5Y neuroblastoma cells The possible protective effects of curcumin, known for its many beneficial properties including antioxidant and anti-inflammatory effects, was tested on this model in the presence and absence of paraquat, an additional stressor. PINK1 siRNA and control cells were separated into four treatment groups: (i) untreated, (ii) treated with paraquat, (iii) pre-treated with curcumin then treated with paraquat, or (iv) treated with curcumin. Various parameters of cellular and mitochondrial function were then measured. The PINK1 siRNA cells exhibited significantly decreased cell viability, mitochondrial membrane potential (MMP), mitochondrial respiration and ATP production, and increased apoptosis. Paraquat-treated cells exhibited decreased cell viability, increased apoptosis, a more fragmented mitochondrial network and decreased MMP. Curcumin pre-treatment followed by paraquat exposure rescued cell viability and increased MMP and mitochondrial respiration in control cells, and significantly decreased apoptosis and increased MMP and maximal respiration in PINK1 siRNA cells. These results highlight a protective effect of curcumin against mitochondrial dysfunction and apoptosis in PINK1-deficient and paraquat-exposed cells. More studies are warranted to further elucidate the potential neuroprotective properties of curcumin.

@article{lumkwana_autophagic_2017,
	title = {Autophagic flux control in neurodegeneration: {Progress} and precision targeting-{Where} do we stand?},
	issn = {1873-5118},
	shorttitle = {Autophagic flux control in neurodegeneration},
	doi = {10.1016/j.pneurobio.2017.03.006},
	abstract = {Neurodegenerative diseases are characterised by the presence of cytoplasmic and nuclear protein aggregates that result in toxicity and neuronal cell death. Autophagy is a physiological cellular process that engulfs primarily long-lived proteins as well as protein aggregates with subsequent cargo delivery for lysosomal degradation. The rate at which the material is degraded through autophagy is referred to as autophagic flux. Although we have progressed substantially in unravelling the role and regulation of the autophagy machinery, its dysfunction in pathology as well as its dynamic changes in the disease progression remains largely unclear. Furthermore, the magnitude of autophagic flux in neuronal subtypes is largely unknown and it is unclear to what extent the flux may be affected in distinct neurodegenerative disease states. In this review, we provide an introduction to autophagy in neuronal homeostasis and indicate how autophagy is currently measured and modulated for therapeutic purposes. We highlight the need not only to develop enhanced methodologies that target and assess autophagic flux precisely, but also to discern the dynamics of autophagy in different neuronal types and brain regions associated with the disease-specific pathology. Finally, we describe how existing and novel techniques for assessing autophagic flux could be implemented in order to distinguish between molecular defects associated with autophagic cargo and the machinery. In doing so, this review may provide novel insights in the assessment and control of autophagic flux that is aligned with the protein clearance dysfunction in neurodegenerative disorders.},
	language = {eng},
	journal = {Progress in Neurobiology},
	author = {Lumkwana, Dumisile and du Toit, Andre and Kinnear, Craig and Loos, Ben},
	month = apr,
	year = {2017},
	pmid = {28385648},
	note = {00001 },
	keywords = {Alzheimer’s disease, Autophagic flux, Autophagic flux assessment, Autophagic flux modulation, Autophagolysosomes, Autophagosomes, Autophagy, Autophagy defects, Huntington’s disease, Lysosomes, Neurodegeneration, Parkison’s disease},
}

Neurodegenerative diseases are characterised by the presence of cytoplasmic and nuclear protein aggregates that result in toxicity and neuronal cell death. Autophagy is a physiological cellular process that engulfs primarily long-lived proteins as well as protein aggregates with subsequent cargo delivery for lysosomal degradation. The rate at which the material is degraded through autophagy is referred to as autophagic flux. Although we have progressed substantially in unravelling the role and regulation of the autophagy machinery, its dysfunction in pathology as well as its dynamic changes in the disease progression remains largely unclear. Furthermore, the magnitude of autophagic flux in neuronal subtypes is largely unknown and it is unclear to what extent the flux may be affected in distinct neurodegenerative disease states. In this review, we provide an introduction to autophagy in neuronal homeostasis and indicate how autophagy is currently measured and modulated for therapeutic purposes. We highlight the need not only to develop enhanced methodologies that target and assess autophagic flux precisely, but also to discern the dynamics of autophagy in different neuronal types and brain regions associated with the disease-specific pathology. Finally, we describe how existing and novel techniques for assessing autophagic flux could be implemented in order to distinguish between molecular defects associated with autophagic cargo and the machinery. In doing so, this review may provide novel insights in the assessment and control of autophagic flux that is aligned with the protein clearance dysfunction in neurodegenerative disorders.

@article{lombard_implications_2016,
	title = {Implications of direct-to-consumer whole-exome sequencing in {South} {Africa}},
	volume = {106},
	issn = {0256-9574},
	abstract = {This editorial examines a number of vitally important ethical, legal and scientific concerns that have to be addressed to ensure proper and ethical implementation of direct-to-consumer whole-exome sequencing in South Africa. Individuals taking part in this endeavour must be fully informed of the positive and negative sequelae.},
	language = {eng},
	number = {2},
	journal = {South African Medical Journal = Suid-Afrikaanse Tydskrif Vir Geneeskunde},
	author = {Lombard, Zané and Baine, Fiona and Krause, Amanda and Lochan, Anneline and Macualay, Shelley and Spencer, Careni and Aldous, Colleen and De Vries, Jantina and Fieggen, Karen and Henderson, Bertram and Hoal, Eileen and Kinnear, Craig and Kinsley, Noelene and September, Alison and Urban, Michael and Soodyall, Himla and Pepper, Michael and Ramsay, Michele},
	month = jan,
	year = {2016},
	pmid = {26821891},
	note = {00001 },
	keywords = {Genetic Counseling, Genetic Privacy, Genome-Wide Association Study, Humans, Sequence Analysis, DNA, South Africa},
	pages = {139--140},
}

This editorial examines a number of vitally important ethical, legal and scientific concerns that have to be addressed to ensure proper and ethical implementation of direct-to-consumer whole-exome sequencing in South Africa. Individuals taking part in this endeavour must be fully informed of the positive and negative sequelae.

@article{mouton_mybph_2016,
	title = {{MYBPH} acts as modifier of cardiac hypertrophy in hypertrophic cardiomyopathy ({HCM}) patients},
	volume = {135},
	issn = {1432-1203},
	doi = {10.1007/s00439-016-1649-7},
	abstract = {Left ventricular hypertrophy is a risk factor for cardiovascular morbidity and mortality. Hypertrophic cardiomyopathy (HCM) is considered a model disease to study causal molecular factors underlying isolated cardiac hypertrophy. However, HCM manifests with various clinical symptoms, even in families bearing the same genetic defects, suggesting that additional factors contribute to hypertrophy. The gene encoding the cardiac myosin binding protein C (cMYBPC) is one of the most frequently implicated genes in HCM. Recently another myosin binding protein, myosin binding protein H (MYBPH) was shown to function in concert with cMYBPC in regulating cardiomyocyte contraction. Given the similarity in sequence, structure and the critical role MYBPH plays in sarcomere contraction, we proposed that MYBPH may be involved in HCM pathogenesis. Family-based genetic association analysis was employed to investigate the contribution of MYBPH in modifying hypertrophy. Seven single nucleotide polymorphisms and haplotypes in MYBPH were investigated for hypertrophy modifying effects in 388 individuals (27 families), in which three unique South African HCM-causing founder mutations (p.R403W and pA797T in β-myosin heavy chain gene (MYH7) and p.R92W in the cardiac troponin T gene (TNNT2)) segregate. We observed a significant association between rs2250509 and hypertrophy traits in the p.A797T MYH7 mutation group. Additionally, haplotype GGTACTT significantly affected hypertrophy within the same mutation group. MYBPH was for the first time assessed as a candidate hypertrophy modifying gene. We identified a novel association between MYBPH and hypertrophy traits in HCM patients carrying the p.A797T MYH7 mutation, suggesting that variation in MYBPH can modulate the severity of hypertrophy in HCM.},
	language = {eng},
	number = {5},
	journal = {Human Genetics},
	author = {Mouton, J. M. and van der Merwe, L. and Goosen, A. and Revera, M. and Brink, P. A. and Moolman-Smook, J. C. and Kinnear, C.},
	month = may,
	year = {2016},
	pmid = {26969327},
	note = {00001 },
	keywords = {Adult, Cardiomegaly, Cardiomyopathy, Hypertrophic, Cohort Studies, Cytoskeletal Proteins, DNA Mutational Analysis, Female, Follow-Up Studies, Genetic Testing, Humans, Male, Middle Aged, Mutation, Polymorphism, Genetic, Prognosis},
	pages = {477--483},
}

Left ventricular hypertrophy is a risk factor for cardiovascular morbidity and mortality. Hypertrophic cardiomyopathy (HCM) is considered a model disease to study causal molecular factors underlying isolated cardiac hypertrophy. However, HCM manifests with various clinical symptoms, even in families bearing the same genetic defects, suggesting that additional factors contribute to hypertrophy. The gene encoding the cardiac myosin binding protein C (cMYBPC) is one of the most frequently implicated genes in HCM. Recently another myosin binding protein, myosin binding protein H (MYBPH) was shown to function in concert with cMYBPC in regulating cardiomyocyte contraction. Given the similarity in sequence, structure and the critical role MYBPH plays in sarcomere contraction, we proposed that MYBPH may be involved in HCM pathogenesis. Family-based genetic association analysis was employed to investigate the contribution of MYBPH in modifying hypertrophy. Seven single nucleotide polymorphisms and haplotypes in MYBPH were investigated for hypertrophy modifying effects in 388 individuals (27 families), in which three unique South African HCM-causing founder mutations (p.R403W and pA797T in β-myosin heavy chain gene (MYH7) and p.R92W in the cardiac troponin T gene (TNNT2)) segregate. We observed a significant association between rs2250509 and hypertrophy traits in the p.A797T MYH7 mutation group. Additionally, haplotype GGTACTT significantly affected hypertrophy within the same mutation group. MYBPH was for the first time assessed as a candidate hypertrophy modifying gene. We identified a novel association between MYBPH and hypertrophy traits in HCM patients carrying the p.A797T MYH7 mutation, suggesting that variation in MYBPH can modulate the severity of hypertrophy in HCM.

@article{haylett_altered_2016,
	title = {Altered {Mitochondrial} {Respiration} and {Other} {Features} of {Mitochondrial} {Function} in {Parkin}-{Mutant} {Fibroblasts} from {Parkinson}'s {Disease} {Patients}},
	volume = {2016},
	issn = {2090-8083},
	doi = {10.1155/2016/1819209},
	abstract = {Mutations in the parkin gene are the most common cause of early-onset Parkinson's disease (PD). Parkin, an E3 ubiquitin ligase, is involved in respiratory chain function, mitophagy, and mitochondrial dynamics. Human cellular models with parkin null mutations are particularly valuable for investigating the mitochondrial functions of parkin. However, published results reporting on patient-derived parkin-mutant fibroblasts have been inconsistent. This study aimed to functionally compare parkin-mutant fibroblasts from PD patients with wild-type control fibroblasts using a variety of assays to gain a better understanding of the role of mitochondrial dysfunction in PD. To this end, dermal fibroblasts were obtained from three PD patients with homozygous whole exon deletions in parkin and three unaffected controls. Assays of mitochondrial respiration, mitochondrial network integrity, mitochondrial membrane potential, and cell growth were performed as informative markers of mitochondrial function. Surprisingly, it was found that mitochondrial respiratory rates were markedly higher in the parkin-mutant fibroblasts compared to control fibroblasts (p = 0.0093), while exhibiting more fragmented mitochondrial networks (p = 0.0304). Moreover, cell growth of the parkin-mutant fibroblasts was significantly higher than that of controls (p = 0.0001). These unanticipated findings are suggestive of a compensatory mechanism to preserve mitochondrial function and quality control in the absence of parkin in fibroblasts, which warrants further investigation.},
	language = {eng},
	journal = {Parkinson's Disease},
	author = {Haylett, William and Swart, Chrisna and van der Westhuizen, Francois and van Dyk, Hayley and van der Merwe, Lize and van der Merwe, Celia and Loos, Ben and Carr, Jonathan and Kinnear, Craig and Bardien, Soraya},
	year = {2016},
	pmid = {27034887},
	pmcid = {PMC4807059},
	note = {00002 },
	pages = {1819209},
}

Mutations in the parkin gene are the most common cause of early-onset Parkinson's disease (PD). Parkin, an E3 ubiquitin ligase, is involved in respiratory chain function, mitophagy, and mitochondrial dynamics. Human cellular models with parkin null mutations are particularly valuable for investigating the mitochondrial functions of parkin. However, published results reporting on patient-derived parkin-mutant fibroblasts have been inconsistent. This study aimed to functionally compare parkin-mutant fibroblasts from PD patients with wild-type control fibroblasts using a variety of assays to gain a better understanding of the role of mitochondrial dysfunction in PD. To this end, dermal fibroblasts were obtained from three PD patients with homozygous whole exon deletions in parkin and three unaffected controls. Assays of mitochondrial respiration, mitochondrial network integrity, mitochondrial membrane potential, and cell growth were performed as informative markers of mitochondrial function. Surprisingly, it was found that mitochondrial respiratory rates were markedly higher in the parkin-mutant fibroblasts compared to control fibroblasts (p = 0.0093), while exhibiting more fragmented mitochondrial networks (p = 0.0304). Moreover, cell growth of the parkin-mutant fibroblasts was significantly higher than that of controls (p = 0.0001). These unanticipated findings are suggestive of a compensatory mechanism to preserve mitochondrial function and quality control in the absence of parkin in fibroblasts, which warrants further investigation.

@article{glanzmann_new_2016,
	title = {A new tool for prioritization of sequence variants from whole exome sequencing data},
	volume = {11},
	doi = {10.1186/s13029-016-0056-8},
	abstract = {BACKGROUND: Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly provide important insights into disease mechanisms. In developing countries, bioinformatics capacity and expertise is severely limited and wet bench scientists are required to take on the challenging task of understanding and implementing the barrage of bioinformatics tools that are available to them.
RESULTS: We designed a novel method for the filtration of WES data called TAPER™ (Tool for Automated selection and Prioritization for Efficient Retrieval of sequence variants).
CONCLUSIONS: TAPER™ implements a set of logical steps by which to prioritize candidate variants that could be associated with disease and this is aimed for implementation in biomedical laboratories with limited bioinformatics capacity. TAPER™ is free, can be setup on a Windows operating system (from Windows 7 and above) and does not require any programming knowledge. In summary, we have developed a freely available tool that simplifies variant prioritization from WES data in order to facilitate discovery of disease-causing genes.},
	language = {eng},
	journal = {Source Code for Biology and Medicine},
	author = {Glanzmann, Brigitte and Herbst, Hendri and Kinnear, Craig J. and Möller, Marlo and Gamieldien, Junaid and Bardien, Soraya},
	year = {2016},
	pmid = {27375772},
	pmcid = {PMC4929716},
	note = {00000 },
	keywords = {Bioinformatics capacity, TAPER™, Variant identification, Whole exome sequencing},
	pages = {10},
}

BACKGROUND: Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly provide important insights into disease mechanisms. In developing countries, bioinformatics capacity and expertise is severely limited and wet bench scientists are required to take on the challenging task of understanding and implementing the barrage of bioinformatics tools that are available to them. RESULTS: We designed a novel method for the filtration of WES data called TAPER™ (Tool for Automated selection and Prioritization for Efficient Retrieval of sequence variants). CONCLUSIONS: TAPER™ implements a set of logical steps by which to prioritize candidate variants that could be associated with disease and this is aimed for implementation in biomedical laboratories with limited bioinformatics capacity. TAPER™ is free, can be setup on a Windows operating system (from Windows 7 and above) and does not require any programming knowledge. In summary, we have developed a freely available tool that simplifies variant prioritization from WES data in order to facilitate discovery of disease-causing genes.

@article{jabot-hanin_major_2016,
	title = {Major {Loci} on {Chromosomes} 8q and 3q {Control} {Interferon} γ {Production} {Triggered} by {Bacillus} {Calmette}-{Guerin} and 6-{kDa} {Early} {Secretory} {Antigen} {Target}, {Respectively}, in {Various} {Populations}},
	volume = {213},
	issn = {1537-6613},
	doi = {10.1093/infdis/jiv757},
	abstract = {BACKGROUND: Interferon γ (IFN-γ) release assays (IGRAs) provide an in vitro measurement of antimycobacterial immunity that is widely used as a test for Mycobacterium tuberculosis infection. IGRA outcomes are highly heritable in various populations, but the nature of the involved genetic factors remains unknown.
METHODS: We conducted a genome-wide linkage analysis of IGRA phenotypes in families from a tuberculosis household contact study in France and a replication study in families from South Africa to confirm the loci identified.
RESULTS: We identified a major locus on chromosome 8q controlling IFN-γ production in response to stimulation with live bacillus Calmette-Guerin (BCG; LOD score, 3.81; P = 1.40 × 10(-5)). We also detected a second locus, on chromosome 3q, that controlled IFN-γ levels in response to stimulation with 6-kDa early secretory antigen target, when accounting for the IFN-γ production shared with that induced by BCG (LOD score, 3.72; P = 1.8 × 10(-5)). Both loci were replicated in South African families, where tuberculosis is hyperendemic. These loci differ from those previously identified as controlling the response to the tuberculin skin test (TST1 and TST2) and the production of TNF-α (TNF1).
CONCLUSIONS: The identification of 2 new linkage signals in populations of various ethnic origins living in different M. tuberculosis exposure settings provides new clues about the genetic control of human antimycobacterial immunity.},
	language = {eng},
	number = {7},
	journal = {The Journal of Infectious Diseases},
	author = {Jabot-Hanin, Fabienne and Cobat, Aurélie and Feinberg, Jacqueline and Grange, Ghislain and Remus, Natascha and Poirier, Christine and Boland-Auge, Anne and Besse, Céline and Bustamante, Jacinta and Boisson-Dupuis, Stéphanie and Casanova, Jean-Laurent and Schurr, Erwin and Alcaïs, Alexandre and Hoal, Eileen G. and Delacourt, Christophe and Abel, Laurent},
	month = apr,
	year = {2016},
	pmid = {26690346},
	pmcid = {PMC4779307},
	note = {00002 },
	keywords = {Antigens, Bacterial, Bacterial Proteins, Chromosomes, Human, Pair 3, Chromosomes, Human, Pair 8, Cohort Studies, Female, France, Gene Expression Regulation, Bacterial, Genetic Linkage, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Interferon-gamma, Male, Mycobacterium bovis, Phenotype, Prospective Studies, South Africa, Tuberculosis, genetic control, genetic linkage analysis, interferon gamma release assays, mycobacteria},
	pages = {1173--1179},
}

BACKGROUND: Interferon γ (IFN-γ) release assays (IGRAs) provide an in vitro measurement of antimycobacterial immunity that is widely used as a test for Mycobacterium tuberculosis infection. IGRA outcomes are highly heritable in various populations, but the nature of the involved genetic factors remains unknown. METHODS: We conducted a genome-wide linkage analysis of IGRA phenotypes in families from a tuberculosis household contact study in France and a replication study in families from South Africa to confirm the loci identified. RESULTS: We identified a major locus on chromosome 8q controlling IFN-γ production in response to stimulation with live bacillus Calmette-Guerin (BCG; LOD score, 3.81; P = 1.40 × 10(-5)). We also detected a second locus, on chromosome 3q, that controlled IFN-γ levels in response to stimulation with 6-kDa early secretory antigen target, when accounting for the IFN-γ production shared with that induced by BCG (LOD score, 3.72; P = 1.8 × 10(-5)). Both loci were replicated in South African families, where tuberculosis is hyperendemic. These loci differ from those previously identified as controlling the response to the tuberculin skin test (TST1 and TST2) and the production of TNF-α (TNF1). CONCLUSIONS: The identification of 2 new linkage signals in populations of various ethnic origins living in different M. tuberculosis exposure settings provides new clues about the genetic control of human antimycobacterial immunity.

@article{bowker_polymorphisms_2016,
	title = {Polymorphisms in the {Pattern} {Recognition} {Receptor} {Mincle} {Gene} ({CLEC4E}) and {Association} with {Tuberculosis}},
	volume = {194},
	issn = {1432-1750},
	doi = {10.1007/s00408-016-9915-y},
	abstract = {The mechanisms involved in interactions between Mycobacterium tuberculosis and host innate immune cells determine outcome. Antigen-presenting cells, including macrophages and dendritic cells, express many pattern recognition receptors to identify pathogen-associated molecular patterns, thereby initiating an immune response. A major mycobacterial virulence factor, trehalose-6',6-dimycolate, is recognised by the macrophage-inducible C-type lectin, Mincle, which leads to the activation of the Syk-Card9 signalling pathway in macrophages. Mincle is encoded by CLEC4E, and we investigated polymorphisms in this gene to assess its role in tuberculosis susceptibility. Four tagging single nucleotide polymorphisms (SNPs) (rs10841845, rs10841847, rs10841856 and rs4620776) were genotyped using TaqMan(®) SNP assays in 416 tuberculosis cases and 405 healthy controls. Logistic regression models were used for analysis. No association was detected with any of the SNPs analysed. This research highlights tuberculosis disease complexity where recognition proteins which specifically bind mycobacterial glycolipids cannot be conclusively associated with the disease in genetic studies.},
	language = {eng},
	number = {5},
	journal = {Lung},
	author = {Bowker, Nicholas and Salie, Muneeb and Schurz, Haiko and van Helden, Paul D. and Kinnear, Craig J. and Hoal, Eileen G. and Möller, Marlo},
	month = oct,
	year = {2016},
	pmid = {27363694},
	note = {00001 },
	keywords = {CLEC4E, Mincle, Mycobacterium tuberculosis, Polymorphism, Susceptibility},
	pages = {763--767},
}

The mechanisms involved in interactions between Mycobacterium tuberculosis and host innate immune cells determine outcome. Antigen-presenting cells, including macrophages and dendritic cells, express many pattern recognition receptors to identify pathogen-associated molecular patterns, thereby initiating an immune response. A major mycobacterial virulence factor, trehalose-6',6-dimycolate, is recognised by the macrophage-inducible C-type lectin, Mincle, which leads to the activation of the Syk-Card9 signalling pathway in macrophages. Mincle is encoded by CLEC4E, and we investigated polymorphisms in this gene to assess its role in tuberculosis susceptibility. Four tagging single nucleotide polymorphisms (SNPs) (rs10841845, rs10841847, rs10841856 and rs4620776) were genotyped using TaqMan(®) SNP assays in 416 tuberculosis cases and 405 healthy controls. Logistic regression models were used for analysis. No association was detected with any of the SNPs analysed. This research highlights tuberculosis disease complexity where recognition proteins which specifically bind mycobacterial glycolipids cannot be conclusively associated with the disease in genetic studies.

@article{uren_fine-scale_2016,
	title = {Fine-{Scale} {Human} {Population} {Structure} in {Southern} {Africa} {Reflects} {Ecogeographic} {Boundaries}},
	volume = {204},
	issn = {1943-2631},
	doi = {10.1534/genetics.116.187369},
	abstract = {Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for {\textgreater}100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N{\textbar}u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.},
	language = {eng},
	number = {1},
	journal = {Genetics},
	author = {Uren, Caitlin and Kim, Minju and Martin, Alicia R. and Bobo, Dean and Gignoux, Christopher R. and van Helden, Paul D. and Möller, Marlo and Hoal, Eileen G. and Henn, Brenna M.},
	month = sep,
	year = {2016},
	pmid = {27474727},
	pmcid = {PMC5012395},
	note = {00003 },
	keywords = {KhoeSan, ancestry, pastoralism, population structure},
	pages = {303--314},
}

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for \textgreater100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N\textbaru-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.

@article{glanzmann_complete_2016,
	title = {The complete genome sequence of the {African} buffalo ({Syncerus} caffer)},
	volume = {17},
	issn = {1471-2164},
	doi = {10.1186/s12864-016-3364-0},
	abstract = {BACKGROUND: The African buffalo (Syncerus caffer) is an important role player in the savannah ecosystem. It has become a species of relevance because of its role as a wildlife maintenance host for an array of infectious and zoonotic diseases some of which include corridor disease, foot-and-mouth disease and bovine tuberculosis. To date, no complete genome sequence for S. caffer had been available for study and the genomes of other species such as the domestic cow (Bos taurus) had been used as a proxy for any genetics analysis conducted on this species. Here, the high coverage genome sequence of the African buffalo (S. caffer) is presented.
RESULTS: A total of 19,765 genes were predicted and 19,296 genes could be successfully annotated to S. caffer while 469 genes remained unannotated. Moreover, in order to extend a detailed annotation of S. caffer, gene clusters were constructed using twelve additional mammalian genomes. The S. caffer genome contains 10,988 gene clusters, of which 62 are shared exclusively between B. taurus and S. caffer.
CONCLUSIONS: This study provides a unique genomic perspective for the S. caffer, allowing for the identification of novel variants that may play a role in the natural history and physiological adaptations.},
	language = {eng},
	number = {1},
	journal = {BMC genomics},
	author = {Glanzmann, Brigitte and Möller, Marlo and le Roex, Nikki and Tromp, Gerard and Hoal, Eileen G. and van Helden, Paul D.},
	month = dec,
	year = {2016},
	pmid = {27927182},
	pmcid = {PMC5142436},
	note = {00000 },
	keywords = {Bos taurus, Genetic diversity, Genome assembly, Syncerus caffer},
	pages = {1001},
}

BACKGROUND: The African buffalo (Syncerus caffer) is an important role player in the savannah ecosystem. It has become a species of relevance because of its role as a wildlife maintenance host for an array of infectious and zoonotic diseases some of which include corridor disease, foot-and-mouth disease and bovine tuberculosis. To date, no complete genome sequence for S. caffer had been available for study and the genomes of other species such as the domestic cow (Bos taurus) had been used as a proxy for any genetics analysis conducted on this species. Here, the high coverage genome sequence of the African buffalo (S. caffer) is presented. RESULTS: A total of 19,765 genes were predicted and 19,296 genes could be successfully annotated to S. caffer while 469 genes remained unannotated. Moreover, in order to extend a detailed annotation of S. caffer, gene clusters were constructed using twelve additional mammalian genomes. The S. caffer genome contains 10,988 gene clusters, of which 62 are shared exclusively between B. taurus and S. caffer. CONCLUSIONS: This study provides a unique genomic perspective for the S. caffer, allowing for the identification of novel variants that may play a role in the natural history and physiological adaptations.

@article{uys_risk_2015,
	title = {The {Risk} of {Tuberculosis} {Reinfection} {Soon} after {Cure} of a {First} {Disease} {Episode} {Is} {Extremely} {High} in a {Hyperendemic} {Community}},
	volume = {10},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0144487},
	abstract = {Elevated rates of reinfection tuberculosis in various hyperendemic regions have been reported and, in particular, it has been shown that in a high-incidence setting near Cape Town, South Africa, the rate of reinfection tuberculosis (TB) disease after cure of a previous TB disease episode is about four times greater than the rate of first-time TB disease. It is not known whether this elevated rate is caused by a high reinfection rate due, for instance, to living circumstances, or a high rate of progress to disease specific to the patients, or both. In order to address that question we analysed an extensive data set from clinics attended by TB patients in the high-incidence setting near Cape Town, South Africa and found that, in fact, the (average) rate of reinfection (as opposed to the rate of reinfection disease) after cure of a previous TB disease episode is initially about 0.85 per annum. This rate diminishes rapidly over time and after about ten years this rate is similar to the rate of infection in the general population. Also, the rate of progress to disease after reinfection is initially high but declines in subsequent years down to the figure typical for the general population. These findings suggest that the first few months after cure of a TB disease episode form a critical period for controlling reinfection disease in a hyperendemic setting and that monitoring such cured patients could pre-empt a reinfection progressing to active disease.},
	language = {eng},
	number = {12},
	journal = {PloS One},
	author = {Uys, Pieter and Brand, Hilmarie and Warren, Robin and van der Spuy, Gian and Hoal, Eileen G. and van Helden, Paul D.},
	year = {2015},
	pmid = {26649422},
	pmcid = {PMC4674135},
	note = {00001 },
	pages = {e0144487},
}

Elevated rates of reinfection tuberculosis in various hyperendemic regions have been reported and, in particular, it has been shown that in a high-incidence setting near Cape Town, South Africa, the rate of reinfection tuberculosis (TB) disease after cure of a previous TB disease episode is about four times greater than the rate of first-time TB disease. It is not known whether this elevated rate is caused by a high reinfection rate due, for instance, to living circumstances, or a high rate of progress to disease specific to the patients, or both. In order to address that question we analysed an extensive data set from clinics attended by TB patients in the high-incidence setting near Cape Town, South Africa and found that, in fact, the (average) rate of reinfection (as opposed to the rate of reinfection disease) after cure of a previous TB disease episode is initially about 0.85 per annum. This rate diminishes rapidly over time and after about ten years this rate is similar to the rate of infection in the general population. Also, the rate of progress to disease after reinfection is initially high but declines in subsequent years down to the figure typical for the general population. These findings suggest that the first few months after cure of a TB disease episode form a critical period for controlling reinfection disease in a hyperendemic setting and that monitoring such cured patients could pre-empt a reinfection progressing to active disease.

@article{schurz_tlr1_2015,
	title = {{TLR1}, 2, 4, 6 and 9 {Variants} {Associated} with {Tuberculosis} {Susceptibility}: {A} {Systematic} {Review} and {Meta}-{Analysis}},
	volume = {10},
	issn = {1932-6203},
	shorttitle = {{TLR1}, 2, 4, 6 and 9 {Variants} {Associated} with {Tuberculosis} {Susceptibility}},
	doi = {10.1371/journal.pone.0139711},
	abstract = {BACKGROUND: Studies investigating the influence of toll-like receptor (TLR) polymorphisms and tuberculosis susceptibility have yielded varying and often contradictory results in different ethnic groups. A meta-analysis was conducted to investigate the relationship between TLR variants and susceptibility to tuberculosis, both across and within specific ethnic groups.
METHODS: An extensive database search was performed for studies investigating the relationship between TLR and tuberculosis (TB) susceptibility. Data was subsequently extracted from included studies and statistically analysed.
RESULTS: 32 articles involving 18907 individuals were included in this meta-analysis, and data was extracted for 14 TLR polymorphisms. Various genetic models were employed. An increased risk of TB was found for individuals with the TLR2 rs3804100 CC and the TLR9 rs352139 GA and GG genotypes, while decreased risk was identified for those with the AG genotype of TLR1 rs4833095. The T allele of TLR6 rs5743810 conferred protection across all ethnic groups. TLR2 rs5743708 subgroup analysis identified the A allele to increase susceptibility to TB in the Asian ethnic group, while conferring protection in the Hispanic group. The T allele of TLR4 rs4986791 was also found to increase the risk of TB in the Asian subgroup. All other TLR gene variants investigated were not found to be associated with TB in this meta-analysis.
DISCUSSION: Although general associations were identified, most TLR variants showed no significant association with TB, indicating that additional studies investigating a wider range of pattern recognition receptors is required to gain a better understanding of this complex disease.},
	language = {eng},
	number = {10},
	journal = {PloS One},
	author = {Schurz, Haiko and Daya, Michelle and Möller, Marlo and Hoal, Eileen G. and Salie, Muneeb},
	year = {2015},
	pmid = {26430737},
	pmcid = {PMC4592262},
	note = {00000 },
	pages = {e0139711},
}

BACKGROUND: Studies investigating the influence of toll-like receptor (TLR) polymorphisms and tuberculosis susceptibility have yielded varying and often contradictory results in different ethnic groups. A meta-analysis was conducted to investigate the relationship between TLR variants and susceptibility to tuberculosis, both across and within specific ethnic groups. METHODS: An extensive database search was performed for studies investigating the relationship between TLR and tuberculosis (TB) susceptibility. Data was subsequently extracted from included studies and statistically analysed. RESULTS: 32 articles involving 18907 individuals were included in this meta-analysis, and data was extracted for 14 TLR polymorphisms. Various genetic models were employed. An increased risk of TB was found for individuals with the TLR2 rs3804100 CC and the TLR9 rs352139 GA and GG genotypes, while decreased risk was identified for those with the AG genotype of TLR1 rs4833095. The T allele of TLR6 rs5743810 conferred protection across all ethnic groups. TLR2 rs5743708 subgroup analysis identified the A allele to increase susceptibility to TB in the Asian ethnic group, while conferring protection in the Hispanic group. The T allele of TLR4 rs4986791 was also found to increase the risk of TB in the Asian subgroup. All other TLR gene variants investigated were not found to be associated with TB in this meta-analysis. DISCUSSION: Although general associations were identified, most TLR variants showed no significant association with TB, indicating that additional studies investigating a wider range of pattern recognition receptors is required to gain a better understanding of this complex disease.

@article{salie_activating_2015,
	title = {Activating {KIRs} alter susceptibility to pulmonary tuberculosis in a {South} {African} population},
	issn = {1873-281X},
	doi = {10.1016/j.tube.2015.09.003},
	abstract = {We investigate the role of killer immunoglobulin-like receptor (KIR) genes and human leukocyte antigen class-I (HLA) variants in susceptibility to tuberculosis in a South African population. In a sample set comprising 408 TB cases and 351 healthy controls, we show that the KIR3DS1 gene and KIR genotypes with five or more activating KIRs, and the presence of 3DS1, protect against developing active TB in the South African Coloured population. Several HLA class-I alleles were identified as susceptibility factors for TB disease. However, none of the KIR-HLA compound genotypes were found to be associated with TB. Our data suggests that the KIR genes may play an important role in TB disease.},
	language = {ENG},
	journal = {Tuberculosis (Edinburgh, Scotland)},
	author = {Salie, Muneeb and Daya, Michelle and Möller, Marlo and Hoal, Eileen G.},
	month = oct,
	year = {2015},
	pmid = {26542219},
	note = {00000 },
	keywords = {HLA, KIR, Susceptibility, Tuberculosis},
}

We investigate the role of killer immunoglobulin-like receptor (KIR) genes and human leukocyte antigen class-I (HLA) variants in susceptibility to tuberculosis in a South African population. In a sample set comprising 408 TB cases and 351 healthy controls, we show that the KIR3DS1 gene and KIR genotypes with five or more activating KIRs, and the presence of 3DS1, protect against developing active TB in the South African Coloured population. Several HLA class-I alleles were identified as susceptibility factors for TB disease. However, none of the KIR-HLA compound genotypes were found to be associated with TB. Our data suggests that the KIR genes may play an important role in TB disease.

@article{mouton_ascribing_2015,
	title = {Ascribing novel functions to the sarcomeric protein, myosin binding protein {H} ({MyBPH}) in cardiac sarcomere contraction},
	volume = {331},
	issn = {1090-2422},
	doi = {10.1016/j.yexcr.2014.11.006},
	abstract = {Myosin binding protein H (MyBPH) is a protein of unknown function, which shares sequence and structural similarities with myosin binding protein C (cMyBPC), a protein frequently implicated in hypertrophic cardiomyopathy (HCM). Given the similarity between cMyBPC and MyBPH, we proposed that MyBPH, like cMyBPC, could be involved in HCM pathogenesis and we therefore sought to determine its function. We identified MyBPH-interacting proteins by using yeast two-hybrid (Y2H) analysis. The role of MyBPH and cMyBPC in cardiac cell contractility was analysed by measuring the planar cell surface area of differentiated H9c2 rat cardiomyocytes in response to β-adrenergic stress after siRNA knockdown of MyBPH and cMyBPC. Individual knockdown of either protein had no effect on cardiac contractility, while concurrent knockdowns reduced cardiac contractility. These proteins therefore functionally compensate for one another and are critical for cardiac contractility. We further show that both proteins co-localise with the autophagosomal membrane protein LC3, suggesting that both proteins are involved in autophagosomal membrane maturation processes. The results of this study ascribe novel functions to MyBPH, which may contribute to our understanding of its role in the sarcomere. This study provides evidence for a potential role of MyBPH in HCM, which warrants further investigation.},
	language = {eng},
	number = {2},
	journal = {Experimental Cell Research},
	author = {Mouton, Jomien and Loos, Ben and Moolman-Smook, Johanna C. and Kinnear, Craig J.},
	month = feb,
	year = {2015},
	pmid = {25449695},
	note = {00000 },
	keywords = {Actins, Animals, Autophagy, Cardiomyopathy, Hypertrophic, Carrier Proteins, Cells, Cultured, Cytoskeletal Proteins, Microtubule-Associated Proteins, Myocardial Contraction, Myocytes, Cardiac, Myosin Heavy Chains, Protein Binding, RNA Interference, RNA, Small Interfering, Rats, Sarcomeres, Two-Hybrid System Techniques, Ubiquitin-Conjugating Enzymes},
	pages = {338--351},
}

Myosin binding protein H (MyBPH) is a protein of unknown function, which shares sequence and structural similarities with myosin binding protein C (cMyBPC), a protein frequently implicated in hypertrophic cardiomyopathy (HCM). Given the similarity between cMyBPC and MyBPH, we proposed that MyBPH, like cMyBPC, could be involved in HCM pathogenesis and we therefore sought to determine its function. We identified MyBPH-interacting proteins by using yeast two-hybrid (Y2H) analysis. The role of MyBPH and cMyBPC in cardiac cell contractility was analysed by measuring the planar cell surface area of differentiated H9c2 rat cardiomyocytes in response to β-adrenergic stress after siRNA knockdown of MyBPH and cMyBPC. Individual knockdown of either protein had no effect on cardiac contractility, while concurrent knockdowns reduced cardiac contractility. These proteins therefore functionally compensate for one another and are critical for cardiac contractility. We further show that both proteins co-localise with the autophagosomal membrane protein LC3, suggesting that both proteins are involved in autophagosomal membrane maturation processes. The results of this study ascribe novel functions to MyBPH, which may contribute to our understanding of its role in the sarcomere. This study provides evidence for a potential role of MyBPH in HCM, which warrants further investigation.

@article{mouton_diagnostic_2015,
	title = {Diagnostic disparity and identification of two {TNNI3} gene mutations, one novel and one arising de novo, in {South} {African} patients with restrictive cardiomyopathy and focal ventricular hypertrophy},
	volume = {26},
	issn = {1680-0745},
	doi = {10.5830/CVJA-2015-019},
	abstract = {INTRODUCTION: The minimum criterion for the diagnosis of hypertrophic cardiomyopathy (HCM) is thickening of the left ventricular wall, typically in an asymmetrical or focal fashion, and it requires no functional deficit. Using this criterion, we identified a family with four affected individuals and a single unrelated individual essentially with restrictive cardiomyopathy (RCM). Mutations in genes coding for the thin filaments of cardiac muscle have been described in RCM and HCM with 'restrictive features'. One such gene encodes for cardiac troponin I (TNNI3), a sub-unit of the troponin complex involved in the regulation of striated muscle contraction. We hypothesised that mutations in TNNI3 could underlie this particular phenotype, and we therefore screened TNNI3 for mutations in 115 HCM probands.
METHODS: Clinical investigation involved examination, echocardiography, chest X-ray and an electrocardiogram of both the index cases and close relatives. The study cohort consisted of 113 South African HCM probands, with and without known founder HCM mutations, and 100 ethnically matched control individuals. Mutation screening of TNNI3 for diseasecausing mutations were performed using high-resolution melt (HRM) analysis.
RESULTS: HRM analyses identified three previously described HCM-causing mutations (p.Pro82Ser, p.Arg162Gln, p.Arg170Gln) and a novel exonic variant (p.Leu144His). A previous study involving the same amino acid identified a p.Leu144Gln mutation in a patient presenting with RCM, with clinical features of HCM. We observed the novel p.Leu144His mutation in three siblings with clinical RCM and varying degrees of ventricular hypertrophy. The isolated index case with the de novo p.Arg170Gln mutation presented with a similar phenotype. Both mutations were absent in a healthy control group.
CONCLUSION: We have identified a novel disease-causing p.Leu144His mutation and a de novo p.Arg170Gln mutation associated with RCM and focal ventricular hypertrophy, often below the typical diagnostic threshold for HCM. Our study provides information regarding TNNI3 mutations underlying RCM in contrast to other causes of a similar presentation, such as constrictive pericarditis or infiltration of cardiac muscle, all with marked right-sided cardiac manifestations. This study therefore highlights the need for extensive mutation screening of genes encoding for sarcomeric proteins, such as TNNI3 to identify the underlying cause of this particular phenotype.},
	language = {eng},
	number = {2},
	journal = {Cardiovascular Journal of Africa},
	author = {Mouton, Jomien M. and Pellizzon, Adriano S. and Goosen, Althea and Kinnear, Craig J. and Herbst, Philip G. and Brink, Paul A. and Moolman-Smook, Johanna C.},
	month = apr,
	year = {2015},
	pmid = {25940119},
	note = {00000 },
	pages = {63--69},
}

INTRODUCTION: The minimum criterion for the diagnosis of hypertrophic cardiomyopathy (HCM) is thickening of the left ventricular wall, typically in an asymmetrical or focal fashion, and it requires no functional deficit. Using this criterion, we identified a family with four affected individuals and a single unrelated individual essentially with restrictive cardiomyopathy (RCM). Mutations in genes coding for the thin filaments of cardiac muscle have been described in RCM and HCM with 'restrictive features'. One such gene encodes for cardiac troponin I (TNNI3), a sub-unit of the troponin complex involved in the regulation of striated muscle contraction. We hypothesised that mutations in TNNI3 could underlie this particular phenotype, and we therefore screened TNNI3 for mutations in 115 HCM probands. METHODS: Clinical investigation involved examination, echocardiography, chest X-ray and an electrocardiogram of both the index cases and close relatives. The study cohort consisted of 113 South African HCM probands, with and without known founder HCM mutations, and 100 ethnically matched control individuals. Mutation screening of TNNI3 for diseasecausing mutations were performed using high-resolution melt (HRM) analysis. RESULTS: HRM analyses identified three previously described HCM-causing mutations (p.Pro82Ser, p.Arg162Gln, p.Arg170Gln) and a novel exonic variant (p.Leu144His). A previous study involving the same amino acid identified a p.Leu144Gln mutation in a patient presenting with RCM, with clinical features of HCM. We observed the novel p.Leu144His mutation in three siblings with clinical RCM and varying degrees of ventricular hypertrophy. The isolated index case with the de novo p.Arg170Gln mutation presented with a similar phenotype. Both mutations were absent in a healthy control group. CONCLUSION: We have identified a novel disease-causing p.Leu144His mutation and a de novo p.Arg170Gln mutation associated with RCM and focal ventricular hypertrophy, often below the typical diagnostic threshold for HCM. Our study provides information regarding TNNI3 mutations underlying RCM in contrast to other causes of a similar presentation, such as constrictive pericarditis or infiltration of cardiac muscle, all with marked right-sided cardiac manifestations. This study therefore highlights the need for extensive mutation screening of genes encoding for sarcomeric proteins, such as TNNI3 to identify the underlying cause of this particular phenotype.

@article{salie_association_2015,
	title = {Association of toll-like receptors with susceptibility to tuberculosis suggests sex-specific effects of {TLR8} polymorphisms},
	volume = {34},
	issn = {1567-7257},
	doi = {10.1016/j.meegid.2015.07.004},
	abstract = {BACKGROUND: Toll-like receptors (TLRs) are involved in the recognition of conserved microbial structures, leading to activation of an inflammatory response and formation of an adaptive immune response.
METHODS: Twenty-three polymorphisms in five TLR genes were genotyped in 729 tuberculosis cases and 487 healthy controls in a population-based case-control association study in a South African population.
RESULTS: We detected sex-specific associations for TLR8 polymorphisms, with rs3761624 (OR=1.54, p{\textless}0.001), rs3764879 (OR=1.41, p=0.011) and rs3764880 (OR=1.42, p=0.011) associated in females and rs3764879 (OR=0.72, p=0.013) and rs3764880 (OR=0.75, p=0.036) associated in males. Epistatic interactions between the TLR genes were investigated and the TLR1\_rs4833095 polymorphism was shown to interact with TLR2\_rs3804100 and (GT)n microsatellite (p=0.002) and alter susceptibility to TB. We also studied the role of TLRs in disease caused by different Mycobacterium tuberculosis genotypes in 257 tuberculosis cases, and identified associations between specific TLR polymorphisms and disease caused by specific strains.
CONCLUSION: This study provides further evidence that the TLRs play an important role in the outcome of tuberculosis disease, and suggests a partial explanation for the male bias in tuberculosis ratios.},
	language = {eng},
	journal = {Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases},
	author = {Salie, Muneeb and Daya, Michelle and Lucas, Lance A. and Warren, Robin M. and van der Spuy, Gian D. and van Helden, Paul D. and Hoal, Eileen G. and Möller, Marlo},
	month = aug,
	year = {2015},
	pmid = {26160538},
	pages = {221--229},
}

BACKGROUND: Toll-like receptors (TLRs) are involved in the recognition of conserved microbial structures, leading to activation of an inflammatory response and formation of an adaptive immune response. METHODS: Twenty-three polymorphisms in five TLR genes were genotyped in 729 tuberculosis cases and 487 healthy controls in a population-based case-control association study in a South African population. RESULTS: We detected sex-specific associations for TLR8 polymorphisms, with rs3761624 (OR=1.54, p\textless0.001), rs3764879 (OR=1.41, p=0.011) and rs3764880 (OR=1.42, p=0.011) associated in females and rs3764879 (OR=0.72, p=0.013) and rs3764880 (OR=0.75, p=0.036) associated in males. Epistatic interactions between the TLR genes were investigated and the TLR1_rs4833095 polymorphism was shown to interact with TLR2_rs3804100 and (GT)n microsatellite (p=0.002) and alter susceptibility to TB. We also studied the role of TLRs in disease caused by different Mycobacterium tuberculosis genotypes in 257 tuberculosis cases, and identified associations between specific TLR polymorphisms and disease caused by specific strains. CONCLUSION: This study provides further evidence that the TLRs play an important role in the outcome of tuberculosis disease, and suggests a partial explanation for the male bias in tuberculosis ratios.

@article{daya_investigating_2015,
	title = {Investigating the {Role} of {Gene}-{Gene} {Interactions} in {TB} {Susceptibility}},
	volume = {10},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0123970},
	abstract = {Tuberculosis (TB) is the second leading cause of mortality from infectious disease worldwide. One of the factors involved in developing disease is the genetics of the host, yet the field of TB susceptibility genetics has not yielded the answers that were expected. A commonly posited explanation for the missing heritability of complex disease is gene-gene interactions, also referred to as epistasis. In this study we investigate the role of gene-gene interactions in genetic susceptibility to TB using a cohort recruited from a high TB incidence community from Cape Town, South Africa. Our discovery data set incorporates genotypes from a large a number of candidate gene studies as well as genome-wide data. After limiting our search space to pairs of putative TB susceptibility genes, as well as pairs of genes that have been curated in online databases as potential interactors, we use statistical modelling to identify pairs of interacting SNPs. We attempt to validate the top models identified in our discovery data set using an independent genome-wide TB case-control data set from The Gambia. A number of models were successfully validated, indicating that interplay between the NRG1 - NRG3, GRIK1 - GRIK3 and IL23R - ATG4C gene pairs may modify susceptibility to TB. Gene pairs involved in the NF-κB pathway were also identified in the discovery data set (SFTPD - NOD2, ISG15 - TLR8 and NLRC5 - IL12RB1), but could not be tested in the Gambian study group due to lack of overlapping data.},
	language = {eng},
	number = {4},
	journal = {PloS One},
	author = {Daya, Michelle and van der Merwe, Lize and van Helden, Paul D. and Möller, Marlo and Hoal, Eileen G.},
	year = {2015},
	pmid = {25919455},
	pmcid = {PMC4412713},
	note = {00000 },
	pages = {e0123970},
}

Tuberculosis (TB) is the second leading cause of mortality from infectious disease worldwide. One of the factors involved in developing disease is the genetics of the host, yet the field of TB susceptibility genetics has not yielded the answers that were expected. A commonly posited explanation for the missing heritability of complex disease is gene-gene interactions, also referred to as epistasis. In this study we investigate the role of gene-gene interactions in genetic susceptibility to TB using a cohort recruited from a high TB incidence community from Cape Town, South Africa. Our discovery data set incorporates genotypes from a large a number of candidate gene studies as well as genome-wide data. After limiting our search space to pairs of putative TB susceptibility genes, as well as pairs of genes that have been curated in online databases as potential interactors, we use statistical modelling to identify pairs of interacting SNPs. We attempt to validate the top models identified in our discovery data set using an independent genome-wide TB case-control data set from The Gambia. A number of models were successfully validated, indicating that interplay between the NRG1 - NRG3, GRIK1 - GRIK3 and IL23R - ATG4C gene pairs may modify susceptibility to TB. Gene pairs involved in the NF-κB pathway were also identified in the discovery data set (SFTPD - NOD2, ISG15 - TLR8 and NLRC5 - IL12RB1), but could not be tested in the Gambian study group due to lack of overlapping data.

@article{le_roex_disease_2015,
	title = {Disease {Control} in {Wildlife}: {Evaluating} a {Test} and {Cull} {Programme} for {Bovine} {Tuberculosis} in {African} {Buffalo}},
	issn = {1865-1682},
	shorttitle = {Disease {Control} in {Wildlife}},
	doi = {10.1111/tbed.12329},
	abstract = {Providing an evidence base for wildlife population management is difficult, due to limited opportunities for experimentation and study replication at the population level. We utilized an opportunity to assess the outcome of a test and cull programme aimed at limiting the spread of Mycobacterium bovis in African buffalo. Buffalo act as reservoirs of M. bovis, the causative agent of bovine tuberculosis (BTB), which can have major economic, ecological and public health impacts through the risk of infection to other wildlife species, livestock and surrounding communities. BTB prevalence data were collected in conjunction with disease control operations in Hluhluwe-iMfolozi Park, South Africa, from 1999 to 2006. A total of 4733 buffalo (250-950 per year) were tested for BTB using the single comparative intradermal tuberculin (SCIT) test, with BTB-positive animals culled, and negative animals released. BTB prevalence was spatially and temporally variable, ranging from 2.3\% to 54.7\%. Geographic area was a strong predictor of BTB transmission in HiP, owing to relatively stable herds and home ranges. Herds experiencing more intensive and frequent captures showed reduced per capita disease transmission risk and less increase in herd prevalence over time. Disease hot spots did not expand spatially over time, and BTB prevalence in all but the hot spot areas was maintained between 10\% and 15\% throughout the study period. Our data suggest that HiP's test and cull programme was effective at reducing BTB transmission in buffalo, with capture effort and interval found to be the crucial components of the programme. The programme was thus successful with respect to the original goals; however, there are additional factors that should be considered in future cost/benefit analyses and decision-making. These findings may be utilized and expanded in future collaborative work between wildlife managers, veterinarians and scientists, to optimize wildlife disease control programmes and mitigate conflict at the interface of conservation, agricultural and urban areas.},
	language = {ENG},
	journal = {Transboundary and Emerging Diseases},
	author = {le Roex, N. and Cooper, D. and van Helden, P. D. and Hoal, E. G. and Jolles, A. E.},
	month = jan,
	year = {2015},
	pmid = {25620619},
	note = {00000 },
}

Providing an evidence base for wildlife population management is difficult, due to limited opportunities for experimentation and study replication at the population level. We utilized an opportunity to assess the outcome of a test and cull programme aimed at limiting the spread of Mycobacterium bovis in African buffalo. Buffalo act as reservoirs of M. bovis, the causative agent of bovine tuberculosis (BTB), which can have major economic, ecological and public health impacts through the risk of infection to other wildlife species, livestock and surrounding communities. BTB prevalence data were collected in conjunction with disease control operations in Hluhluwe-iMfolozi Park, South Africa, from 1999 to 2006. A total of 4733 buffalo (250-950 per year) were tested for BTB using the single comparative intradermal tuberculin (SCIT) test, with BTB-positive animals culled, and negative animals released. BTB prevalence was spatially and temporally variable, ranging from 2.3% to 54.7%. Geographic area was a strong predictor of BTB transmission in HiP, owing to relatively stable herds and home ranges. Herds experiencing more intensive and frequent captures showed reduced per capita disease transmission risk and less increase in herd prevalence over time. Disease hot spots did not expand spatially over time, and BTB prevalence in all but the hot spot areas was maintained between 10% and 15% throughout the study period. Our data suggest that HiP's test and cull programme was effective at reducing BTB transmission in buffalo, with capture effort and interval found to be the crucial components of the programme. The programme was thus successful with respect to the original goals; however, there are additional factors that should be considered in future cost/benefit analyses and decision-making. These findings may be utilized and expanded in future collaborative work between wildlife managers, veterinarians and scientists, to optimize wildlife disease control programmes and mitigate conflict at the interface of conservation, agricultural and urban areas.

@article{le_roex_selective_2015,
	title = {Selective breeding: {The} future of {TB} management in {African} buffalo?},
	volume = {149},
	issn = {1873-6254},
	shorttitle = {Selective breeding},
	doi = {10.1016/j.actatropica.2015.05.012},
	abstract = {The high prevalence of bovine tuberculosis (BTB) in African buffalo (Syncerus caffer) in regions of southern African has a negative economic impact on the trade of animals and animal products, represents an ecological threat to biodiversity, and poses a health risk to local communities through the wildlife-cattle-human interface. Test and cull methods may not be logistically feasible in many free-range wildlife systems, and with the presence of co-existing BTB hosts and the limited effectiveness of the BCG vaccine in buffalo, there is a need for alternative methods of BTB management. Selective breeding for increased resistance to BTB in buffalo may be a viable method of BTB management in the future, particularly if genetic information can be incorporated into these schemes. To explore this possibility, we discuss the different strategies that can be employed in selective breeding programmes, and consider the implementation of genetic improvement schemes. We reflect on the suitability of applying this strategy for enhanced BTB resistance in African buffalo, and address the challenges of this approach that must be taken into account. Conclusions and the implications for management are presented.},
	language = {ENG},
	journal = {Acta Tropica},
	author = {le Roex, N. and Berrington, C. M. and Hoal, E. G. and van Helden, P. D.},
	month = may,
	year = {2015},
	pmid = {25985909},
	note = {00000 },
	pages = {38--44},
}

The high prevalence of bovine tuberculosis (BTB) in African buffalo (Syncerus caffer) in regions of southern African has a negative economic impact on the trade of animals and animal products, represents an ecological threat to biodiversity, and poses a health risk to local communities through the wildlife-cattle-human interface. Test and cull methods may not be logistically feasible in many free-range wildlife systems, and with the presence of co-existing BTB hosts and the limited effectiveness of the BCG vaccine in buffalo, there is a need for alternative methods of BTB management. Selective breeding for increased resistance to BTB in buffalo may be a viable method of BTB management in the future, particularly if genetic information can be incorporated into these schemes. To explore this possibility, we discuss the different strategies that can be employed in selective breeding programmes, and consider the implementation of genetic improvement schemes. We reflect on the suitability of applying this strategy for enhanced BTB resistance in African buffalo, and address the challenges of this approach that must be taken into account. Conclusions and the implications for management are presented.

@article{daya_using_2014,
	title = {Using multi-way admixture mapping to elucidate {TB} susceptibility in the {South} {African} {Coloured} population},
	volume = {15},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-15-1021},
	abstract = {BACKGROUND: The admixed South African Coloured population is ideally suited to the discovery of tuberculosis susceptibility genetic variants and their probable ethnic origins, but previous attempts at finding such variants using genome-wide admixture mapping were hampered by the inaccuracy of local ancestry inference. In this study, we infer local ancestry using the novel algorithm implemented in RFMix, with the emphasis on identifying regions of excess San or Bantu ancestry, which we hypothesize may harbour TB susceptibility genes.
RESULTS: Using simulated data, we demonstrate reasonable accuracy of local ancestry inference by RFMix, with a tendency towards miss-calling San ancestry as Bantu. Regions with either excess San ancestry or excess African (San or Bantu) ancestry are less likely to be affected by this bias, and we therefore proceeded to identify such regions, found in cases but not in controls (642 cases and 91 controls). A number of promising regions were found (overall p-values of 7.19×10-5 for San ancestry and {\textless}2.00×10-16 for African ancestry), including chromosomes 15q15 and 17q22, which are close to genomic regions previously implicated in TB. Promising immune-related susceptibility genes such as the GADD45A, OSM and B7-H5 genes are also harboured in the identified regions.
CONCLUSION: Admixture mapping is feasible in the South African Coloured population and a number of novel TB susceptibility genomic regions were uncovered.},
	language = {eng},
	journal = {BMC genomics},
	author = {Daya, Michelle and van der Merwe, Lize and Gignoux, Christopher R. and van Helden, Paul D. and Möller, Marlo and Hoal, Eileen G.},
	year = {2014},
	pmid = {25422094},
	pmcid = {PMC4256931},
	note = {00000 },
	pages = {1021},
}

BACKGROUND: The admixed South African Coloured population is ideally suited to the discovery of tuberculosis susceptibility genetic variants and their probable ethnic origins, but previous attempts at finding such variants using genome-wide admixture mapping were hampered by the inaccuracy of local ancestry inference. In this study, we infer local ancestry using the novel algorithm implemented in RFMix, with the emphasis on identifying regions of excess San or Bantu ancestry, which we hypothesize may harbour TB susceptibility genes. RESULTS: Using simulated data, we demonstrate reasonable accuracy of local ancestry inference by RFMix, with a tendency towards miss-calling San ancestry as Bantu. Regions with either excess San ancestry or excess African (San or Bantu) ancestry are less likely to be affected by this bias, and we therefore proceeded to identify such regions, found in cases but not in controls (642 cases and 91 controls). A number of promising regions were found (overall p-values of 7.19×10-5 for San ancestry and \textless2.00×10-16 for African ancestry), including chromosomes 15q15 and 17q22, which are close to genomic regions previously implicated in TB. Promising immune-related susceptibility genes such as the GADD45A, OSM and B7-H5 genes are also harboured in the identified regions. CONCLUSION: Admixture mapping is feasible in the South African Coloured population and a number of novel TB susceptibility genomic regions were uncovered.

@article{salie_associations_2014,
	title = {Associations between human leukocyte antigen class {I} variants and the {Mycobacterium} tuberculosis subtypes causing disease},
	volume = {209},
	issn = {1537-6613},
	doi = {10.1093/infdis/jit443},
	abstract = {BACKGROUND: The development of active tuberculosis disease has been shown to be multifactorial. Interactions between host and bacterial genotype may influence disease outcome, with some studies indicating the adaptation of M. tuberculosis strains to specific human populations. Here we investigate the role of the human leukocyte antigen (HLA) class I genes in this biological process.
METHODS: Three hundred patients with tuberculosis from South Africa were typed for their HLA class I alleles by direct sequencing. Mycobacterium tuberculosis genotype classification was done by IS6110 restriction fragment length polymorphism genotyping and spoligotyping.
RESULTS: We showed that Beijing strain occurred more frequently in individuals with multiple disease episodes (P {\textless} .001) with the HLA-B27 allele lowering the odds of having an additional episode (odds ratio, 0.21; P = .006). Associations were also identified for specific HLA types and disease caused by the Beijing, LAM, LCC, and Quebec strains. HLA types were also associated with disease caused by strains from the Euro-American or East Asian lineages, and the frequencies of these alleles in their sympatric human populations identified potential coevolutionary events between host and pathogen.
CONCLUSIONS: This is the first report of the association of human HLA types and M. tuberculosis strain genotype, highlighting that both host and pathogen genetics need to be taken into consideration when studying tuberculosis disease development.},
	language = {eng},
	number = {2},
	journal = {The Journal of Infectious Diseases},
	author = {Salie, Muneeb and van der Merwe, Lize and Möller, Marlo and Daya, Michelle and van der Spuy, Gian D. and van Helden, Paul D. and Martin, Maureen P. and Gao, Xiao-Jiang and Warren, Robin M. and Carrington, Mary and Hoal, Eileen G.},
	month = jan,
	year = {2014},
	pmid = {23945374},
	pmcid = {PMC3873786},
	note = {00006 },
	keywords = {Adult, Alleles, DNA Transposable Elements, Female, Genotype, Histocompatibility Antigens Class I, Host-Pathogen Interactions, Humans, Male, Middle Aged, Molecular Typing, Mycobacterium tuberculosis, Polymorphism, Restriction Fragment Length, Sequence Analysis, DNA, South Africa, Tuberculosis, Young Adult},
	pages = {216--223},
}

BACKGROUND: The development of active tuberculosis disease has been shown to be multifactorial. Interactions between host and bacterial genotype may influence disease outcome, with some studies indicating the adaptation of M. tuberculosis strains to specific human populations. Here we investigate the role of the human leukocyte antigen (HLA) class I genes in this biological process. METHODS: Three hundred patients with tuberculosis from South Africa were typed for their HLA class I alleles by direct sequencing. Mycobacterium tuberculosis genotype classification was done by IS6110 restriction fragment length polymorphism genotyping and spoligotyping. RESULTS: We showed that Beijing strain occurred more frequently in individuals with multiple disease episodes (P \textless .001) with the HLA-B27 allele lowering the odds of having an additional episode (odds ratio, 0.21; P = .006). Associations were also identified for specific HLA types and disease caused by the Beijing, LAM, LCC, and Quebec strains. HLA types were also associated with disease caused by strains from the Euro-American or East Asian lineages, and the frequencies of these alleles in their sympatric human populations identified potential coevolutionary events between host and pathogen. CONCLUSIONS: This is the first report of the association of human HLA types and M. tuberculosis strain genotype, highlighting that both host and pathogen genetics need to be taken into consideration when studying tuberculosis disease development.

@article{chimusa_genome-wide_2014,
	title = {Genome-wide association study of ancestry-specific {TB} risk in the {South} {African} {Coloured} population},
	volume = {23},
	issn = {1460-2083},
	doi = {10.1093/hmg/ddt462},
	abstract = {The worldwide burden of tuberculosis (TB) remains an enormous problem, and is particularly severe in the admixed South African Coloured (SAC) population residing in the Western Cape. Despite evidence from twin studies suggesting a strong genetic component to TB resistance, only a few loci have been identified to date. In this work, we conduct a genome-wide association study (GWAS), meta-analysis and trans-ethnic fine mapping to attempt the replication of previously identified TB susceptibility loci. Our GWAS results confirm the WT1 chr11 susceptibility locus (rs2057178: odds ratio = 0.62, P = 2.71e(-06)) previously identified by Thye et al., but fail to replicate previously identified polymorphisms in the TLR8 gene and locus 18q11.2. Our study demonstrates that the genetic contribution to TB risk varies between continental populations, and illustrates the value of including admixed populations in studies of TB risk and other complex phenotypes. Our evaluation of local ancestry based on the real and simulated data demonstrates that case-only admixture mapping is currently impractical in multi-way admixed populations, such as the SAC, due to spurious deviations in average local ancestry generated by current local ancestry inference methods. This study provides insights into identifying disease genes and ancestry-specific disease risk in multi-way admixed populations.},
	language = {eng},
	number = {3},
	journal = {Human Molecular Genetics},
	author = {Chimusa, Emile R. and Zaitlen, Noah and Daya, Michelle and Möller, Marlo and van Helden, Paul D. and Mulder, Nicola J. and Price, Alkes L. and Hoal, Eileen G.},
	month = feb,
	year = {2014},
	pmid = {24057671},
	pmcid = {PMC3888262},
	note = {00020 },
	keywords = {African Continental Ancestry Group, Case-Control Studies, Cytoplasmic Dyneins, European Continental Ancestry Group, Female, Genetic Predisposition to Disease, Genetics, Population, Genome-Wide Association Study, HapMap Project, Humans, Male, Polymorphism, Single Nucleotide, South Africa, Tuberculosis, WT1 Proteins},
	pages = {796--809},
}

The worldwide burden of tuberculosis (TB) remains an enormous problem, and is particularly severe in the admixed South African Coloured (SAC) population residing in the Western Cape. Despite evidence from twin studies suggesting a strong genetic component to TB resistance, only a few loci have been identified to date. In this work, we conduct a genome-wide association study (GWAS), meta-analysis and trans-ethnic fine mapping to attempt the replication of previously identified TB susceptibility loci. Our GWAS results confirm the WT1 chr11 susceptibility locus (rs2057178: odds ratio = 0.62, P = 2.71e(-06)) previously identified by Thye et al., but fail to replicate previously identified polymorphisms in the TLR8 gene and locus 18q11.2. Our study demonstrates that the genetic contribution to TB risk varies between continental populations, and illustrates the value of including admixed populations in studies of TB risk and other complex phenotypes. Our evaluation of local ancestry based on the real and simulated data demonstrates that case-only admixture mapping is currently impractical in multi-way admixed populations, such as the SAC, due to spurious deviations in average local ancestry generated by current local ancestry inference methods. This study provides insights into identifying disease genes and ancestry-specific disease risk in multi-way admixed populations.

@article{kidd_exome_2014,
	title = {Exome capture from saliva produces high quality genomic and metagenomic data},
	volume = {15},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-15-262},
	abstract = {BACKGROUND: Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also has the potential to facilitate the generation of genomic data from DNA collected via saliva or buccal cells. DNA samples derived from these cell types tend to have a lower human DNA yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. However, thousands of samples have been previously collected from these cell types, and saliva collection has the advantage that it is a non-invasive and appropriate for a wide variety of research.
RESULTS: We demonstrate successful enrichment and sequencing of 15 South African KhoeSan exomes and 2 full genomes with samples initially derived from saliva. The expanded exome dataset enables us to characterize genetic diversity free from ascertainment bias for multiple KhoeSan populations, including new exome data from six HGDP Namibian San, revealing substantial population structure across the Kalahari Desert region. Additionally, we discover and independently verify thirty-one previously unknown KIR alleles using methods we developed to accurately map and call the highly polymorphic HLA and KIR loci from exome capture data. Finally, we show that exome capture of saliva-derived DNA yields sufficient non-human sequences to characterize oral microbial communities, including detection of bacteria linked to oral disease (e.g. Prevotella melaninogenica). For comparison, two samples were sequenced using standard full genome library preparation without exome capture and we found no systematic bias of metagenomic information between exome-captured and non-captured data.
CONCLUSIONS: DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads. We find that individuals from the Kalahari carry a higher oral pathogenic microbial load than samples surveyed in the Human Microbiome Project. Additionally, rare variants present in the exomes suggest strong population structure across different KhoeSan populations.},
	language = {eng},
	journal = {BMC genomics},
	author = {Kidd, Jeffrey M. and Sharpton, Thomas J. and Bobo, Dean and Norman, Paul J. and Martin, Alicia R. and Carpenter, Meredith L. and Sikora, Martin and Gignoux, Christopher R. and Nemat-Gorgani, Neda and Adams, Alexandra and Guadalupe, Moraima and Guo, Xiaosen and Feng, Qiang and Li, Yingrui and Liu, Xiao and Parham, Peter and Hoal, Eileen G. and Feldman, Marcus W. and Pollard, Katherine S. and Wall, Jeffrey D. and Bustamante, Carlos D. and Henn, Brenna M.},
	year = {2014},
	pmid = {24708091},
	pmcid = {PMC4051168},
	note = {00004 },
	keywords = {Exome, Genome, Human, Genomics, Genotype, HLA Antigens, High-Throughput Nucleotide Sequencing, Humans, Metagenomics, Microbiota, Molecular Sequence Data, Mouth, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Receptors, KIR, Saliva},
	pages = {262},
}

BACKGROUND: Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also has the potential to facilitate the generation of genomic data from DNA collected via saliva or buccal cells. DNA samples derived from these cell types tend to have a lower human DNA yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. However, thousands of samples have been previously collected from these cell types, and saliva collection has the advantage that it is a non-invasive and appropriate for a wide variety of research. RESULTS: We demonstrate successful enrichment and sequencing of 15 South African KhoeSan exomes and 2 full genomes with samples initially derived from saliva. The expanded exome dataset enables us to characterize genetic diversity free from ascertainment bias for multiple KhoeSan populations, including new exome data from six HGDP Namibian San, revealing substantial population structure across the Kalahari Desert region. Additionally, we discover and independently verify thirty-one previously unknown KIR alleles using methods we developed to accurately map and call the highly polymorphic HLA and KIR loci from exome capture data. Finally, we show that exome capture of saliva-derived DNA yields sufficient non-human sequences to characterize oral microbial communities, including detection of bacteria linked to oral disease (e.g. Prevotella melaninogenica). For comparison, two samples were sequenced using standard full genome library preparation without exome capture and we found no systematic bias of metagenomic information between exome-captured and non-captured data. CONCLUSIONS: DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads. We find that individuals from the Kalahari carry a higher oral pathogenic microbial load than samples surveyed in the Human Microbiome Project. Additionally, rare variants present in the exomes suggest strong population structure across different KhoeSan populations.

@article{daya_role_2014,
	title = {The role of ancestry in {TB} susceptibility of an admixed {South} {African} population},
	volume = {94},
	issn = {1873-281X},
	doi = {10.1016/j.tube.2014.03.012},
	abstract = {Genetic susceptibility to tuberculosis (TB) has been well established and this, taken together with variation in susceptibility observed between different geographic and ethnic populations, implies that susceptibility to TB may in part be affected by ethnicity. In a previous genome-wide TB case-control study (642 cases and 91 controls) of the admixed South African Coloured (SAC) population, we found a positive correlation between African San ancestry and TB susceptibility, and negative correlations with European and Asian ancestries. Since genome-wide data was available for only a small number of controls in the previous study, we endeavored to validate this finding by genotyping a panel of ancestry informative markers (AIMs) in additional individuals, yielding a data set of 918 cases and 507 controls. Ancestry proportions were estimated using the AIMs for each of the source populations of the SAC (African San, African non-San, European, South Asian and East Asian). Using logistic regression models to test for association between TB and ancestry, we confirmed the substantial effect of ancestry on TB susceptibility. We also investigated the effect of adjusting for ancestry in candidate gene TB association studies of the SAC. We report a polymorphism that is no longer significantly associated with TB after adjustment for ancestry, a polymorphism that is significantly associated with TB only after adjustment for ancestry, and a polymorphism where the association significance remains unchanged. By comparing the allele frequencies of these polymorphisms in the source populations of the SAC, we demonstrate that association results are likely to be affected by adjustment for ancestry if allele frequencies differ markedly in the source populations of the SAC.},
	language = {eng},
	number = {4},
	journal = {Tuberculosis (Edinburgh, Scotland)},
	author = {Daya, Michelle and van der Merwe, Lize and van Helden, Paul D. and Möller, Marlo and Hoal, Eileen G.},
	month = jul,
	year = {2014},
	pmid = {24832562},
	note = {00002 },
	keywords = {Adult, African Continental Ancestry Group, Asian Continental Ancestry Group, Case-Control Studies, European Continental Ancestry Group, Female, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, South Africa, Tuberculosis, Young Adult},
	pages = {413--420},
}

Genetic susceptibility to tuberculosis (TB) has been well established and this, taken together with variation in susceptibility observed between different geographic and ethnic populations, implies that susceptibility to TB may in part be affected by ethnicity. In a previous genome-wide TB case-control study (642 cases and 91 controls) of the admixed South African Coloured (SAC) population, we found a positive correlation between African San ancestry and TB susceptibility, and negative correlations with European and Asian ancestries. Since genome-wide data was available for only a small number of controls in the previous study, we endeavored to validate this finding by genotyping a panel of ancestry informative markers (AIMs) in additional individuals, yielding a data set of 918 cases and 507 controls. Ancestry proportions were estimated using the AIMs for each of the source populations of the SAC (African San, African non-San, European, South Asian and East Asian). Using logistic regression models to test for association between TB and ancestry, we confirmed the substantial effect of ancestry on TB susceptibility. We also investigated the effect of adjusting for ancestry in candidate gene TB association studies of the SAC. We report a polymorphism that is no longer significantly associated with TB after adjustment for ancestry, a polymorphism that is significantly associated with TB only after adjustment for ancestry, and a polymorphism where the association significance remains unchanged. By comparing the allele frequencies of these polymorphisms in the source populations of the SAC, we demonstrate that association results are likely to be affected by adjustment for ancestry if allele frequencies differ markedly in the source populations of the SAC.

@article{daya_panel_2013,
	title = {A panel of ancestry informative markers for the complex five-way admixed {South} {African} coloured population},
	volume = {8},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0082224},
	abstract = {Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South Africa, is the admixed group known as the South African Coloured (SAC). A small set of AIMs that is optimized to distinguish between the five source populations of this population (African San, African non-San, European, South Asian, and East Asian) will enable researchers to cost-effectively reduce false-positive findings resulting from ignoring admixture in genetic association studies of the population. Using genome-wide data to find SNPs with large allele frequency differences between the source populations of the SAC, as quantified by Rosenberg et. al's In-statistic, we developed a panel of AIMs by experimenting with various selection strategies. Subsets of different sizes were evaluated by measuring the correlation between ancestry proportions estimated by each AIM subset with ancestry proportions estimated using genome-wide data. We show that a panel of 96 AIMs can be used to assess ancestry proportions and to adjust for the confounding effect of the complex five-way admixture that occurred in the South African Coloured population.},
	language = {eng},
	number = {12},
	journal = {PloS One},
	author = {Daya, Michelle and van der Merwe, Lize and Galal, Ushma and Möller, Marlo and Salie, Muneeb and Chimusa, Emile R. and Galanter, Joshua M. and van Helden, Paul D. and Henn, Brenna M. and Gignoux, Chris R. and Hoal, Eileen},
	year = {2013},
	pmid = {24376522},
	pmcid = {PMC3869660},
	keywords = {African Continental Ancestry Group, Ethnic Groups, Gene Pool, Genealogy and Heraldry, Genetic Markers, Genetics, Population, Genome, Human, Humans, South Africa},
	pages = {e82224},
}

Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South Africa, is the admixed group known as the South African Coloured (SAC). A small set of AIMs that is optimized to distinguish between the five source populations of this population (African San, African non-San, European, South Asian, and East Asian) will enable researchers to cost-effectively reduce false-positive findings resulting from ignoring admixture in genetic association studies of the population. Using genome-wide data to find SNPs with large allele frequency differences between the source populations of the SAC, as quantified by Rosenberg et. al's In-statistic, we developed a panel of AIMs by experimenting with various selection strategies. Subsets of different sizes were evaluated by measuring the correlation between ancestry proportions estimated by each AIM subset with ancestry proportions estimated using genome-wide data. We show that a panel of 96 AIMs can be used to assess ancestry proportions and to adjust for the confounding effect of the complex five-way admixture that occurred in the South African Coloured population.

@article{van_helden_new_2013,
	title = {A new {TB} vaccine: fact or fiction?},
	volume = {36},
	issn = {1878-1667},
	shorttitle = {A new {TB} vaccine},
	doi = {10.1016/j.cimid.2012.07.003},
	abstract = {Vaccination has been spectacularly successful in eradicating or controlling some infectious diseases, and is particularly attractive as an approach to tackling other infectious diseases. Although vaccination against tuberculosis has been done for nearly 100 years, it is clearly not that successful since the disease still occurs at epidemic levels in animals and humans in many areas. New approaches to vaccination against TB in humans and animals are currently in the pipeline, but none show either complete protection or sterilization. However, there is evidence to suggest that vaccination may deliver some positive outcomes. Not only should we be investigating new vaccines, but also how vaccines and candidates are used and delivered. There are many reasons to think that this task will not be simple, or perhaps not possible in some cases. We present different aspects of the development of vaccines against TB, outline some complications and suggest some new ways to consider this problem.},
	language = {eng},
	number = {3},
	journal = {Comparative Immunology, Microbiology and Infectious Diseases},
	author = {van Helden, Paul D. and Hoal, Eileen G.},
	month = may,
	year = {2013},
	pmid = {22921282},
	note = {00004 },
	keywords = {Animals, BCG Vaccine, Disease Models, Animal, Humans, Mass Vaccination, Mycobacterium tuberculosis, Tuberculosis, Tuberculosis Vaccines},
	pages = {287--294},
}

Vaccination has been spectacularly successful in eradicating or controlling some infectious diseases, and is particularly attractive as an approach to tackling other infectious diseases. Although vaccination against tuberculosis has been done for nearly 100 years, it is clearly not that successful since the disease still occurs at epidemic levels in animals and humans in many areas. New approaches to vaccination against TB in humans and animals are currently in the pipeline, but none show either complete protection or sterilization. However, there is evidence to suggest that vaccination may deliver some positive outcomes. Not only should we be investigating new vaccines, but also how vaccines and candidates are used and delivered. There are many reasons to think that this task will not be simple, or perhaps not possible in some cases. We present different aspects of the development of vaccines against TB, outline some complications and suggest some new ways to consider this problem.

@article{hemmings_bdnf_2013,
	title = {{BDNF} {Val66Met} and {DRD2} {Taq1A} polymorphisms interact to influence {PTSD} symptom severity: a preliminary investigation in a {South} {African} population},
	volume = {40},
	issn = {1878-4216},
	shorttitle = {{BDNF} {Val66Met} and {DRD2} {Taq1A} polymorphisms interact to influence {PTSD} symptom severity},
	doi = {10.1016/j.pnpbp.2012.10.011},
	abstract = {BACKGROUND: We evaluated the role that selected variants in serotonin transporter (5-HTT), dopamine receptor 2 (DRD2) and brain-derived neurotrophic factor (BDNF) genes play in PTSD symptom severity in an at-risk population. We also investigated the interaction between the genetic variants to determine whether these variables and the interactions between the variables influenced the severity of PTSD symptoms.
METHODS: PTSD symptoms were quantitatively assessed using the Davidson Trauma Scale (DTS) in 150 participants from an at-risk South African population. All participants were genotyped for the 5-HTTLPR, DRD2 Taq1A and BDNF Val66Met polymorphisms. Gene-gene interactions were investigated using various linear models. All analyses were adjusted for age, gender, major depressive disorder diagnosis, level of resilience, level of social support and alcohol dependence.
RESULTS: A significant interaction effect between DRD2 Taq1A and BDNF Val66Met variants on DTS score was observed. On the background of the BDNF Val66Val genotype, DTS score increased significantly with the addition of a DRD2 Taq1A A1 allele. However, on the BDNF Met66 allele background, the addition of an A1 allele was found to reduce total DTS score.
CONCLUSIONS: This study provides preliminary evidence for an epistatic interaction between BDNF Val66Met and DRD2 Taq1A polymorphisms on the severity of PTSD symptoms, where both too little and too much dopamine can result in increased PTSD symptom severity.},
	language = {eng},
	journal = {Progress in Neuro-Psychopharmacology \& Biological Psychiatry},
	author = {Hemmings, Sian M. J. and Martin, Lindi I. and Klopper, Marisa and van der Merwe, Lize and Aitken, Lisa and de Wit, Erika and Black, Gillian F. and Hoal, Eileen G. and Walzl, Gerhard and Seedat, Soraya},
	month = jan,
	year = {2013},
	pmid = {23103549},
	note = {00012 },
	keywords = {Adult, Alleles, Brain-Derived Neurotrophic Factor, Epistasis, Genetic, Female, Genetic Predisposition to Disease, Genotype, Humans, Male, Polymorphism, Single Nucleotide, Questionnaires, Receptors, Dopamine D2, Resilience, Psychological, Serotonin Plasma Membrane Transport Proteins, Severity of Illness Index, Social Support, Stress Disorders, Post-Traumatic},
	pages = {273--280},
}

BACKGROUND: We evaluated the role that selected variants in serotonin transporter (5-HTT), dopamine receptor 2 (DRD2) and brain-derived neurotrophic factor (BDNF) genes play in PTSD symptom severity in an at-risk population. We also investigated the interaction between the genetic variants to determine whether these variables and the interactions between the variables influenced the severity of PTSD symptoms. METHODS: PTSD symptoms were quantitatively assessed using the Davidson Trauma Scale (DTS) in 150 participants from an at-risk South African population. All participants were genotyped for the 5-HTTLPR, DRD2 Taq1A and BDNF Val66Met polymorphisms. Gene-gene interactions were investigated using various linear models. All analyses were adjusted for age, gender, major depressive disorder diagnosis, level of resilience, level of social support and alcohol dependence. RESULTS: A significant interaction effect between DRD2 Taq1A and BDNF Val66Met variants on DTS score was observed. On the background of the BDNF Val66Val genotype, DTS score increased significantly with the addition of a DRD2 Taq1A A1 allele. However, on the BDNF Met66 allele background, the addition of an A1 allele was found to reduce total DTS score. CONCLUSIONS: This study provides preliminary evidence for an epistatic interaction between BDNF Val66Met and DRD2 Taq1A polymorphisms on the severity of PTSD symptoms, where both too little and too much dopamine can result in increased PTSD symptom severity.

@article{van_helden_one_2013,
	title = {One world, one health. {Humans}, animals and the environment are inextricably linked--a fact that needs to be remembered and exploited in our modern approach to health},
	volume = {14},
	issn = {1469-3178},
	doi = {10.1038/embor.2013.61},
	language = {eng},
	number = {6},
	journal = {EMBO reports},
	author = {van Helden, Paul D. and van Helden, Lesley S. and Hoal, Eileen G.},
	month = jun,
	year = {2013},
	pmid = {23681441},
	pmcid = {PMC3674448},
	note = {00000 },
	keywords = {Animals, Biodiversity, Birds, Cats, Cattle, Disease Reservoirs, Health, Humans, Influenza in Birds, Influenza, Human, Metagenome, Toxoplasmosis, Toxoplasmosis, Animal, Tuberculosis, Pulmonary, Zoonoses},
	pages = {497--501},
}

@article{le_roex_gene_2013,
	title = {Gene polymorphisms in {African} buffalo associated with susceptibility to bovine tuberculosis infection},
	volume = {8},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0064494},
	abstract = {Bovine tuberculosis (BTB) is a chronic, highly infectious disease that affects humans, cattle and numerous species of wildlife. In developing countries such as South Africa, the existence of extensive wildlife-human-livestock interfaces poses a significant risk of Mycobacterium bovis transmission between these groups, and has far-reaching ecological, economic and public health impacts. The African buffalo (Syncerus caffer), acts as a maintenance host for Mycobacterium bovis, and maintains and transmits the disease within the buffalo and to other species. In this study we aimed to investigate genetic susceptibility of buffalo for Mycobacterium bovis infection. Samples from 868 African buffalo of the Cape buffalo subspecies were used in this study. SNPs (n = 69), with predicted functional consequences in genes related to the immune system, were genotyped in this buffalo population by competitive allele-specific SNP genotyping. Case-control association testing and statistical analyses identified three SNPs associated with BTB status in buffalo. These SNPs, SNP41, SNP137 and SNP144, are located in the SLC7A13, DMBT1 and IL1α genes, respectively. SNP137 remained significantly associated after permutation testing. The three genetic polymorphisms identified are located in promising candidate genes for further exploration into genetic susceptibility to BTB in buffalo and other bovids, such as the domestic cow. These polymorphisms/genes may also hold potential for marker-assisted breeding programmes, with the aim of breeding more BTB-resistant animals and herds within both the national parks and the private sector.},
	language = {eng},
	number = {5},
	journal = {PloS One},
	author = {le Roex, Nikki and Koets, Ad P. and van Helden, Paul D. and Hoal, Eileen G.},
	year = {2013},
	pmid = {23691232},
	pmcid = {PMC3654904},
	note = {00004 },
	keywords = {Africa, Animals, Buffaloes, Cattle, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Tuberculosis, Bovine},
	pages = {e64494},
}

Bovine tuberculosis (BTB) is a chronic, highly infectious disease that affects humans, cattle and numerous species of wildlife. In developing countries such as South Africa, the existence of extensive wildlife-human-livestock interfaces poses a significant risk of Mycobacterium bovis transmission between these groups, and has far-reaching ecological, economic and public health impacts. The African buffalo (Syncerus caffer), acts as a maintenance host for Mycobacterium bovis, and maintains and transmits the disease within the buffalo and to other species. In this study we aimed to investigate genetic susceptibility of buffalo for Mycobacterium bovis infection. Samples from 868 African buffalo of the Cape buffalo subspecies were used in this study. SNPs (n = 69), with predicted functional consequences in genes related to the immune system, were genotyped in this buffalo population by competitive allele-specific SNP genotyping. Case-control association testing and statistical analyses identified three SNPs associated with BTB status in buffalo. These SNPs, SNP41, SNP137 and SNP144, are located in the SLC7A13, DMBT1 and IL1α genes, respectively. SNP137 remained significantly associated after permutation testing. The three genetic polymorphisms identified are located in promising candidate genes for further exploration into genetic susceptibility to BTB in buffalo and other bovids, such as the domestic cow. These polymorphisms/genes may also hold potential for marker-assisted breeding programmes, with the aim of breeding more BTB-resistant animals and herds within both the national parks and the private sector.

@article{le_roex_bovine_2013,
	title = {Bovine {TB} in livestock and wildlife: what's in the genes?},
	volume = {45},
	issn = {1531-2267},
	shorttitle = {Bovine {TB} in livestock and wildlife},
	doi = {10.1152/physiolgenomics.00061.2013},
	abstract = {Bovine tuberculosis (BTB) is a chronic, infectious disease found in domestic livestock and wildlife. It is caused predominantly by Mycobacterium bovis, which forms part of the Mycobacterium tuberculosis complex. BTB has serious implications for the movement of animals and animal products, biodiversity, and public health and is of significant economic concern. The existence of wildlife maintenance hosts makes it extremely difficult to eradicate BTB, even when established control strategies are in place, creating the need for alternative methods for controlling this disease. There are multiple factors that influence the outcome of infection by a pathogen, one of which is the host's genome. The identification of genetic variants involved in the susceptibility to BTB would supply a new selection of potential drug targets as well as the possibility for the breeding of animals with greater disease resistance. In this review, we collate the results of the BTB heritability and association studies performed in cattle and wildlife, discuss considerations and other methodologies (such as gene expression work) to be taken into account when performing genetic studies, and make some recommendations for future work in this area.},
	language = {eng},
	number = {15},
	journal = {Physiological Genomics},
	author = {le Roex, Nikki and van Helden, Paul D. and Koets, Ad P. and Hoal, Eileen G.},
	month = aug,
	year = {2013},
	pmid = {23757394},
	note = {00007 },
	keywords = {Animals, Animals, Wild, Breeding, Cattle, Disease Resistance, Gene Expression Profiling, Genetic Association Studies, Genetic Predisposition to Disease, Genetic Variation, Inheritance Patterns, Livestock, Tuberculosis, Bovine},
	pages = {631--637},
}

Bovine tuberculosis (BTB) is a chronic, infectious disease found in domestic livestock and wildlife. It is caused predominantly by Mycobacterium bovis, which forms part of the Mycobacterium tuberculosis complex. BTB has serious implications for the movement of animals and animal products, biodiversity, and public health and is of significant economic concern. The existence of wildlife maintenance hosts makes it extremely difficult to eradicate BTB, even when established control strategies are in place, creating the need for alternative methods for controlling this disease. There are multiple factors that influence the outcome of infection by a pathogen, one of which is the host's genome. The identification of genetic variants involved in the susceptibility to BTB would supply a new selection of potential drug targets as well as the possibility for the breeding of animals with greater disease resistance. In this review, we collate the results of the BTB heritability and association studies performed in cattle and wildlife, discuss considerations and other methodologies (such as gene expression work) to be taken into account when performing genetic studies, and make some recommendations for future work in this area.

@article{cobat_identification_2013,
	title = {Identification of a major locus, {TNF1}, that controls {BCG}-triggered tumor necrosis factor production by leukocytes in an area hyperendemic for tuberculosis},
	volume = {57},
	issn = {1537-6591},
	doi = {10.1093/cid/cit438},
	abstract = {BACKGROUND: Tumor necrosis factor (TNF) is a key immune regulator of tuberculosis resistance, as exemplified by the highly increased risk of tuberculosis disease among individuals receiving TNF-blocker therapy.
METHODS: We determined the extent of TNF production after stimulation with BCG or BCG plus interferon gamma (IFN-γ) using a whole blood assay in 392 children belonging to 135 nuclear families from an area hyperendemic for tuberculosis in South Africa. We conducted classical univariate and bivariate genome-wide linkage analysis of TNF production using the data from both stimulation protocols by means of an extension of the maximum-likelihood-binomial method for quantitative trait loci to multivariate analysis.
RESULTS: Stimulation of whole blood by either BCG or BCG plus IFN-γ resulted in a range of TNF release across subjects. Extent of TNF production following both stimulation protocols was highly correlated (r = 0.81). We failed to identify genetic linkage of TNF release when considering each stimulus separately. However, using a multivariate approach, we detected a major pleiotropic locus (P {\textless} 10(-5)) on chromosome region 11p15, termed TNF locus 1 (TNF1), that controlled TNF production after stimulation by both BCG alone and BCG plus IFN-γ.
CONCLUSIONS: The TNF1 locus was mapped in the vicinity of the TST1 locus, previously identified in the same family sample, that controls tuberculin skin test (TST) negativity per se, that is, T-cell-independent resistance to Mycobacterium tuberculosis infection. This suggested that there is a connection between TST negativity per se and TNF production.},
	language = {eng},
	number = {7},
	journal = {Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America},
	author = {Cobat, Aurelie and Hoal, Eileen G. and Gallant, Caroline J. and Simkin, Leah and Black, Gillian F. and Stanley, Kim and Jaïs, Jean-Philippe and Yu, Ting-Heng and Boland-Auge, Anne and Grange, Ghislain and Delacourt, Christophe and van Helden, Paul and Casanova, Jean-Laurent and Abel, Laurent and Alcaïs, Alexandre and Schurr, Erwin},
	month = oct,
	year = {2013},
	pmid = {23800941},
	pmcid = {PMC3765013},
	note = {00006 },
	keywords = {Adult, Analysis of Variance, BCG Vaccine, Chi-Square Distribution, Child, Chromosomes, Human, Pair 11, Endemic Diseases, Family, Genetic Pleiotropy, Humans, Interferon-gamma, Interferon-gamma Release Tests, Leukocytes, Linkage Disequilibrium, Mycobacterium bovis, Phenotype, Quantitative Trait Loci, South Africa, Tuberculosis, Tumor Necrosis Factor-alpha},
	pages = {963--970},
}

BACKGROUND: Tumor necrosis factor (TNF) is a key immune regulator of tuberculosis resistance, as exemplified by the highly increased risk of tuberculosis disease among individuals receiving TNF-blocker therapy. METHODS: We determined the extent of TNF production after stimulation with BCG or BCG plus interferon gamma (IFN-γ) using a whole blood assay in 392 children belonging to 135 nuclear families from an area hyperendemic for tuberculosis in South Africa. We conducted classical univariate and bivariate genome-wide linkage analysis of TNF production using the data from both stimulation protocols by means of an extension of the maximum-likelihood-binomial method for quantitative trait loci to multivariate analysis. RESULTS: Stimulation of whole blood by either BCG or BCG plus IFN-γ resulted in a range of TNF release across subjects. Extent of TNF production following both stimulation protocols was highly correlated (r = 0.81). We failed to identify genetic linkage of TNF release when considering each stimulus separately. However, using a multivariate approach, we detected a major pleiotropic locus (P \textless 10(-5)) on chromosome region 11p15, termed TNF locus 1 (TNF1), that controlled TNF production after stimulation by both BCG alone and BCG plus IFN-γ. CONCLUSIONS: The TNF1 locus was mapped in the vicinity of the TST1 locus, previously identified in the same family sample, that controls tuberculin skin test (TST) negativity per se, that is, T-cell-independent resistance to Mycobacterium tuberculosis infection. This suggested that there is a connection between TST negativity per se and TNF production.

@article{chimusa_determining_2013,
	title = {Determining ancestry proportions in complex admixture scenarios in {South} {Africa} using a novel proxy ancestry selection method},
	volume = {8},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0073971},
	abstract = {Admixed populations can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Admixture mapping has been used successfully, but is not designed to cope with populations that have more than two or three ancestral populations. The inference of admixture proportions and local ancestry and the imputation of missing genotypes in admixed populations are crucial in both understanding variation in disease and identifying novel disease loci. These inferences make use of reference populations, and accuracy depends on the choice of ancestral populations. Using an insufficient or inaccurate ancestral panel can result in erroneously inferred ancestry and affect the detection power of GWAS and meta-analysis when using imputation. Current algorithms are inadequate for multi-way admixed populations. To address these challenges we developed PROXYANC, an approach to select the best proxy ancestral populations. From the simulation of a multi-way admixed population we demonstrate the capability and accuracy of PROXYANC and illustrate the importance of the choice of ancestry in both estimating admixture proportions and imputing missing genotypes. We applied this approach to a complex, uniquely admixed South African population. Using genome-wide SNP data from over 764 individuals, we accurately estimate the genetic contributions from the best ancestral populations: isiXhosa [Formula: see text], ‡Khomani SAN [Formula: see text], European [Formula: see text], Indian [Formula: see text], and Chinese [Formula: see text]. We also demonstrate that the ancestral allele frequency differences correlate with increased linkage disequilibrium in the South African population, which originates from admixture events rather than population bottlenecks.
NOMENCLATURE: The collective term for people of mixed ancestry in southern Africa is "Coloured," and this is officially recognized in South Africa as a census term, and for self-classification. Whilst we acknowledge that some cultures may use this term in a derogatory manner, these connotations are not present in South Africa, and are certainly not intended here.},
	language = {eng},
	number = {9},
	journal = {PloS One},
	author = {Chimusa, Emile R. and Daya, Michelle and Möller, Marlo and Ramesar, Raj and Henn, Brenna M. and van Helden, Paul D. and Mulder, Nicola J. and Hoal, Eileen G.},
	year = {2013},
	pmid = {24066090},
	pmcid = {PMC3774743},
	note = {00005 },
	keywords = {Genetics, Population, Genome, Human, Genotype, Humans, South Africa},
	pages = {e73971},
}

Admixed populations can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Admixture mapping has been used successfully, but is not designed to cope with populations that have more than two or three ancestral populations. The inference of admixture proportions and local ancestry and the imputation of missing genotypes in admixed populations are crucial in both understanding variation in disease and identifying novel disease loci. These inferences make use of reference populations, and accuracy depends on the choice of ancestral populations. Using an insufficient or inaccurate ancestral panel can result in erroneously inferred ancestry and affect the detection power of GWAS and meta-analysis when using imputation. Current algorithms are inadequate for multi-way admixed populations. To address these challenges we developed PROXYANC, an approach to select the best proxy ancestral populations. From the simulation of a multi-way admixed population we demonstrate the capability and accuracy of PROXYANC and illustrate the importance of the choice of ancestry in both estimating admixture proportions and imputing missing genotypes. We applied this approach to a complex, uniquely admixed South African population. Using genome-wide SNP data from over 764 individuals, we accurately estimate the genetic contributions from the best ancestral populations: isiXhosa [Formula: see text], ‡Khomani SAN [Formula: see text], European [Formula: see text], Indian [Formula: see text], and Chinese [Formula: see text]. We also demonstrate that the ancestral allele frequency differences correlate with increased linkage disequilibrium in the South African population, which originates from admixture events rather than population bottlenecks. NOMENCLATURE: The collective term for people of mixed ancestry in southern Africa is "Coloured," and this is officially recognized in South Africa as a census term, and for self-classification. Whilst we acknowledge that some cultures may use this term in a derogatory manner, these connotations are not present in South Africa, and are certainly not intended here.

@article{wright_association_2012,
	title = {Association of {MB}-{COMT} polymorphisms with schizophrenia-susceptibility and symptom severity in an {African} cohort},
	volume = {39},
	issn = {1878-4216},
	doi = {10.1016/j.pnpbp.2012.06.006},
	abstract = {The catechol-O-methyltransferase (COMT) gene is an attractive schizophrenia candidate gene, encoding a catabolic dopamine enzyme. The enzyme exists as two distinct isoforms, with the membrane bound enzyme (i.e. MB-COMT) being predominantly expressed in the brain. Since African populations remain underrepresented in genetic/genomic research, we performed an association study to determine whether MB-COMT genetic variants are associated with schizophrenia-susceptibility and symptom severity in the South African Xhosa population. Fourteen candidate polymorphisms were selected by means of a literature search and in silico analyses and were subsequently genotyped in a cohort of 238 Xhosa schizophrenia patients and 240 healthy Xhosa controls. Genetic association was tested with schizophrenia-susceptibility as well as symptom severity within the patient group. Polymorphisms of interest were also analysed using functional assays. Two SNPs, rs2020917 (OR=0.54, 95\% CI 0.37-0.79; P=0.0011) and rs737865 (OR=0.52, 95\% CI 0.36-0.74; P=0.0002), in the P2 promoter region were significantly associated with schizophrenia as well as an increase (increase=11.2\%, 95\% CI 3.7\%-19.2\%; P=0.0031) in reporter gene expression. The minor alleles of these SNPs were underrepresented in the schizophrenia cohort, indicating a possible protective effect. The P2 region also formed part of a haplotype found to be associated with the severity of the negative symptoms of the disorder. The data generated by this study indicate that genetic variation of MB-COMT could be associated with schizophrenia and negative symptom severity in the Xhosa population and may therefore be one of the genomic loci contributing towards the disorder in the South African community. Future large-scale studies in other African schizophrenia populations are required to further elucidate the significance of these findings.},
	language = {eng},
	number = {1},
	journal = {Progress in Neuro-Psychopharmacology \& Biological Psychiatry},
	author = {Wright, Galen E. B. and Niehaus, Dana J. H. and van der Merwe, Lize and Koen, Liezl and Korkie, Lundi J. and Kinnear, Craig J. and Drögemöller, Britt I. and Warnich, Louise},
	month = oct,
	year = {2012},
	pmid = {22705295},
	note = {00006 },
	keywords = {Adult, African Continental Ancestry Group, Alleles, Case-Control Studies, Catechol O-Methyltransferase, Cell Line, Female, Genetic Association Studies, Genetic Predisposition to Disease, Genotype, Haplotypes, Humans, Isoenzymes, Male, Membrane Proteins, Polymorphism, Single Nucleotide, Promoter Regions, Genetic, Psychiatric Status Rating Scales, Schizophrenia, Symptom Assessment},
	pages = {163--169},
}

The catechol-O-methyltransferase (COMT) gene is an attractive schizophrenia candidate gene, encoding a catabolic dopamine enzyme. The enzyme exists as two distinct isoforms, with the membrane bound enzyme (i.e. MB-COMT) being predominantly expressed in the brain. Since African populations remain underrepresented in genetic/genomic research, we performed an association study to determine whether MB-COMT genetic variants are associated with schizophrenia-susceptibility and symptom severity in the South African Xhosa population. Fourteen candidate polymorphisms were selected by means of a literature search and in silico analyses and were subsequently genotyped in a cohort of 238 Xhosa schizophrenia patients and 240 healthy Xhosa controls. Genetic association was tested with schizophrenia-susceptibility as well as symptom severity within the patient group. Polymorphisms of interest were also analysed using functional assays. Two SNPs, rs2020917 (OR=0.54, 95% CI 0.37-0.79; P=0.0011) and rs737865 (OR=0.52, 95% CI 0.36-0.74; P=0.0002), in the P2 promoter region were significantly associated with schizophrenia as well as an increase (increase=11.2%, 95% CI 3.7%-19.2%; P=0.0031) in reporter gene expression. The minor alleles of these SNPs were underrepresented in the schizophrenia cohort, indicating a possible protective effect. The P2 region also formed part of a haplotype found to be associated with the severity of the negative symptoms of the disorder. The data generated by this study indicate that genetic variation of MB-COMT could be associated with schizophrenia and negative symptom severity in the Xhosa population and may therefore be one of the genomic loci contributing towards the disorder in the South African community. Future large-scale studies in other African schizophrenia populations are required to further elucidate the significance of these findings.

@article{muller_comparative_2012,
	title = {Comparative analysis of a putative tuberculosis-susceptibility gene, {MC3R}, and pseudogene sequences in cattle, {African} buffalo, hyena, rhinoceros and other {African} bovids and ruminants},
	volume = {136},
	issn = {1424-859X},
	doi = {10.1159/000335464},
	abstract = {Studies in humans have suggested the possible involvement of melanocortin-3-receptor (MC3R) and other components of the central melanocortin system in host defense against mycobacteria. We report a genomic DNA nucleotide sequence highly homologous to human MC3R in several bovids and non-bovid African wildlife species. Nucleotide sequence analysis indicates that the orthologous genes of cattle and buffalo are highly homologous (89.4 and 90\%, respectively) to the human MC3R gene. Sequence results also identified a typical non-functional, duplicated pseudogene, MC3RP, in 7 species from the family Bovidae. No pseudogene was found in animals outside Bovidae. The presence of the pseudogene in tuberculosis-susceptible species could have possible immunomodulatory effects on susceptibility to bovine tuberculosis infection, as well as a considerable influence on energy metabolism and food conversion efficiency.},
	language = {eng},
	number = {2},
	journal = {Cytogenetic and Genome Research},
	author = {Müller, A. and Möller, M. and Adams, L. A. and Warren, R. M. and Hoal, E. G. and van Helden, P. D.},
	year = {2012},
	pmid = {22286663},
	note = {00001 },
	keywords = {Amino Acid Sequence, Animals, Base Sequence, Buffaloes, Cattle, Genetic Predisposition to Disease, Humans, Hyaenidae, Molecular Sequence Data, Perissodactyla, Phylogeny, Pseudogenes, Receptor, Melanocortin, Type 3, Ruminants, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Species Specificity, Tuberculosis, Tuberculosis, Bovine},
	pages = {117--122},
}

Studies in humans have suggested the possible involvement of melanocortin-3-receptor (MC3R) and other components of the central melanocortin system in host defense against mycobacteria. We report a genomic DNA nucleotide sequence highly homologous to human MC3R in several bovids and non-bovid African wildlife species. Nucleotide sequence analysis indicates that the orthologous genes of cattle and buffalo are highly homologous (89.4 and 90%, respectively) to the human MC3R gene. Sequence results also identified a typical non-functional, duplicated pseudogene, MC3RP, in 7 species from the family Bovidae. No pseudogene was found in animals outside Bovidae. The presence of the pseudogene in tuberculosis-susceptible species could have possible immunomodulatory effects on susceptibility to bovine tuberculosis infection, as well as a considerable influence on energy metabolism and food conversion efficiency.

@article{le_roex_novel_2012,
	title = {Novel {SNP} {Discovery} in {African} {Buffalo}, {Syncerus} caffer, using high-throughput {Sequencing}},
	volume = {7},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0048792},
	abstract = {The African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43-54\% of the Bowtie SNPs and 57-58\% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.},
	language = {eng},
	number = {11},
	journal = {PloS One},
	author = {le Roex, Nikki and Noyes, Harry and Brass, Andrew and Bradley, Daniel G. and Kemp, Steven J. and Kay, Suzanne and van Helden, Paul D. and Hoal, Eileen G.},
	year = {2012},
	pmid = {23144973},
	pmcid = {PMC3492240},
	note = {00008 },
	keywords = {Animals, Buffaloes, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Selection, Genetic, Sequence Analysis, DNA},
	pages = {e48792},
}

The African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43-54% of the Bowtie SNPs and 57-58% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.

@article{boardman_investigating_2011,
	title = {Investigating {SAPAP3} variants in the etiology of obsessive-compulsive disorder and trichotillomania in the {South} {African} white population},
	volume = {52},
	issn = {1532-8384},
	doi = {10.1016/j.comppsych.2010.05.007},
	abstract = {BACKGROUND: Obsessive-compulsive disorder (OCD) is a debilitating psychiatric disorder characterized by repeated obsessions and compulsions. Trichotillomania (TTM), a psychiatric disorder characterized by repetitive hairpulling, is presently classified as an impulse control disorder, but has also been viewed as an obsessive-compulsive spectrum disorder. Both conditions are complex disorders, with evidence from family and twin studies indicating that their etiology includes a genetic component. Results from a recent knockout animal model suggest that SAP90/PSD95-associated protein 3 (SAPAP3) may be involved in the pathophysiology of both disorders.
METHODS: Seven polymorphic variants distributed across the gene encoding SAPAP3 were genotyped in South African white OCD (n = 172), TTM (n = 45), and control (n = 153) subjects. Single-locus and haplotype analyses were conducted to determine association between genetic variants and subjects with OCD, TTM, and controls.
RESULTS: Although single-locus analysis revealed a significant association between rs11583978 in SAPAP3 and TTM, this association was nonsignificant after correction for multiple testing. In the OCD group, a significant association was observed between earlier age at onset and the A-T-A-T (rs11583978-rs7541937-rs6662980-rs4652867) haplotype compared with the C-G-G-G haplotype.
CONCLUSIONS: This study generated preliminary evidence to link SAPAP3 variants to the development of earlier onset OCD. Future studies should concentrate on locating the susceptibility variant(s) by focusing on functional polymorphisms within SAPAP3.},
	language = {eng},
	number = {2},
	journal = {Comprehensive Psychiatry},
	author = {Boardman, Leigh and van der Merwe, Lize and Lochner, Christine and Kinnear, Craig J. and Seedat, Soraya and Stein, Dan J. and Moolman-Smook, Johanna C. and Hemmings, Sian M. J.},
	month = apr,
	year = {2011},
	pmid = {21295225},
	note = {00037 },
	keywords = {Adolescent, Adult, Age of Onset, Aged, Child, European Continental Ancestry Group, Female, Genetic Variation, Genotype, Haplotypes, Humans, Male, Middle Aged, Nerve Tissue Proteins, Obsessive-Compulsive Disorder, Polymorphism, Single Nucleotide, Psychiatric Status Rating Scales, South Africa, Trichotillomania},
	pages = {181--187},
}

BACKGROUND: Obsessive-compulsive disorder (OCD) is a debilitating psychiatric disorder characterized by repeated obsessions and compulsions. Trichotillomania (TTM), a psychiatric disorder characterized by repetitive hairpulling, is presently classified as an impulse control disorder, but has also been viewed as an obsessive-compulsive spectrum disorder. Both conditions are complex disorders, with evidence from family and twin studies indicating that their etiology includes a genetic component. Results from a recent knockout animal model suggest that SAP90/PSD95-associated protein 3 (SAPAP3) may be involved in the pathophysiology of both disorders. METHODS: Seven polymorphic variants distributed across the gene encoding SAPAP3 were genotyped in South African white OCD (n = 172), TTM (n = 45), and control (n = 153) subjects. Single-locus and haplotype analyses were conducted to determine association between genetic variants and subjects with OCD, TTM, and controls. RESULTS: Although single-locus analysis revealed a significant association between rs11583978 in SAPAP3 and TTM, this association was nonsignificant after correction for multiple testing. In the OCD group, a significant association was observed between earlier age at onset and the A-T-A-T (rs11583978-rs7541937-rs6662980-rs4652867) haplotype compared with the C-G-G-G haplotype. CONCLUSIONS: This study generated preliminary evidence to link SAPAP3 variants to the development of earlier onset OCD. Future studies should concentrate on locating the susceptibility variant(s) by focusing on functional polymorphisms within SAPAP3.

@article{uys_myomegalin_2011,
	title = {Myomegalin is a novel {A}-kinase anchoring protein involved in the phosphorylation of cardiac myosin binding protein {C}},
	volume = {12},
	issn = {1471-2121},
	doi = {10.1186/1471-2121-12-18},
	abstract = {BACKGROUND: Cardiac contractility is regulated by dynamic phosphorylation of sarcomeric proteins by kinases such as cAMP-activated protein kinase A (PKA). Efficient phosphorylation requires that PKA be anchored close to its targets by A-kinase anchoring proteins (AKAPs). Cardiac Myosin Binding Protein-C (cMyBPC) and cardiac troponin I (cTNI) are hypertrophic cardiomyopathy (HCM)-causing sarcomeric proteins which regulate contractility in response to PKA phosphorylation.
RESULTS: During a yeast 2-hybrid (Y2H) library screen using a trisphosphorylation mimic of the C1-C2 region of cMyBPC, we identified isoform 4 of myomegalin (MMGL) as an interactor of this N-terminal cMyBPC region. As MMGL has previously been shown to interact with phosphodiesterase 4D, we speculated that it may be a PKA-anchoring protein (AKAP).To investigate this possibility, we assessed the ability of MMGL isoform 4 to interact with PKA regulatory subunits R1A and R2A using Y2H-based direct protein-protein interaction assays. Additionally, to further elucidate the function of MMGL, we used it as bait to screen a cardiac cDNA library. Other PKA targets, viz. CARP, COMMD4, ENO1, ENO3 and cTNI were identified as putative interactors, with cTNI being the most frequent interactor.We further assessed and confirmed these interactions by fluorescent 3D-co-localization in differentiated H9C2 cells as well as by in vivo co-immunoprecipitation. We also showed that quantitatively more interaction occurs between MMGL and cTNI under β-adrenergic stress. Moreover, siRNA-mediated knockdown of MMGL leads to reduction of cMyBPC levels under conditions of adrenergic stress, indicating that MMGL-assisted phosphorylation is requisite for protection of cMyBPC against proteolytic cleavage.
CONCLUSIONS: This study ascribes a novel function to MMGL isoform 4: it meets all criteria for classification as an AKAP, and we show that is involved in the phosphorylation of cMyBPC as well as cTNI, hence MMGL is an important regulator of cardiac contractility. This has further implications for understanding the patho-aetiology of HCM-causing mutations in the genes encoding cMyBPC and cTNI, and raises the question of whether MMGL might itself be considered a candidate HCM-causing or modifying factor.},
	language = {eng},
	journal = {BMC cell biology},
	author = {Uys, Gerrida M. and Ramburan, Amsha and Loos, Benjamin and Kinnear, Craig J. and Korkie, Lundi J. and Mouton, Jomien and Riedemann, Johann and Moolman-Smook, Johanna C.},
	year = {2011},
	pmid = {21569246},
	pmcid = {PMC3103437},
	note = {00023 },
	keywords = {A Kinase Anchor Proteins, Animals, Carrier Proteins, Cyclic AMP-Dependent Protein Kinase RIalpha Subunit, Microtubule-Associated Proteins, Myocytes, Cardiac, Phosphorylation, Protein Interaction Domains and Motifs, Protein Isoforms, RNA Interference, RNA, Small Interfering, Rats, Receptors, Adrenergic, beta, Troponin I, Two-Hybrid System Techniques},
	pages = {18},
}

BACKGROUND: Cardiac contractility is regulated by dynamic phosphorylation of sarcomeric proteins by kinases such as cAMP-activated protein kinase A (PKA). Efficient phosphorylation requires that PKA be anchored close to its targets by A-kinase anchoring proteins (AKAPs). Cardiac Myosin Binding Protein-C (cMyBPC) and cardiac troponin I (cTNI) are hypertrophic cardiomyopathy (HCM)-causing sarcomeric proteins which regulate contractility in response to PKA phosphorylation. RESULTS: During a yeast 2-hybrid (Y2H) library screen using a trisphosphorylation mimic of the C1-C2 region of cMyBPC, we identified isoform 4 of myomegalin (MMGL) as an interactor of this N-terminal cMyBPC region. As MMGL has previously been shown to interact with phosphodiesterase 4D, we speculated that it may be a PKA-anchoring protein (AKAP).To investigate this possibility, we assessed the ability of MMGL isoform 4 to interact with PKA regulatory subunits R1A and R2A using Y2H-based direct protein-protein interaction assays. Additionally, to further elucidate the function of MMGL, we used it as bait to screen a cardiac cDNA library. Other PKA targets, viz. CARP, COMMD4, ENO1, ENO3 and cTNI were identified as putative interactors, with cTNI being the most frequent interactor.We further assessed and confirmed these interactions by fluorescent 3D-co-localization in differentiated H9C2 cells as well as by in vivo co-immunoprecipitation. We also showed that quantitatively more interaction occurs between MMGL and cTNI under β-adrenergic stress. Moreover, siRNA-mediated knockdown of MMGL leads to reduction of cMyBPC levels under conditions of adrenergic stress, indicating that MMGL-assisted phosphorylation is requisite for protection of cMyBPC against proteolytic cleavage. CONCLUSIONS: This study ascribes a novel function to MMGL isoform 4: it meets all criteria for classification as an AKAP, and we show that is involved in the phosphorylation of cMyBPC as well as cTNI, hence MMGL is an important regulator of cardiac contractility. This has further implications for understanding the patho-aetiology of HCM-causing mutations in the genes encoding cMyBPC and cTNI, and raises the question of whether MMGL might itself be considered a candidate HCM-causing or modifying factor.

@article{de_wit_gene-gene_2011,
	title = {Gene-gene interaction between tuberculosis candidate genes in a {South} {African} population},
	volume = {22},
	issn = {1432-1777},
	doi = {10.1007/s00335-010-9280-8},
	abstract = {In a complex disease such as tuberculosis (TB) it is increasingly evident that gene-gene interactions play a far more important role in an individual's susceptibility to develop the disease than single polymorphisms on their own, as one gene can enhance or hinder the expression of another gene. Gene-gene interaction analysis is a new approach to elucidate susceptibility to TB. The possibility of gene-gene interactions was assessed, focusing on 11 polymorphisms in nine genes (DC-SIGN, IFN-γ, IFNGR1, IL-8, IL-1Ra, MBL, NRAMP1, RANTES, and SP-D) that have been associated with TB, some repeatedly. An optimal model, which best describes and predicts TB case-control status, was constructed. Significant interactions were detected between eight pairs of variants. The models fitted the observed data extremely well, with p {\textless} 0.0001 for all eight models. A highly significant interaction was detected between INFGR1 and NRAMP1, which is not surprising because macrophage activation is greatly enhanced by IFN-γ and IFN-γ response elements that are present in the human NRAMP1 promoter region, providing further evidence for their interaction. This study enabled us to test the theory that disease outcome may be due to interaction of several gene effects. With eight instances of statistically significant gene-gene interactions, the importance of epistasis is clearly identifiable in this study. Methods for studying gene-gene interactions are based on a multilocus and multigene approach, consistent with the nature of complex-trait diseases, and may provide the paradigm for future genetic studies of TB.},
	language = {eng},
	number = {1-2},
	journal = {Mammalian Genome: Official Journal of the International Mammalian Genome Society},
	author = {de Wit, Erika and van der Merwe, Lize and van Helden, Paul D. and Hoal, Eileen G.},
	month = feb,
	year = {2011},
	pmid = {20799037},
	note = {00030 },
	keywords = {Adult, African Continental Ancestry Group, Case-Control Studies, Epistasis, Genetic, Female, Genetic Predisposition to Disease, Genotype, Humans, Male, Polymorphism, Single Nucleotide, South Africa, Tuberculosis},
	pages = {100--110},
}

In a complex disease such as tuberculosis (TB) it is increasingly evident that gene-gene interactions play a far more important role in an individual's susceptibility to develop the disease than single polymorphisms on their own, as one gene can enhance or hinder the expression of another gene. Gene-gene interaction analysis is a new approach to elucidate susceptibility to TB. The possibility of gene-gene interactions was assessed, focusing on 11 polymorphisms in nine genes (DC-SIGN, IFN-γ, IFNGR1, IL-8, IL-1Ra, MBL, NRAMP1, RANTES, and SP-D) that have been associated with TB, some repeatedly. An optimal model, which best describes and predicts TB case-control status, was constructed. Significant interactions were detected between eight pairs of variants. The models fitted the observed data extremely well, with p \textless 0.0001 for all eight models. A highly significant interaction was detected between INFGR1 and NRAMP1, which is not surprising because macrophage activation is greatly enhanced by IFN-γ and IFN-γ response elements that are present in the human NRAMP1 promoter region, providing further evidence for their interaction. This study enabled us to test the theory that disease outcome may be due to interaction of several gene effects. With eight instances of statistically significant gene-gene interactions, the importance of epistasis is clearly identifiable in this study. Methods for studying gene-gene interactions are based on a multilocus and multigene approach, consistent with the nature of complex-trait diseases, and may provide the paradigm for future genetic studies of TB.

@article{adams_polymorphisms_2011,
	title = {Polymorphisms in {MC3R} promoter and {CTSZ} 3'{UTR} are associated with tuberculosis susceptibility},
	volume = {19},
	issn = {1476-5438},
	doi = {10.1038/ejhg.2011.1},
	abstract = {We have validated the association of two genes on chromosome 20q13.31-33 with tuberculosis susceptibility. A previous genome-wide linkage study performed by Cooke et al identified the genes melanocortin-3-receptor (MC3R) and cathepsin Z (CTSZ) as possible candidates in tuberculosis susceptibility. MC3R has been implicated in obesity studies and is known to play a role in many biological systems including the regulation of energy homeostasis and fat metabolism. CTSZ has been detected in immune cells, such as macrophages and monocytes, and it is hypothesized that the protein may play a role in the immune response. In our South African population a case-control study confirmed the previously reported association with a single-nucleotide polymorphism (SNP) in CTSZ and found an association in MC3R with a SNP not previously implicated in tuberculosis susceptibility. Six SNPs in MC3R and eight in CTSZ were genotyped and haplotypes were inferred. SNP rs6127698 in the promoter region of MC3R (cases = 498; controls = 506) and rs34069356 in the 3'UTR of CTSZ (cases = 396; controls = 298) both showed significant association with tuberculosis susceptibility (P = 0.0004 and {\textless} 0.0001, respectively), indicating that pathways involving these proteins, not previously researched in this disease, could yield novel therapies for tuberculosis.},
	language = {eng},
	number = {6},
	journal = {European journal of human genetics: EJHG},
	author = {Adams, Lindsey A. and Möller, Marlo and Nebel, Almut and Schreiber, Stefan and van der Merwe, Lize and van Helden, Paul D. and Hoal, Eileen G.},
	month = jun,
	year = {2011},
	pmid = {21368909},
	pmcid = {PMC3110050},
	note = {00013 },
	keywords = {3' Untranslated Regions, Adult, African Continental Ancestry Group, Case-Control Studies, Cathepsin Z, Female, Gene Frequency, Genetic Predisposition to Disease, Genotype, Haplotypes, Humans, Linkage Disequilibrium, Male, Polymorphism, Single Nucleotide, Promoter Regions, Genetic, Receptor, Melanocortin, Type 3, South Africa, Tuberculosis},
	pages = {676--681},
}

We have validated the association of two genes on chromosome 20q13.31-33 with tuberculosis susceptibility. A previous genome-wide linkage study performed by Cooke et al identified the genes melanocortin-3-receptor (MC3R) and cathepsin Z (CTSZ) as possible candidates in tuberculosis susceptibility. MC3R has been implicated in obesity studies and is known to play a role in many biological systems including the regulation of energy homeostasis and fat metabolism. CTSZ has been detected in immune cells, such as macrophages and monocytes, and it is hypothesized that the protein may play a role in the immune response. In our South African population a case-control study confirmed the previously reported association with a single-nucleotide polymorphism (SNP) in CTSZ and found an association in MC3R with a SNP not previously implicated in tuberculosis susceptibility. Six SNPs in MC3R and eight in CTSZ were genotyped and haplotypes were inferred. SNP rs6127698 in the promoter region of MC3R (cases = 498; controls = 506) and rs34069356 in the 3'UTR of CTSZ (cases = 396; controls = 298) both showed significant association with tuberculosis susceptibility (P = 0.0004 and \textless 0.0001, respectively), indicating that pathways involving these proteins, not previously researched in this disease, could yield novel therapies for tuberculosis.

@article{carugati_mycobacterial_2011,
	title = {Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat analysis and {Beijing}/{W} family of {Mycobacterium} tuberculosis},
	volume = {49},
	issn = {1098-660X},
	doi = {10.1128/JCM.02089-09},
	language = {eng},
	number = {7},
	journal = {Journal of Clinical Microbiology},
	author = {Carugati, Manuela and Zanini, Fabio and Schiroli, Consuelo and Gori, Andrea and Franzetti, Fabio and Hanekom, M. and van der Spuy, G. D. and Gey van Pittius, N. C. and McEvoy, C. R. E. and Ndabambi, S. L. and Victor, T. C. and Hoal, E. G. and van Helden, P. D. and Warren, R. M.},
	month = jul,
	year = {2011},
	pmid = {21719734},
	pmcid = {PMC3147889},
	note = {00000 },
	keywords = {Bacterial Typing Techniques, DNA, Bacterial, Genotype, Humans, Interspersed Repetitive Sequences, Italy, Minisatellite Repeats, Mycobacterium tuberculosis, Tuberculosis},
	pages = {2780; author reply 2781},
}

@article{moller_past_2010,
	title = {Past, present and future directions in human genetic susceptibility to tuberculosis},
	volume = {58},
	issn = {1574-695X},
	doi = {10.1111/j.1574-695X.2009.00600.x},
	abstract = {The historical impression that tuberculosis was an inherited disorder has come full circle and substantial evidence now exists of the human genetic contribution to susceptibility to tuberculosis. This evidence has come from several whole-genome linkage scans, and numerous case-control association studies where the candidate genes were derived from the genome screens, animal models and hypotheses pertaining to the disease pathways. Although many of the associated genes have not been validated in all studies, the list of those that have been is growing, and includes NRAMP1, IFNG, NOS2A, MBL, VDR and some TLR. Certain of these genes have consistently been associated with tuberculosis in diverse populations. The future investigation of susceptibility to tuberculosis is almost certain to include genome-wide association studies, admixture mapping and the search for rare variants and epigenetic mechanisms. The genetic identification of more vulnerable individuals is expected to inform personalized treatment and perhaps vaccination strategies.},
	language = {eng},
	number = {1},
	journal = {FEMS immunology and medical microbiology},
	author = {Möller, Marlo and de Wit, Erika and Hoal, Eileen G.},
	month = feb,
	year = {2010},
	pmid = {19780822},
	note = {00090 },
	keywords = {Animals, Bacterial Proteins, Case-Control Studies, Genetic Predisposition to Disease, Genome-Wide Association Study, Guinea Pigs, Humans, Mice, Mycobacterium tuberculosis, Rabbits, Tuberculosis},
	pages = {3--26},
}

The historical impression that tuberculosis was an inherited disorder has come full circle and substantial evidence now exists of the human genetic contribution to susceptibility to tuberculosis. This evidence has come from several whole-genome linkage scans, and numerous case-control association studies where the candidate genes were derived from the genome screens, animal models and hypotheses pertaining to the disease pathways. Although many of the associated genes have not been validated in all studies, the list of those that have been is growing, and includes NRAMP1, IFNG, NOS2A, MBL, VDR and some TLR. Certain of these genes have consistently been associated with tuberculosis in diverse populations. The future investigation of susceptibility to tuberculosis is almost certain to include genome-wide association studies, admixture mapping and the search for rare variants and epigenetic mechanisms. The genetic identification of more vulnerable individuals is expected to inform personalized treatment and perhaps vaccination strategies.

@article{cobat_high_2010,
	title = {High heritability of antimycobacterial immunity in an area of hyperendemicity for tuberculosis disease},
	volume = {201},
	issn = {1537-6613},
	doi = {10.1086/648611},
	abstract = {Human antimycobacterial immunity is a critical component of tuberculosis (TB) pathogenesis that is often used to infer the presence of TB infection. We report high heritability ({\textgreater}50\%) for in vitro secretion of tumor necrosis factor alpha and interferon gamma (IFN-gamma), and the frequency of antigen-specific IFN-gamma(+)CD4(+) and IFN-gamma(+)CD8(+) cells in the response of whole blood to mycobacterial challenge. In principal component analysis, the first 3 components explain 78\% of the overall variance consistent with the effect of pleiotropic regulatory genes of human antimycobacterial immunity. These results directly demonstrate the pivotal role played by host genetics in quantitative measures of antimycobacterial immunity underlying immune diagnosis of TB infection.},
	language = {eng},
	number = {1},
	journal = {The Journal of Infectious Diseases},
	author = {Cobat, Aurelie and Gallant, Caroline J. and Simkin, Leah and Black, Gillian F. and Stanley, Kim and Hughes, Jane and Doherty, T. Mark and Hanekom, Willem A. and Eley, Brian and Beyers, Nulda and Jaïs, Jean-Philippe and van Helden, Paul and Abel, Laurent and Hoal, Eileen G. and Alcaïs, Alexandre and Schurr, Erwin},
	month = jan,
	year = {2010},
	pmid = {19938975},
	note = {00030 },
	keywords = {Adolescent, CD4-Positive T-Lymphocytes, CD8-Positive T-Lymphocytes, Cells, Cultured, Child, Endemic Diseases, Female, Genotype, Humans, Immunity, Innate, Interferon-gamma, Male, Mycobacterium tuberculosis, Phenotype, Principal Component Analysis, South Africa, Tuberculosis, Tumor Necrosis Factor-alpha, Young Adult},
	pages = {15--19},
}

Human antimycobacterial immunity is a critical component of tuberculosis (TB) pathogenesis that is often used to infer the presence of TB infection. We report high heritability (\textgreater50%) for in vitro secretion of tumor necrosis factor alpha and interferon gamma (IFN-gamma), and the frequency of antigen-specific IFN-gamma(+)CD4(+) and IFN-gamma(+)CD8(+) cells in the response of whole blood to mycobacterial challenge. In principal component analysis, the first 3 components explain 78% of the overall variance consistent with the effect of pleiotropic regulatory genes of human antimycobacterial immunity. These results directly demonstrate the pivotal role played by host genetics in quantitative measures of antimycobacterial immunity underlying immune diagnosis of TB infection.

@article{moller_functional_2010,
	title = {A functional haplotype in the 3'untranslated region of {TNFRSF1B} is associated with tuberculosis in two {African} populations},
	volume = {181},
	issn = {1535-4970},
	doi = {10.1164/rccm.200905-0678OC},
	abstract = {RATIONALE: Susceptibility to tuberculosis is not only determined by Mycobacterium tuberculosis infection, but also by the genetic component of the host. The pleiotropic cytokine tumor necrosis factor-alpha is essential to control tuberculosis infection, and various tumor necrosis factor family members and their respective receptors may contribute to tuberculosis risk.
OBJECTIVES: To investigate four functionally relevant polymorphisms in the tumor necrosis factor receptor 2-encoding gene, tumor necrosis factor receptor superfamily member 1B, for association with tuberculosis susceptibility.
METHODS: Genotyping of four polymorphisms was performed in independent populations from South Africa (429 cases and 482 control subjects) and Ghana (640 cases and 1,158 control subjects), and the association of the variants with tuberculosis was tested using two case-control association studies.
MEASUREMENTS AND MAIN RESULTS: Single-point and haplotype analysis in South Africans revealed an association in the 3'untranslated region of the investigated gene. The T allele of rs3397 alone and/or the 3' untranslated region haplotype GTT may confer protection against tuberculosis insofar as both allele and haplotype frequencies were significantly lower in case subjects than in controls. The GTT genotype had previously been shown to increase the decay of tumor necrosis factor receptor 2 messenger ribonucleic acid, and messenger ribonucleic acid destabilization may represent a key molecular mechanism for disease susceptibility. Interestingly, the association signal appeared to be restricted to women. The genetic finding was validated in female participants from Ghana. The combined P value in the haplotype analysis was P = 0.00011.
CONCLUSIONS: Our finding emphasizes the importance of tumor necrosis factor/tumor necrosis factor receptor-mediated immune responses in the pathogenesis of tuberculosis.},
	language = {eng},
	number = {4},
	journal = {American Journal of Respiratory and Critical Care Medicine},
	author = {Möller, Marlo and Flachsbart, Friederike and Till, Andreas and Thye, Thorsten and Horstmann, Rolf D. and Meyer, Christian G. and Osei, Ivy and van Helden, Paul D. and Hoal, Eileen G. and Schreiber, Stefan and Nebel, Almut and Franke, Andre},
	month = feb,
	year = {2010},
	pmid = {20007930},
	pmcid = {PMC2822974},
	note = {00022 },
	keywords = {3' Untranslated Regions, African Continental Ancestry Group, Alleles, Female, Gene Frequency, Genetic Association Studies, Genetic Predisposition to Disease, Genotype, Ghana, Haplotypes, Humans, Male, Polymorphism, Single Nucleotide, Receptors, Tumor Necrosis Factor, Type II, Sex Factors, South Africa, Tuberculosis, Pulmonary},
	pages = {388--393},
}

RATIONALE: Susceptibility to tuberculosis is not only determined by Mycobacterium tuberculosis infection, but also by the genetic component of the host. The pleiotropic cytokine tumor necrosis factor-alpha is essential to control tuberculosis infection, and various tumor necrosis factor family members and their respective receptors may contribute to tuberculosis risk. OBJECTIVES: To investigate four functionally relevant polymorphisms in the tumor necrosis factor receptor 2-encoding gene, tumor necrosis factor receptor superfamily member 1B, for association with tuberculosis susceptibility. METHODS: Genotyping of four polymorphisms was performed in independent populations from South Africa (429 cases and 482 control subjects) and Ghana (640 cases and 1,158 control subjects), and the association of the variants with tuberculosis was tested using two case-control association studies. MEASUREMENTS AND MAIN RESULTS: Single-point and haplotype analysis in South Africans revealed an association in the 3'untranslated region of the investigated gene. The T allele of rs3397 alone and/or the 3' untranslated region haplotype GTT may confer protection against tuberculosis insofar as both allele and haplotype frequencies were significantly lower in case subjects than in controls. The GTT genotype had previously been shown to increase the decay of tumor necrosis factor receptor 2 messenger ribonucleic acid, and messenger ribonucleic acid destabilization may represent a key molecular mechanism for disease susceptibility. Interestingly, the association signal appeared to be restricted to women. The genetic finding was validated in female participants from Ghana. The combined P value in the haplotype analysis was P = 0.00011. CONCLUSIONS: Our finding emphasizes the importance of tumor necrosis factor/tumor necrosis factor receptor-mediated immune responses in the pathogenesis of tuberculosis.

@article{gallant_tuberculin_2010,
	title = {Tuberculin skin test and in vitro assays provide complementary measures of antimycobacterial immunity in children and adolescents},
	volume = {137},
	issn = {1931-3543},
	doi = {10.1378/chest.09-1852},
	abstract = {BACKGROUND: Although many studies have compared in vitro TB diagnostic tests with the venerable tuberculin skin test (TST), there is little understanding of the quantitative relationship between critical measures of antimycobacterial immunity used to detect TB infection. We, therefore, decided to determine the degree of redundancy between quantitative read-outs of in vivo and in vitro assays of antimycobacterial immunity.
METHODS: We enrolled 475 healthy HIV-negative children and young adults living in a hyperendemic area of TB. We measured in vivo TST responses, and a 1:10 diluted 3- or 7-day whole-blood assay was used to determine the in vitro antigen-specific interferon (IFN)-gamma cytokine release. The frequency of antigen-specific IFN-gamma(+)CD4(+) and IFN-gamma(+)CD8(+) cells was tested using intracellular cytokine staining after 1 day incubation.
RESULTS: In vivo TST responses segregated into two well-separated groups with either no measurable response (TST induration {\textless} 5 mm; n = 164) or a normally distributed group with TST indurations {\textgreater} or = 5 mm with peak at 15 mm (n = 260). In vitro assays provided a less pronounced separation of responders and nonresponders. Correlation analysis of responses among persons with TST {\textgreater} or = 5 mm demonstrated that extent of TST response was poorly correlated with IFN-gamma release (coefficients of correlation rho = 0.17-0.22) and frequency of IFN-gamma(+)CD4(+)/CD8(+) cells (rho = 0.05-0.17) across three stimulating antigens (Mycobacterium bovis bacillus Calmette-Guérin, purified protein derivative, early-secreted antigenic target-6).
CONCLUSION: We conclude that in vivo and in vitro assays are nonredundant, complementary measures of antimycobacterial immunity. Both TST and in vitro assays provided valuable information about antimycobacterial immunity and by inference latent TB in the studied high-incidence TB settings.},
	language = {eng},
	number = {5},
	journal = {Chest},
	author = {Gallant, Caroline J. and Cobat, Aurelie and Simkin, Leah and Black, Gillian F. and Stanley, Kim and Hughes, Jane and Doherty, T. Mark and Hanekom, Willem A. and Eley, Brian and Beyers, Nulda and Jaïs, Jean-Philippe and van Helden, Paul and Abel, Laurent and Alcaïs, Alexandre and Hoal, Eileen G. and Schurr, Erwin},
	month = may,
	year = {2010},
	pmid = {20040612},
	note = {00021 },
	keywords = {Adolescent, Antibodies, Bacterial, CD4-Positive T-Lymphocytes, CD8-Positive T-Lymphocytes, Cell Count, Child, Diagnostic Techniques and Procedures, Female, Humans, Immunity, In Vitro Techniques, Interferon-gamma, Male, Mycobacterium tuberculosis, South Africa, Tuberculin Test, Tuberculosis},
	pages = {1071--1077},
}

BACKGROUND: Although many studies have compared in vitro TB diagnostic tests with the venerable tuberculin skin test (TST), there is little understanding of the quantitative relationship between critical measures of antimycobacterial immunity used to detect TB infection. We, therefore, decided to determine the degree of redundancy between quantitative read-outs of in vivo and in vitro assays of antimycobacterial immunity. METHODS: We enrolled 475 healthy HIV-negative children and young adults living in a hyperendemic area of TB. We measured in vivo TST responses, and a 1:10 diluted 3- or 7-day whole-blood assay was used to determine the in vitro antigen-specific interferon (IFN)-gamma cytokine release. The frequency of antigen-specific IFN-gamma(+)CD4(+) and IFN-gamma(+)CD8(+) cells was tested using intracellular cytokine staining after 1 day incubation. RESULTS: In vivo TST responses segregated into two well-separated groups with either no measurable response (TST induration \textless 5 mm; n = 164) or a normally distributed group with TST indurations \textgreater or = 5 mm with peak at 15 mm (n = 260). In vitro assays provided a less pronounced separation of responders and nonresponders. Correlation analysis of responses among persons with TST \textgreater or = 5 mm demonstrated that extent of TST response was poorly correlated with IFN-gamma release (coefficients of correlation rho = 0.17-0.22) and frequency of IFN-gamma(+)CD4(+)/CD8(+) cells (rho = 0.05-0.17) across three stimulating antigens (Mycobacterium bovis bacillus Calmette-Guérin, purified protein derivative, early-secreted antigenic target-6). CONCLUSION: We conclude that in vivo and in vitro assays are nonredundant, complementary measures of antimycobacterial immunity. Both TST and in vitro assays provided valuable information about antimycobacterial immunity and by inference latent TB in the studied high-incidence TB settings.

@article{moller_current_2010,
	title = {Current findings, challenges and novel approaches in human genetic susceptibility to tuberculosis},
	volume = {90},
	issn = {1873-281X},
	doi = {10.1016/j.tube.2010.02.002},
	abstract = {The evidence for a human genetic component in susceptibility to tuberculosis (TB) is incontrovertible. Quite apart from studies of rare disease events illustrating the importance of key genes in humans and animals, TB at the population level is also influenced by the genetics of the host. Heritability of disease concordance and immune responses to mycobacterial antigens has been clearly shown, and ranges up to 71\%. Linkage studies, designed to identify major susceptibility genes in a disease, have produced a number of candidate loci but few, except for regions on chromosome 5p15, 20p and 20q, have been replicated. The region on 5p15 regulates the intensity of the response to the tuberculin skin test, and another locus on 11p14 appears to control resistance to the bacterium. In addition, numerous genes and pathways have been implicated in candidate gene association studies, with validation of polymorphisms in IFNG, NRAMP1, and NOS2A and equivocal results for IL10, CCL2, DC-SIGN, P2RX7, VDR, TLR2, TLR9 and SP110. Other more recently researched candidate genes such as TNFRSF1B remain to be validated, preferably in meta-analyses. New approaches have provided early evidence for the importance of gene-gene interactions in regulating resistance to disease, and also the prospect that applying host genetics in the field of vaccinomics could lead to a more targeted approach in designing interventions to aid the human immune system in combating mycobacteria. Genome-wide association studies and admixture mapping are approaches that remain to be applied to TB, and it is not clear, as is the case with other complex diseases, how much of the heritability of the TB susceptibility phenotype will be determined by multiple genes of small effect versus rare variants with disproportionately large effects.},
	language = {eng},
	number = {2},
	journal = {Tuberculosis (Edinburgh, Scotland)},
	author = {Möller, Marlo and Hoal, Eileen G.},
	month = mar,
	year = {2010},
	pmid = {20206579},
	note = {00130 },
	keywords = {Female, Genetic Linkage, Genetic Predisposition to Disease, Humans, Male, Mycobacterium tuberculosis, Phenotype, Polymorphism, Single Nucleotide, Tuberculosis},
	pages = {71--83},
}

The evidence for a human genetic component in susceptibility to tuberculosis (TB) is incontrovertible. Quite apart from studies of rare disease events illustrating the importance of key genes in humans and animals, TB at the population level is also influenced by the genetics of the host. Heritability of disease concordance and immune responses to mycobacterial antigens has been clearly shown, and ranges up to 71%. Linkage studies, designed to identify major susceptibility genes in a disease, have produced a number of candidate loci but few, except for regions on chromosome 5p15, 20p and 20q, have been replicated. The region on 5p15 regulates the intensity of the response to the tuberculin skin test, and another locus on 11p14 appears to control resistance to the bacterium. In addition, numerous genes and pathways have been implicated in candidate gene association studies, with validation of polymorphisms in IFNG, NRAMP1, and NOS2A and equivocal results for IL10, CCL2, DC-SIGN, P2RX7, VDR, TLR2, TLR9 and SP110. Other more recently researched candidate genes such as TNFRSF1B remain to be validated, preferably in meta-analyses. New approaches have provided early evidence for the importance of gene-gene interactions in regulating resistance to disease, and also the prospect that applying host genetics in the field of vaccinomics could lead to a more targeted approach in designing interventions to aid the human immune system in combating mycobacteria. Genome-wide association studies and admixture mapping are approaches that remain to be applied to TB, and it is not clear, as is the case with other complex diseases, how much of the heritability of the TB susceptibility phenotype will be determined by multiple genes of small effect versus rare variants with disproportionately large effects.

@article{quintana-murci_strong_2010,
	title = {Strong maternal {Khoisan} contribution to the {South} {African} coloured population: a case of gender-biased admixture},
	volume = {86},
	issn = {1537-6605},
	shorttitle = {Strong maternal {Khoisan} contribution to the {South} {African} coloured population},
	doi = {10.1016/j.ajhg.2010.02.014},
	abstract = {The study of recently admixed populations provides unique tools for understanding recent population dynamics, socio-cultural factors associated with the founding of emerging populations, and the genetic basis of disease by means of admixture mapping. Historical records and recent autosomal data indicate that the South African Coloured population forms a unique highly admixed population, resulting from the encounter of different peoples from Africa, Europe, and Asia. However, little is known about the mode by which this admixed population was recently founded. Here we show, through detailed phylogeographic analyses of mitochondrial DNA and Y-chromosome variation in a large sample of South African Coloured individuals, that this population derives from at least five different parental populations (Khoisan, Bantus, Europeans, Indians, and Southeast Asians), who have differently contributed to the foundation of the South African Coloured. In addition, our analyses reveal extraordinarily unbalanced gender-specific contributions of the various population genetic components, the most striking being the massive maternal contribution of Khoisan peoples (more than 60\%) and the almost negligible maternal contribution of Europeans with respect to their paternal counterparts. The overall picture of gender-biased admixture depicted in this study indicates that the modern South African Coloured population results mainly from the early encounter of European and African males with autochthonous Khoisan females of the Cape of Good Hope around 350 years ago.},
	language = {eng},
	number = {4},
	journal = {American Journal of Human Genetics},
	author = {Quintana-Murci, Lluis and Harmant, Christine and Quach, Hélène and Balanovsky, Oleg and Zaporozhchenko, Valery and Bormans, Connie and van Helden, Paul D. and Hoal, Eileen G. and Behar, Doron M.},
	month = apr,
	year = {2010},
	pmid = {20346436},
	pmcid = {PMC2850426},
	note = {00056 },
	keywords = {African Continental Ancestry Group, Chromosomes, Human, Y, DNA, Mitochondrial, Female, Genetic Linkage, Genetics, Population, Humans, Male, Mothers, Polymorphism, Single Nucleotide, Sex Factors},
	pages = {611--620},
}

The study of recently admixed populations provides unique tools for understanding recent population dynamics, socio-cultural factors associated with the founding of emerging populations, and the genetic basis of disease by means of admixture mapping. Historical records and recent autosomal data indicate that the South African Coloured population forms a unique highly admixed population, resulting from the encounter of different peoples from Africa, Europe, and Asia. However, little is known about the mode by which this admixed population was recently founded. Here we show, through detailed phylogeographic analyses of mitochondrial DNA and Y-chromosome variation in a large sample of South African Coloured individuals, that this population derives from at least five different parental populations (Khoisan, Bantus, Europeans, Indians, and Southeast Asians), who have differently contributed to the foundation of the South African Coloured. In addition, our analyses reveal extraordinarily unbalanced gender-specific contributions of the various population genetic components, the most striking being the massive maternal contribution of Khoisan peoples (more than 60%) and the almost negligible maternal contribution of Europeans with respect to their paternal counterparts. The overall picture of gender-biased admixture depicted in this study indicates that the modern South African Coloured population results mainly from the early encounter of European and African males with autochthonous Khoisan females of the Cape of Good Hope around 350 years ago.

@article{de_wit_genome-wide_2010,
	title = {Genome-wide analysis of the structure of the {South} {African} {Coloured} {Population} in the {Western} {Cape}},
	volume = {128},
	issn = {1432-1203},
	doi = {10.1007/s00439-010-0836-1},
	abstract = {Admixed populations present unique opportunities to discover the genetic factors underlying many multifactorial diseases. The geographical position and complex history of South Africa has led to the establishment of the unique admixed population known as the South African Coloured. Not much is known about the genetic make-up of this population, and the historical record is patchy. We genotyped 959 individuals from the Western Cape area, self-identified as belonging to this population, using the Affymetrix 500k genotyping platform. This resulted in nearly 75,000 autosomal SNPs that could be compared with populations represented in the International HapMap Project and the Human Genome Diversity Project. Analysis by means of both the admixture and linkage models in STRUCTURE revealed that the major ancestral components of this population are predominantly Khoesan (32-43\%), Bantu-speaking Africans (20-36\%), European (21-28\%) and a smaller Asian contribution (9-11\%), depending on the model used. This is consistent with historical data. While of great historical and genealogical interest, this information is also essential for future admixture mapping of disease genes in this population.},
	language = {eng},
	number = {2},
	journal = {Human Genetics},
	author = {de Wit, Erika and Delport, Wayne and Rugamika, Chimusa E. and Meintjes, Ayton and Möller, Marlo and van Helden, Paul D. and Seoighe, Cathal and Hoal, Eileen G.},
	month = aug,
	year = {2010},
	pmid = {20490549},
	note = {00061 },
	keywords = {African Continental Ancestry Group, Asian Continental Ancestry Group, Ethnic Groups, European Continental Ancestry Group, Genome, Genotype, Geography, Humans, Male, Polymorphism, Single Nucleotide, Population Groups, Research, South Africa},
	pages = {145--153},
}

Admixed populations present unique opportunities to discover the genetic factors underlying many multifactorial diseases. The geographical position and complex history of South Africa has led to the establishment of the unique admixed population known as the South African Coloured. Not much is known about the genetic make-up of this population, and the historical record is patchy. We genotyped 959 individuals from the Western Cape area, self-identified as belonging to this population, using the Affymetrix 500k genotyping platform. This resulted in nearly 75,000 autosomal SNPs that could be compared with populations represented in the International HapMap Project and the Human Genome Diversity Project. Analysis by means of both the admixture and linkage models in STRUCTURE revealed that the major ancestral components of this population are predominantly Khoesan (32-43%), Bantu-speaking Africans (20-36%), European (21-28%) and a smaller Asian contribution (9-11%), depending on the model used. This is consistent with historical data. While of great historical and genealogical interest, this information is also essential for future admixture mapping of disease genes in this population.

@article{moller_analysis_2010,
	title = {Analysis of eight genes modulating interferon gamma and human genetic susceptibility to tuberculosis: a case-control association study},
	volume = {10},
	issn = {1471-2334},
	shorttitle = {Analysis of eight genes modulating interferon gamma and human genetic susceptibility to tuberculosis},
	doi = {10.1186/1471-2334-10-154},
	abstract = {BACKGROUND: Interferon gamma is a major macrophage-activating cytokine during infection with Mycobacterium tuberculosis, the causative pathogen of tuberculosis, and its role has been well established in animal models and in humans. This cytokine is produced by activated T helper 1 cells, which can best deal with intracellular pathogens such as M. tuberculosis. Based on the hypothesis that genes which regulate interferon gamma may influence tuberculosis susceptibility, we investigated polymorphisms in eight candidate genes.
METHODS: Fifty-four polymorphisms in eight candidate genes were genotyped in over 800 tuberculosis cases and healthy controls in a population-based case-control association study in a South African population. Genotyping methods used included the SNPlex Genotyping System, capillary electrophoresis of fluorescently labelled PCR products, TaqMan SNP genotyping assays or the amplification mutation refraction system. Single polymorphisms as well as haplotypes of the variants were tested for association with TB using statistical analyses.
RESULTS: A haplotype in interleukin 12B was nominally associated with tuberculosis (p = 0.02), but after permutation testing, done to assess the significance for the entire analysis, this was not globally significant. In addition a novel allele was found for the interleukin 12B D5S2941 microsatellite.
CONCLUSIONS: This study highlights the importance of using larger sample sizes when attempting validation of previously reported genetic associations. Initial studies may be false positives or may propose a stronger genetic effect than subsequently found to be the case.},
	language = {eng},
	journal = {BMC infectious diseases},
	author = {Möller, Marlo and Nebel, Almut and van Helden, Paul D. and Schreiber, Stefan and Hoal, Eileen G.},
	year = {2010},
	pmid = {20525402},
	pmcid = {PMC2891757},
	note = {00022 },
	keywords = {Adolescent, Adult, Female, Genetic Predisposition to Disease, Genotype, Humans, Interferon-gamma, Male, Molecular Sequence Data, Mycobacterium tuberculosis, Polymorphism, Genetic, South Africa, Tuberculosis, Young Adult},
	pages = {154},
}

BACKGROUND: Interferon gamma is a major macrophage-activating cytokine during infection with Mycobacterium tuberculosis, the causative pathogen of tuberculosis, and its role has been well established in animal models and in humans. This cytokine is produced by activated T helper 1 cells, which can best deal with intracellular pathogens such as M. tuberculosis. Based on the hypothesis that genes which regulate interferon gamma may influence tuberculosis susceptibility, we investigated polymorphisms in eight candidate genes. METHODS: Fifty-four polymorphisms in eight candidate genes were genotyped in over 800 tuberculosis cases and healthy controls in a population-based case-control association study in a South African population. Genotyping methods used included the SNPlex Genotyping System, capillary electrophoresis of fluorescently labelled PCR products, TaqMan SNP genotyping assays or the amplification mutation refraction system. Single polymorphisms as well as haplotypes of the variants were tested for association with TB using statistical analyses. RESULTS: A haplotype in interleukin 12B was nominally associated with tuberculosis (p = 0.02), but after permutation testing, done to assess the significance for the entire analysis, this was not globally significant. In addition a novel allele was found for the interleukin 12B D5S2941 microsatellite. CONCLUSIONS: This study highlights the importance of using larger sample sizes when attempting validation of previously reported genetic associations. Initial studies may be false positives or may propose a stronger genetic effect than subsequently found to be the case.

@article{gallant_impact_2010,
	title = {Impact of age and sex on mycobacterial immunity in an area of high tuberculosis incidence},
	volume = {14},
	issn = {1815-7920},
	abstract = {SETTING: The extent of immune reactivity measured by the tuberculin skin test (TST) and interferon-gamma (IFN-gamma) T-cell assays is usually not analysed.
OBJECTIVE: To determine the impact of age and sex on assay positivity and on the extent of reactivity of both TST and T-cell assays in young persons in an area of South Africa with high TB transmission.
RESULTS: Age had a strong impact on assay positivity for all seven immune phenotypes tested (P {\textless} 0.0007). Among positive responders, the extent of purified protein derivative (PPD) triggered IFN-gamma release (P {\textless} 0.003) was sensitive to age. ESAT-6 triggered IFN-gamma release (day 7, P = 0.03) and the frequency of PPD-specific IFN-gamma(+)CD4(+) (P = 0.03) and IFN-gamma(+)CD8(+) cells (P = 0.04) were weakly dependent on age. By contrast, the extent of TST induration was insensitive to age (P {\textgreater} 0.05), and sex had no significant impact on any phenotype measured (P {\textgreater} 0.05). The high proportion of positive responders in the 1-10 year age-group observed with long-term whole blood assays, but not with 3-day assays and TST, suggests that long-term whole blood assays may be confounded by bacille Calmette-Guérin vaccination in this age group.
CONCLUSION: There is a significant impact of age, but not sex, on different assays of immune reactivity in this high TB transmission setting.},
	language = {eng},
	number = {8},
	journal = {The International Journal of Tuberculosis and Lung Disease: The Official Journal of the International Union Against Tuberculosis and Lung Disease},
	author = {Gallant, C. J. and Cobat, A. and Simkin, L. and Black, G. F. and Stanley, K. and Hughes, J. and Doherty, T. M. and Hanekom, W. A. and Eley, B. and Beyers, N. and Jaïs, J.-P. and van Helden, P. and Abel, L. and Alcaïs, A. and Hoal, E. G. and Schurr, E.},
	month = aug,
	year = {2010},
	pmid = {20626938},
	note = {00012 },
	keywords = {Adolescent, Age Distribution, Age Factors, Antigens, Bacterial, Child, Child, Preschool, Female, Follow-Up Studies, Humans, Immunity, Innate, Incidence, Infant, Interferon-gamma, Male, Mycobacterium tuberculosis, Phenotype, Retrospective Studies, Sex Distribution, Sex Factors, South Africa, Tuberculin Test, Tuberculosis, Young Adult},
	pages = {952--959},
}

SETTING: The extent of immune reactivity measured by the tuberculin skin test (TST) and interferon-gamma (IFN-gamma) T-cell assays is usually not analysed. OBJECTIVE: To determine the impact of age and sex on assay positivity and on the extent of reactivity of both TST and T-cell assays in young persons in an area of South Africa with high TB transmission. RESULTS: Age had a strong impact on assay positivity for all seven immune phenotypes tested (P \textless 0.0007). Among positive responders, the extent of purified protein derivative (PPD) triggered IFN-gamma release (P \textless 0.003) was sensitive to age. ESAT-6 triggered IFN-gamma release (day 7, P = 0.03) and the frequency of PPD-specific IFN-gamma(+)CD4(+) (P = 0.03) and IFN-gamma(+)CD8(+) cells (P = 0.04) were weakly dependent on age. By contrast, the extent of TST induration was insensitive to age (P \textgreater 0.05), and sex had no significant impact on any phenotype measured (P \textgreater 0.05). The high proportion of positive responders in the 1-10 year age-group observed with long-term whole blood assays, but not with 3-day assays and TST, suggests that long-term whole blood assays may be confounded by bacille Calmette-Guérin vaccination in this age group. CONCLUSION: There is a significant impact of age, but not sex, on different assays of immune reactivity in this high TB transmission setting.

@article{moller_investigation_2009,
	title = {Investigation of chromosome 17 candidate genes in susceptibility to {TB} in a {South} {African} population},
	volume = {89},
	issn = {1873-281X},
	doi = {10.1016/j.tube.2008.10.001},
	abstract = {Chromosome 17 is known to contain TB susceptibility genes. Polymorphisms in two of these genes, namely NOS2A and CCL2, have been associated with TB in various populations. To investigate a possible association of gene variants with TB in the South African Coloured population we genotyped SNPs from NOS2A and CCL2 in over 800 TB cases and controls. We found a significant association between TB and two haplotypes, containing the functional rs9282799 and rs8078340 SNPs, in the NOS2A promoter. The T allele of rs8078340, found in the haplotype over-represented in cases (p=0.015, p(c)=0.038, OR=1.4, 95\% CI [1.1-1.8]), was previously shown to decrease the quantity of DNA-protein complex bound as well as the duration of binding and may decrease nitric oxide (NO) production. The C allele of rs8078340 was present in the haplotype more frequent in controls (p=0.011, p(c)=0.029, OR=1.4, 95\% CI [1.1-1.8]). In the single-point analysis of NOS2A, rs2779249 (previously associated with TB in Brazilians) and the functional rs8078340 were nominally associated with disease. No association was found between any of the other SNPs or haplotypes studied and TB. This study presents evidence that haplotypes in the NOS2A promoter influence susceptibility to TB and confirms the importance of NO production in the disease.},
	language = {eng},
	number = {2},
	journal = {Tuberculosis (Edinburgh, Scotland)},
	author = {Möller, Marlo and Nebel, Almut and Valentonyte, Ruta and van Helden, Paul D. and Schreiber, Stefan and Hoal, Eileen G.},
	month = mar,
	year = {2009},
	pmid = {19147409},
	note = {00041 },
	keywords = {Case-Control Studies, Chemokine CCL2, Chromosomes, Human, Pair 17, Gene Frequency, Genetic Predisposition to Disease, Genotype, Haplotypes, Humans, Linkage Disequilibrium, Nitric Oxide Synthase Type II, Polymorphism, Single Nucleotide, South Africa, Tuberculosis},
	pages = {189--194},
}

Chromosome 17 is known to contain TB susceptibility genes. Polymorphisms in two of these genes, namely NOS2A and CCL2, have been associated with TB in various populations. To investigate a possible association of gene variants with TB in the South African Coloured population we genotyped SNPs from NOS2A and CCL2 in over 800 TB cases and controls. We found a significant association between TB and two haplotypes, containing the functional rs9282799 and rs8078340 SNPs, in the NOS2A promoter. The T allele of rs8078340, found in the haplotype over-represented in cases (p=0.015, p(c)=0.038, OR=1.4, 95% CI [1.1-1.8]), was previously shown to decrease the quantity of DNA-protein complex bound as well as the duration of binding and may decrease nitric oxide (NO) production. The C allele of rs8078340 was present in the haplotype more frequent in controls (p=0.011, p(c)=0.029, OR=1.4, 95% CI [1.1-1.8]). In the single-point analysis of NOS2A, rs2779249 (previously associated with TB in Brazilians) and the functional rs8078340 were nominally associated with disease. No association was found between any of the other SNPs or haplotypes studied and TB. This study presents evidence that haplotypes in the NOS2A promoter influence susceptibility to TB and confirms the importance of NO production in the disease.

@article{cobat_two_2009,
	title = {Two loci control tuberculin skin test reactivity in an area hyperendemic for tuberculosis},
	volume = {206},
	issn = {1540-9538},
	doi = {10.1084/jem.20090892},
	abstract = {Approximately 20\% of persons living in areas hyperendemic for tuberculosis (TB) display persistent lack of tuberculin skin test (TST) reactivity and appear to be naturally resistant to infection by Mycobacterium tuberculosis. Among those with a positive response, the intensity of TST reactivity varies greatly. The genetic basis of TST reactivity is not known. We report on a genome-wide linkage search for loci that have an impact on TST reactivity, which is defined either as zero versus nonzero (TST-BINa) or as extent of TST in millimeters (TST-quantitative trait locus [QTL]) in a panel of 128 families, including 350 siblings, from an area of South Africa hyperendemic for TB. We detected a major locus (TST1) on chromosomal region 11p14 (P = 1.4 x 10(-5)), which controls TST-BINa, with a lack of responsiveness indicating T cell-independent resistance to M. tuberculosis. We also detected a second major locus (TST2) on chromosomal region 5p15 (P {\textless} 10(-5)), which controls TST-QTL or the intensity of T cell-mediated delayed type hypersensitivity (DTH) to tuberculin. Fine mapping of this region identified SLC6A3, encoding the dopamine transporter DAT1, as a promising gene for further studies. Our results pave the way for the understanding of the molecular mechanisms involved in resistance to M. tuberculosis infection in endemic areas (TST1) and for the identification of critical regulators of T cell-dependent DTH to tuberculin (TST2).},
	language = {eng},
	number = {12},
	journal = {The Journal of Experimental Medicine},
	author = {Cobat, Aurelie and Gallant, Caroline J. and Simkin, Leah and Black, Gillian F. and Stanley, Kim and Hughes, Jane and Doherty, T. Mark and Hanekom, Willem A. and Eley, Brian and Jaïs, Jean-Philippe and Boland-Auge, Anne and van Helden, Paul and Casanova, Jean-Laurent and Abel, Laurent and Hoal, Eileen G. and Schurr, Erwin and Alcaïs, Alexandre},
	month = nov,
	year = {2009},
	pmid = {19901083},
	pmcid = {PMC2806605},
	note = {00063 },
	keywords = {Chromosome Mapping, Chromosomes, Human, Pair 11, Chromosomes, Human, Pair 5, Dopamine Plasma Membrane Transport Proteins, Endemic Diseases, Female, Humans, Hypersensitivity, Delayed, Male, Mycobacterium tuberculosis, Quantitative Trait Loci, Siblings, South Africa, Tuberculin, Tuberculin Test, Tuberculosis},
	pages = {2583--2591},
}

Approximately 20% of persons living in areas hyperendemic for tuberculosis (TB) display persistent lack of tuberculin skin test (TST) reactivity and appear to be naturally resistant to infection by Mycobacterium tuberculosis. Among those with a positive response, the intensity of TST reactivity varies greatly. The genetic basis of TST reactivity is not known. We report on a genome-wide linkage search for loci that have an impact on TST reactivity, which is defined either as zero versus nonzero (TST-BINa) or as extent of TST in millimeters (TST-quantitative trait locus [QTL]) in a panel of 128 families, including 350 siblings, from an area of South Africa hyperendemic for TB. We detected a major locus (TST1) on chromosomal region 11p14 (P = 1.4 x 10(-5)), which controls TST-BINa, with a lack of responsiveness indicating T cell-independent resistance to M. tuberculosis. We also detected a second major locus (TST2) on chromosomal region 5p15 (P \textless 10(-5)), which controls TST-QTL or the intensity of T cell-mediated delayed type hypersensitivity (DTH) to tuberculin. Fine mapping of this region identified SLC6A3, encoding the dopamine transporter DAT1, as a promising gene for further studies. Our results pave the way for the understanding of the molecular mechanisms involved in resistance to M. tuberculosis infection in endemic areas (TST1) and for the identification of critical regulators of T cell-dependent DTH to tuberculin (TST2).

@article{hemmings_investigating_2008,
	title = {Investigating the role of the brain-derived neurotrophic factor ({BDNF}) val66met variant in obsessive-compulsive disorder ({OCD})},
	volume = {9},
	issn = {1562-2975},
	doi = {10.1080/15622970701245003},
	abstract = {Although evidence from family studies suggest that genetic factors play an important role in mediating obsessive-compulsive disorder (OCD), results from genetic case-control association analyses have been inconsistent. Discrepant findings may be attributed to the lack of phenotypic resolution, and population stratification. The aim of the present study was to investigate the role that the val66met variant within the gene encoding brain-derived neurotrophic factor (BDNF) may play in mediating the development of selected OCD subtypes accounting for the aforementioned confounding factors. One hundred and twelve OCD subjects and 140 controls were selected from the South African Afrikaner population. A significant association was observed in the male subgroup, with the met66 allele implicated as the risk allele in the development of OCD. This allele was also found to be associated with an earlier age at onset of OCD in males. On the other hand, the val66val genotype was associated with more severe OCD in the female population. No evidence of population stratification was observed in Afrikaner control subjects. These preliminary results point towards genetically distinct characteristics of OCD mediated by dysfunctions in BDNF. The present investigation forms part of ongoing research to elucidate the genetic components involved in the aetiology of OCD and OCD-related characteristics.},
	language = {eng},
	number = {2},
	journal = {The World Journal of Biological Psychiatry: The Official Journal of the World Federation of Societies of Biological Psychiatry},
	author = {Hemmings, Sîan M. J. and Kinnear, Craig J. and Van der Merwe, Lize and Lochner, Christine and Corfield, Valerie A. and Moolman-Smook, Johanna C. and Stein, Dan J.},
	year = {2008},
	pmid = {17853300},
	note = {00061 },
	keywords = {Adult, Brain-Derived Neurotrophic Factor, Chromosome Aberrations, Female, Genetic Markers, Genetic Variation, Genotype, Humans, Male, Obsessive-Compulsive Disorder, Population Surveillance, Questionnaires, South Africa},
	pages = {126--134},
}

Although evidence from family studies suggest that genetic factors play an important role in mediating obsessive-compulsive disorder (OCD), results from genetic case-control association analyses have been inconsistent. Discrepant findings may be attributed to the lack of phenotypic resolution, and population stratification. The aim of the present study was to investigate the role that the val66met variant within the gene encoding brain-derived neurotrophic factor (BDNF) may play in mediating the development of selected OCD subtypes accounting for the aforementioned confounding factors. One hundred and twelve OCD subjects and 140 controls were selected from the South African Afrikaner population. A significant association was observed in the male subgroup, with the met66 allele implicated as the risk allele in the development of OCD. This allele was also found to be associated with an earlier age at onset of OCD in males. On the other hand, the val66val genotype was associated with more severe OCD in the female population. No evidence of population stratification was observed in Afrikaner control subjects. These preliminary results point towards genetically distinct characteristics of OCD mediated by dysfunctions in BDNF. The present investigation forms part of ongoing research to elucidate the genetic components involved in the aetiology of OCD and OCD-related characteristics.

@article{lochner_cluster_2008,
	title = {Cluster analysis of obsessive-compulsive symptomatology: identifying obsessive-compulsive disorder subtypes},
	volume = {45},
	issn = {0333-7308},
	shorttitle = {Cluster analysis of obsessive-compulsive symptomatology},
	abstract = {BACKGROUND: There is increasing evidence that obsessive-compulsive disorder (OCD) is a heterogeneous disorder. Different clinical subtypes may be characterized by differing pathophysiological mechanisms and treatment outcomes.
METHODS: A cluster analysis was performed on 45 items of the Yale-Brown Obsessive-Compulsive Symptoms Checklist (YBOCS-CL) for 261 patients with OCD. Cluster solutions emerging at different linkage distance levels, and the associations of identified clusters with demographic, clinical and relevant genetic variables, were investigated.
RESULTS: A 6-cluster solution emerged at a linkage distance level of 1.5, and a 3-cluster solution emerged at a linkage distance level of 2.1. The 3 clusters in the latter solution were labeled I) Contamination / washing, II) Hoarding / symmetry / ordering, and III) Obsessional / checking. Increased Cluster III scores were associated with earlier age of OCD onset and the Met/Met (L/L) genotype of the COMT Val158Met polymorphism.
CONCLUSION: The data here are consistent with previous work delineating the different symptom subtypes of OCD, also with previous work suggesting that the Met/Met (L/L) genotype of the COMT Val158Met polymorphism may be associated with anxiety symptoms, as well as with previous work suggesting that dopaminergic genes may be particularly important in early-onset OCD.},
	language = {eng},
	number = {3},
	journal = {The Israel Journal of Psychiatry and Related Sciences},
	author = {Lochner, Christine and Hemmings, Sian M. J. and Kinnear, Craig J. and Nel, Daan and Hemmings, Sian M. J. and Seedat, Soraya and Moolman-Smook, Johanna C. and Stein, Dan J.},
	year = {2008},
	pmid = {19398820},
	note = {00025 },
	keywords = {Adolescent, Adult, Aged, Analysis of Variance, Catechol O-Methyltransferase, Cluster Analysis, Female, Genotype, Humans, Male, Middle Aged, Obsessive-Compulsive Disorder, Polymerase Chain Reaction, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Young Adult},
	pages = {164--176},
}

BACKGROUND: There is increasing evidence that obsessive-compulsive disorder (OCD) is a heterogeneous disorder. Different clinical subtypes may be characterized by differing pathophysiological mechanisms and treatment outcomes. METHODS: A cluster analysis was performed on 45 items of the Yale-Brown Obsessive-Compulsive Symptoms Checklist (YBOCS-CL) for 261 patients with OCD. Cluster solutions emerging at different linkage distance levels, and the associations of identified clusters with demographic, clinical and relevant genetic variables, were investigated. RESULTS: A 6-cluster solution emerged at a linkage distance level of 1.5, and a 3-cluster solution emerged at a linkage distance level of 2.1. The 3 clusters in the latter solution were labeled I) Contamination / washing, II) Hoarding / symmetry / ordering, and III) Obsessional / checking. Increased Cluster III scores were associated with earlier age of OCD onset and the Met/Met (L/L) genotype of the COMT Val158Met polymorphism. CONCLUSION: The data here are consistent with previous work delineating the different symptom subtypes of OCD, also with previous work suggesting that the Met/Met (L/L) genotype of the COMT Val158Met polymorphism may be associated with anxiety symptoms, as well as with previous work suggesting that dopaminergic genes may be particularly important in early-onset OCD.

@article{cooke_mapping_2008,
	title = {Mapping of a novel susceptibility locus suggests a role for {MC3R} and {CTSZ} in human tuberculosis},
	volume = {178},
	issn = {1535-4970},
	doi = {10.1164/rccm.200710-1554OC},
	abstract = {RATIONALE: Tuberculosis remains a major cause of morbidity and mortality in the developing world. A better understanding of the mechanisms of disease protection could allow novel strategies to disease management and control.
OBJECTIVES: To identify human genomic loci with evidence of linkage to tuberculosis susceptibility and, within these loci, to identify individual genes influencing tuberculosis susceptibility.
METHODS: Affected sibling pair analysis in South African and Malawian populations. Independent case-control study in West Africa.
MEASUREMENTS AND MAIN RESULTS: Two novel putative loci for tuberculosis susceptibility are identified: chromosome 6p21-q23 and chromosome 20q13.31-33--the latter with the strongest evidence for any locus reported to date in human tuberculosis (single point LOD score of 3.1, P = 10(-4), with a maximum likelihood score [MLS] of 2.8). An independent, multistage genetic association study in West African populations mapped this latter region in detail, finding evidence that variation in the melanocortin 3 receptor (MC3R) and cathepsin Z (CTSZ) genes play a role in the pathogenesis of tuberculosis.
CONCLUSIONS: These results demonstrate how a genomewide approach to the complex phenotype of human tuberculosis can identify novel targets for further research.},
	language = {eng},
	number = {2},
	journal = {American Journal of Respiratory and Critical Care Medicine},
	author = {Cooke, Graham S. and Campbell, Sarah J. and Bennett, Steve and Lienhardt, Christian and McAdam, Keith P. W. J. and Sirugo, Giorgio and Sow, Oumou and Gustafson, Per and Mwangulu, Frank and van Helden, Paul and Fine, Paul and Hoal, Eileen G. and Hill, Adrian V. S.},
	month = jul,
	year = {2008},
	pmid = {18420963},
	pmcid = {PMC2643210},
	note = {00050 },
	keywords = {Africa, Western, African Continental Ancestry Group, Case-Control Studies, Cathepsin K, Cathepsin Z, Cathepsins, Genetic Linkage, Genetic Predisposition to Disease, Humans, Likelihood Functions, Malawi, Microsatellite Repeats, Pedigree, Polymorphism, Genetic, Receptor, Melanocortin, Type 3, Regression Analysis, Siblings, South Africa, Tuberculosis, Pulmonary},
	pages = {203--207},
}

RATIONALE: Tuberculosis remains a major cause of morbidity and mortality in the developing world. A better understanding of the mechanisms of disease protection could allow novel strategies to disease management and control. OBJECTIVES: To identify human genomic loci with evidence of linkage to tuberculosis susceptibility and, within these loci, to identify individual genes influencing tuberculosis susceptibility. METHODS: Affected sibling pair analysis in South African and Malawian populations. Independent case-control study in West Africa. MEASUREMENTS AND MAIN RESULTS: Two novel putative loci for tuberculosis susceptibility are identified: chromosome 6p21-q23 and chromosome 20q13.31-33–the latter with the strongest evidence for any locus reported to date in human tuberculosis (single point LOD score of 3.1, P = 10(-4), with a maximum likelihood score [MLS] of 2.8). An independent, multistage genetic association study in West African populations mapped this latter region in detail, finding evidence that variation in the melanocortin 3 receptor (MC3R) and cathepsin Z (CTSZ) genes play a role in the pathogenesis of tuberculosis. CONCLUSIONS: These results demonstrate how a genomewide approach to the complex phenotype of human tuberculosis can identify novel targets for further research.

@article{moller_host_2007,
	title = {Host susceptibility to tuberculosis: {CARD15} polymorphisms in a {South} {African} population},
	volume = {21},
	issn = {0890-8508},
	shorttitle = {Host susceptibility to tuberculosis},
	doi = {10.1016/j.mcp.2006.10.001},
	abstract = {Tuberculosis (TB) is one of the leading causes of death worldwide. The nucleotide-binding oligomerisation domain 2 protein (NOD2) has recently been recognised as a non-redundant recognition mechanism of Mycobacterium tuberculosis. The caspase recruitment domain-containing protein 15 gene (CARD15), which encodes the NOD2 protein, is a susceptibility gene for Crohn's disease (CD), a granulomatous, chronic inflammatory disorder. CARD15 was therefore investigated as a candidate gene in TB. We genotyped the R702W, G908R and 1007fs variants, previously associated with CD, in TB cases and controls from the admixed South African Coloured population. No statistically significant differences between cases and controls were observed for these variants. We determined that the CD-associated mutations occur at very low frequencies in this population. Our results indicate that CARD15 is not a major susceptibility gene for TB in the South African Coloureds.},
	language = {eng},
	number = {2},
	journal = {Molecular and Cellular Probes},
	author = {Möller, Marlo and Nebel, Almut and Kwiatkowski, Ruta and van Helden, Paul D. and Hoal, Eileen G. and Schreiber, Stefan},
	month = apr,
	year = {2007},
	pmid = {17113749},
	note = {00022 },
	keywords = {Genetic Predisposition to Disease, Genotype, Humans, Mycobacterium tuberculosis, Nod2 Signaling Adaptor Protein, Polymorphism, Genetic, South Africa, Tuberculosis},
	pages = {148--151},
}

Tuberculosis (TB) is one of the leading causes of death worldwide. The nucleotide-binding oligomerisation domain 2 protein (NOD2) has recently been recognised as a non-redundant recognition mechanism of Mycobacterium tuberculosis. The caspase recruitment domain-containing protein 15 gene (CARD15), which encodes the NOD2 protein, is a susceptibility gene for Crohn's disease (CD), a granulomatous, chronic inflammatory disorder. CARD15 was therefore investigated as a candidate gene in TB. We genotyped the R702W, G908R and 1007fs variants, previously associated with CD, in TB cases and controls from the admixed South African Coloured population. No statistically significant differences between cases and controls were observed for these variants. We determined that the CD-associated mutations occur at very low frequencies in this population. Our results indicate that CARD15 is not a major susceptibility gene for TB in the South African Coloureds.

@article{babb_sp110_2007,
	title = {{SP110} polymorphisms are not associated with pulmonary tuberculosis in a {South} {African} population},
	volume = {121},
	issn = {0340-6717},
	doi = {10.1007/s00439-007-0335-1},
	abstract = {Susceptibility to tuberculosis (TB) in mice has recently been attributed to the Ipr1 gene. Polymorphisms in the human homologue, SP110, have been investigated in various populations with only one study finding an association with TB susceptibility. We investigated eight SP110 polymorphisms in a South African population, including two novel polymorphisms. No significant association was found with any of the polymorphisms investigated, including two polymorphisms that were previously found to be associated with TB susceptibility in West African populations.},
	language = {eng},
	number = {3-4},
	journal = {Human Genetics},
	author = {Babb, C. and Keet, E. Hanekom and van Helden, P. D. and Hoal, E. G.},
	month = may,
	year = {2007},
	pmid = {17287948},
	note = {00037 },
	keywords = {Adolescent, African Continental Ancestry Group, Case-Control Studies, Genetic Predisposition to Disease, Humans, Nuclear Proteins, Polymorphism, Genetic, Tuberculosis, Pulmonary},
	pages = {521--522},
}

Susceptibility to tuberculosis (TB) in mice has recently been attributed to the Ipr1 gene. Polymorphisms in the human homologue, SP110, have been investigated in various populations with only one study finding an association with TB susceptibility. We investigated eight SP110 polymorphisms in a South African population, including two novel polymorphisms. No significant association was found with any of the polymorphisms investigated, including two polymorphisms that were previously found to be associated with TB susceptibility in West African populations.

@article{barreiro_length_2007,
	title = {Length variation of {DC}-{SIGN} and {L}-{SIGN} neck-region has no impact on tuberculosis susceptibility},
	volume = {68},
	issn = {0198-8859},
	doi = {10.1016/j.humimm.2006.10.020},
	abstract = {The C-type lectins DC-SIGN and L-SIGN are important pathogen-recognition receptors of the human innate immune system. Both lectins have been shown to interact with a vast range of infectious agents, including Mycobacterium tuberculosis, the etiologic agent of tuberculosis in humans. In addition, DC-SIGN and L-SIGN possess a neck region, made up of a variable number of 23 amino acid tandem repeats, which plays a crucial role in the tetramerization of these proteins and support of the carbohydrate recognition domain. The length of the neck region, which shows variable levels of polymorphism, can critically influence the pathogen binding properties of these two receptors. We therefore investigated the impact of the DC-SIGN and L-SIGN neck-region length variation on the outcome of tuberculosis by screening this polymorphism in a large cohort of Coloured South African origin. The analyses of 711 individuals, including 351 tuberculosis patients and 360 healthy controls, revealed that none of the DC-SIGN and L-SIGN neck-region variants or genotypes seems to influence the individual susceptibility to develop tuberculosis.},
	language = {eng},
	number = {2},
	journal = {Human Immunology},
	author = {Barreiro, Luis B. and Neyrolles, Olivier and Babb, Chantal L. and van Helden, Paul D. and Gicquel, Brigitte and Hoal, Eileen G. and Quintana-Murci, Lluís},
	month = feb,
	year = {2007},
	pmid = {17321900},
	note = {00025 },
	keywords = {Adult, Cell Adhesion Molecules, Cohort Studies, Disease Susceptibility, Female, Humans, Lectins, C-Type, Male, Mycobacterium tuberculosis, Polymorphism, Restriction Fragment Length, Receptors, Cell Surface, South Africa, Tuberculosis, Pulmonary},
	pages = {106--112},
}

The C-type lectins DC-SIGN and L-SIGN are important pathogen-recognition receptors of the human innate immune system. Both lectins have been shown to interact with a vast range of infectious agents, including Mycobacterium tuberculosis, the etiologic agent of tuberculosis in humans. In addition, DC-SIGN and L-SIGN possess a neck region, made up of a variable number of 23 amino acid tandem repeats, which plays a crucial role in the tetramerization of these proteins and support of the carbohydrate recognition domain. The length of the neck region, which shows variable levels of polymorphism, can critically influence the pathogen binding properties of these two receptors. We therefore investigated the impact of the DC-SIGN and L-SIGN neck-region length variation on the outcome of tuberculosis by screening this polymorphism in a large cohort of Coloured South African origin. The analyses of 711 individuals, including 351 tuberculosis patients and 360 healthy controls, revealed that none of the DC-SIGN and L-SIGN neck-region variants or genotypes seems to influence the individual susceptibility to develop tuberculosis.

@article{moller_allelic_2007,
	title = {Allelic variation in {BTNL2} and susceptibility to tuberculosis in a {South} {African} population},
	volume = {9},
	issn = {1286-4579},
	doi = {10.1016/j.micinf.2007.01.011},
	abstract = {Tuberculosis and sarcoidosis show phenotypic features of granulomatous disease. The bacterium Mycobacterium tuberculosis can induce the expression of the sarcoidosis susceptibility gene BTNL2 in monocyte-derived macrophages. BTNL2 was therefore investigated as a candidate gene for tuberculosis in a case-control association study in the South African Coloured population. We sequenced the coding regions of BTNL2 to detect known and novel polymorphisms and genotyped 18 SNPs in 432 pulmonary tuberculosis cases and 482 controls. We did not find a significant association between the truncating rs2076530 SNP, previously associated with sarcoidosis, and tuberculosis. No association was found between any of the other SNPs studied and disease and none of the estimated haplotypes showed any association with TB. Comparative analyses with the South African data from this study and published data on German and American populations revealed that, for a segment of BTNL2, the admixed, but not stratified, South African population resembles the African-Americans more than white populations.},
	language = {eng},
	number = {4},
	journal = {Microbes and Infection / Institut Pasteur},
	author = {Möller, Marlo and Kwiatkowski, Ruta and Nebel, Almut and van Helden, Paul D. and Hoal, Eileen G. and Schreiber, Stefan},
	month = apr,
	year = {2007},
	pmid = {17347014},
	note = {00015 },
	keywords = {Adolescent, Adult, Alleles, Case-Control Studies, Female, Genetic Predisposition to Disease, Genetic Variation, Humans, Linkage Disequilibrium, Male, Membrane Glycoproteins, Middle Aged, Mycobacterium tuberculosis, Polymorphism, Single Nucleotide, Sarcoidosis, South Africa, Tuberculosis},
	pages = {522--528},
}

Tuberculosis and sarcoidosis show phenotypic features of granulomatous disease. The bacterium Mycobacterium tuberculosis can induce the expression of the sarcoidosis susceptibility gene BTNL2 in monocyte-derived macrophages. BTNL2 was therefore investigated as a candidate gene for tuberculosis in a case-control association study in the South African Coloured population. We sequenced the coding regions of BTNL2 to detect known and novel polymorphisms and genotyped 18 SNPs in 432 pulmonary tuberculosis cases and 482 controls. We did not find a significant association between the truncating rs2076530 SNP, previously associated with sarcoidosis, and tuberculosis. No association was found between any of the other SNPs studied and disease and none of the estimated haplotypes showed any association with TB. Comparative analyses with the South African data from this study and published data on German and American populations revealed that, for a segment of BTNL2, the admixed, but not stratified, South African population resembles the African-Americans more than white populations.

@article{babb_vitamin_2007,
	title = {Vitamin {D} receptor gene polymorphisms and sputum conversion time in pulmonary tuberculosis patients},
	volume = {87},
	issn = {1472-9792},
	doi = {10.1016/j.tube.2007.03.001},
	abstract = {A cohort of pulmonary tuberculosis (TB) patients in a South African admixed population was investigated to determine if the vitamin D receptor gene (VDR) polymorphisms FokI, ApaI, and TaqI are associated with TB susceptibility or time to sputum conversion, and to investigate other clinical and demographic factors affecting the rate of response to treatment. Firstly, a case-control association study of 249 TB cases and 352 healthy controls was carried out to investigate association of VDR polymorphisms with TB susceptibility. Secondly, a cohort of pulmonary tuberculosis patients with conversion times for both sputum smear (n=220) and culture (n=222) were analysed to determine factors contributing to mycobacterial resolution in sputum. Age and gender adjusted Cox regression models were constructed. Our results indicate that the extent of disease at diagnosis was predictive of both smear and culture conversion times in the final models. Smoking status and VDR genotype contributed independently to smear conversion time, with ApaI 'AA' genotype and TaqI 'T'-containing genotypes predictive of a faster response to TB chemotherapy. We did not find an association between VDR genotype and TB in the case-control study. We conclude that the time taken for an individual to convert to sputum negativity while on antituberculosis therapy can be independently predicted by the VDR genotype.},
	language = {eng},
	number = {4},
	journal = {Tuberculosis (Edinburgh, Scotland)},
	author = {Babb, C. and van der Merwe, L. and Beyers, N. and Pheiffer, C. and Walzl, G. and Duncan, K. and van Helden, P. and Hoal, E. G.},
	month = jul,
	year = {2007},
	pmid = {17449323},
	note = {00076 },
	keywords = {Adolescent, Adult, Aged, Case-Control Studies, Female, Genetic Predisposition to Disease, Haplotypes, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, Receptors, Calcitriol, Regression Analysis, South Africa, Sputum, Tuberculosis, Pulmonary},
	pages = {295--302},
}

A cohort of pulmonary tuberculosis (TB) patients in a South African admixed population was investigated to determine if the vitamin D receptor gene (VDR) polymorphisms FokI, ApaI, and TaqI are associated with TB susceptibility or time to sputum conversion, and to investigate other clinical and demographic factors affecting the rate of response to treatment. Firstly, a case-control association study of 249 TB cases and 352 healthy controls was carried out to investigate association of VDR polymorphisms with TB susceptibility. Secondly, a cohort of pulmonary tuberculosis patients with conversion times for both sputum smear (n=220) and culture (n=222) were analysed to determine factors contributing to mycobacterial resolution in sputum. Age and gender adjusted Cox regression models were constructed. Our results indicate that the extent of disease at diagnosis was predictive of both smear and culture conversion times in the final models. Smoking status and VDR genotype contributed independently to smear conversion time, with ApaI 'AA' genotype and TaqI 'T'-containing genotypes predictive of a faster response to TB chemotherapy. We did not find an association between VDR genotype and TB in the case-control study. We conclude that the time taken for an individual to convert to sputum negativity while on antituberculosis therapy can be independently predicted by the VDR genotype.

@article{hanekom_evidence_2007,
	title = {Evidence that the spread of {Mycobacterium} tuberculosis strains with the {Beijing} genotype is human population dependent},
	volume = {45},
	issn = {0095-1137},
	doi = {10.1128/JCM.02354-06},
	abstract = {This study describes a comparative analysis of the Beijing mycobacterial interspersed repetitive unit types of Mycobacterium tuberculosis isolates from Cape Town, South Africa, and East Asia. The results show a significant association between the frequency of occurrence of strains from defined Beijing sublineages and the human population from whom they were cultured (P {\textless} 0.0001).},
	language = {eng},
	number = {7},
	journal = {Journal of Clinical Microbiology},
	author = {Hanekom, M. and van der Spuy, G. D. and Gey van Pittius, N. C. and McEvoy, C. R. E. and Ndabambi, S. L. and Victor, T. C. and Hoal, E. G. and van Helden, P. D. and Warren, R. M.},
	month = jul,
	year = {2007},
	pmid = {17475755},
	pmcid = {PMC1933015},
	note = {00057 },
	keywords = {China, Far East, Genotype, Humans, Mycobacterium tuberculosis, Polymorphism, Genetic, Population Dynamics, South Africa, Tuberculosis, Pulmonary},
	pages = {2263--2266},
}

This study describes a comparative analysis of the Beijing mycobacterial interspersed repetitive unit types of Mycobacterium tuberculosis isolates from Cape Town, South Africa, and East Asia. The results show a significant association between the frequency of occurrence of strains from defined Beijing sublineages and the human population from whom they were cultured (P \textless 0.0001).

@article{hemmings_genetic_2006,
	title = {Genetic correlates in trichotillomania--{A} case-control association study in the {South} {African} {Caucasian} population},
	volume = {43},
	issn = {0333-7308},
	abstract = {BACKGROUND: Trichotillomania (TTM), a prevalent and disabling psychiatric disorder characterized by repetitive hair-pulling, is presently classified as an impulse control disorder (ICD). Some have argued, however, that TTM is an obsessive-compulsive spectrum disorder (OCSD). There is some evidence that both disorders (OCD and TTM) are mediated by serotonergic (5-HT) and dopaminergic pathways.
METHODS: The aim of the present investigation was to assess the role of candidate genes encoding components within the 5-HT and dopaminergic neurotransmitter pathways in mediating TTM. South African Caucasian TTM subjects (n=39), OCD (n=250) and control subjects (n=152) were genotyped for variants in 5-HT and dopaminergic candidate genes.
RESULTS: Both genotypic and allelic distributions of the 5-HT receptor 2A (5-HT2A) T102C variant were found to be significantly different between the TTM and control subjects (p=0.028 and p=0.024, respectively), and a trend towards significance was noted between the TTM and OCD subjects (p=0.084 and p=0.080 for genotype and allele analyses, respectively), with the T102T-genotype found to confer susceptibility to the development of TTM.
CONCLUSION: This investigation provides preliminary evidence for the involvement of 5-HT2A in the molecular aetiology of TTM and supports the need for further replication in a larger dataset. The present data are consistent with previous findings that 5-HT2A plays a role in mediating impulse dyscontrol.},
	language = {eng},
	number = {2},
	journal = {The Israel Journal of Psychiatry and Related Sciences},
	author = {Hemmings, Sîan M. J. and Kinnear, Craig J. and Lochner, Christine and Seedat, Soraya and Corfield, Valerie A. and Moolman-Smook, Johanna C. and Stein, Dan J.},
	year = {2006},
	pmid = {16910371},
	note = {00040 },
	keywords = {Alleles, Calcium-Binding Proteins, Case-Control Studies, Dopamine, European Continental Ancestry Group, Genotype, Glycoproteins, Humans, Neural Pathways, Obsessive-Compulsive Disorder, Polymorphism, Genetic, Serotonin, South Africa, Trichotillomania},
	pages = {93--101},
}

BACKGROUND: Trichotillomania (TTM), a prevalent and disabling psychiatric disorder characterized by repetitive hair-pulling, is presently classified as an impulse control disorder (ICD). Some have argued, however, that TTM is an obsessive-compulsive spectrum disorder (OCSD). There is some evidence that both disorders (OCD and TTM) are mediated by serotonergic (5-HT) and dopaminergic pathways. METHODS: The aim of the present investigation was to assess the role of candidate genes encoding components within the 5-HT and dopaminergic neurotransmitter pathways in mediating TTM. South African Caucasian TTM subjects (n=39), OCD (n=250) and control subjects (n=152) were genotyped for variants in 5-HT and dopaminergic candidate genes. RESULTS: Both genotypic and allelic distributions of the 5-HT receptor 2A (5-HT2A) T102C variant were found to be significantly different between the TTM and control subjects (p=0.028 and p=0.024, respectively), and a trend towards significance was noted between the TTM and OCD subjects (p=0.084 and p=0.080 for genotype and allele analyses, respectively), with the T102T-genotype found to confer susceptibility to the development of TTM. CONCLUSION: This investigation provides preliminary evidence for the involvement of 5-HT2A in the molecular aetiology of TTM and supports the need for further replication in a larger dataset. The present data are consistent with previous findings that 5-HT2A plays a role in mediating impulse dyscontrol.

@article{barreiro_promoter_2006,
	title = {Promoter variation in the {DC}-{SIGN}-encoding gene {CD209} is associated with tuberculosis},
	volume = {3},
	issn = {1549-1676},
	doi = {10.1371/journal.pmed.0030020},
	abstract = {BACKGROUND: Tuberculosis, which is caused by Mycobacterium tuberculosis, remains one of the leading causes of mortality worldwide. The C-type lectin DC-SIGN is known to be the major M. tuberculosis receptor on human dendritic cells. We reasoned that if DC-SIGN interacts with M. tuberculosis, as well as with other pathogens, variation in this gene might have a broad range of influence in the pathogenesis of a number of infectious diseases, including tuberculosis.
METHODS AND FINDINGS: We tested whether polymorphisms in CD209, the gene encoding DC-SIGN, are associated with susceptibility to tuberculosis through sequencing and genotyping analyses in a South African cohort. After exclusion of significant population stratification in our cohort, we observed an association between two CD209 promoter variants (-871G and -336A) and decreased risk of developing tuberculosis. By looking at the geographical distribution of these variants, we observed that their allelic combination is mainly confined to Eurasian populations.
CONCLUSIONS: Our observations suggest that the two -871G and -336A variants confer protection against tuberculosis. In addition, the geographic distribution of these two alleles, together with their phylogenetic status, suggest that they may have increased in frequency in non-African populations as a result of host genetic adaptation to a longer history of exposure to tuberculosis. Further characterization of the biological consequences of DC-SIGN variation in tuberculosis will be crucial to better appreciate the role of this lectin in interactions between the host immune system and the tubercle bacillus as well as other pathogens.},
	language = {eng},
	number = {2},
	journal = {PLoS medicine},
	author = {Barreiro, Luis B. and Neyrolles, Olivier and Babb, Chantal L. and Tailleux, Ludovic and Quach, Hélène and McElreavey, Ken and Helden, Paul D. van and Hoal, Eileen G. and Gicquel, Brigitte and Quintana-Murci, Lluis},
	month = feb,
	year = {2006},
	pmid = {16379498},
	pmcid = {PMC1324949},
	note = {00192 },
	keywords = {Adult, African Continental Ancestry Group, Case-Control Studies, Cell Adhesion Molecules, Dendritic Cells, Female, Genetic Predisposition to Disease, Humans, Lectins, C-Type, Male, Middle Aged, Mycobacterium tuberculosis, Phylogeny, Polymorphism, Single Nucleotide, Promoter Regions, Genetic, Receptors, Cell Surface, Risk Factors, South Africa, Tuberculosis, Pulmonary},
	pages = {e20},
}

BACKGROUND: Tuberculosis, which is caused by Mycobacterium tuberculosis, remains one of the leading causes of mortality worldwide. The C-type lectin DC-SIGN is known to be the major M. tuberculosis receptor on human dendritic cells. We reasoned that if DC-SIGN interacts with M. tuberculosis, as well as with other pathogens, variation in this gene might have a broad range of influence in the pathogenesis of a number of infectious diseases, including tuberculosis. METHODS AND FINDINGS: We tested whether polymorphisms in CD209, the gene encoding DC-SIGN, are associated with susceptibility to tuberculosis through sequencing and genotyping analyses in a South African cohort. After exclusion of significant population stratification in our cohort, we observed an association between two CD209 promoter variants (-871G and -336A) and decreased risk of developing tuberculosis. By looking at the geographical distribution of these variants, we observed that their allelic combination is mainly confined to Eurasian populations. CONCLUSIONS: Our observations suggest that the two -871G and -336A variants confer protection against tuberculosis. In addition, the geographic distribution of these two alleles, together with their phylogenetic status, suggest that they may have increased in frequency in non-African populations as a result of host genetic adaptation to a longer history of exposure to tuberculosis. Further characterization of the biological consequences of DC-SIGN variation in tuberculosis will be crucial to better appreciate the role of this lectin in interactions between the host immune system and the tubercle bacillus as well as other pathogens.

@article{lombard_hla_2006,
	title = {{HLA} class {II} disease associations in southern {Africa}},
	volume = {67},
	issn = {0001-2815},
	doi = {10.1111/j.1399-0039.2006.00530.x},
	abstract = {Southern Africa harbors several population groups representing a diversity of gene pool origins. This provides a unique opportunity to study genetic disease predisposition in these populations against a common environmental background. Human leukocyte antigen (HLA) association studies of these populations could improve knowledge on inter-population variation and HLA-related disease susceptibility. The aim of this paper is to review HLA class II disease associations reported for southern African population groups, compare them with findings in other populations and identify those unique to southern Africa. A number of HLA class II disease associations appear to be unique to southern African populations. These include DRB1*14011 association with insulin-dependent diabetes mellitus susceptibility in the Xhosa and DRB1*10 and DQB1*0302 with rheumatoid arthritis susceptibility in the South African (SA) Indian and SA Coloreds, respectively. A noteworthy similarity in class II disease association was observed among southern African Caucasoid and their European parental populations. Unique HLA class II disease associations observed in southern Africa are consistent with the notion that unique environmental and natural selective factors have resulted in certain ethnic-specific HLA class II disease associations, while common HLA class II disease associations found across different populations support the notion that common diseases are caused by common, ancient alleles present in indigenous African populations.},
	language = {eng},
	number = {2},
	journal = {Tissue Antigens},
	author = {Lombard, Z. and Brune, A. E. and Hoal, E. G. and Babb, C. and Van Helden, P. D. and Epplen, J. T. and Bornman, L.},
	month = feb,
	year = {2006},
	pmid = {16441480},
	note = {00031 },
	keywords = {Africa, Southern, Arthritis, Rheumatoid, Diabetes Mellitus, Type 1, Gene Frequency, Genetic Predisposition to Disease, HIV Infections, Histocompatibility Antigens Class II, Humans, Linkage Disequilibrium, Mycobacterium Infections, Polymorphism, Genetic},
	pages = {97--110},
}

Southern Africa harbors several population groups representing a diversity of gene pool origins. This provides a unique opportunity to study genetic disease predisposition in these populations against a common environmental background. Human leukocyte antigen (HLA) association studies of these populations could improve knowledge on inter-population variation and HLA-related disease susceptibility. The aim of this paper is to review HLA class II disease associations reported for southern African population groups, compare them with findings in other populations and identify those unique to southern Africa. A number of HLA class II disease associations appear to be unique to southern African populations. These include DRB1*14011 association with insulin-dependent diabetes mellitus susceptibility in the Xhosa and DRB1*10 and DQB1*0302 with rheumatoid arthritis susceptibility in the South African (SA) Indian and SA Coloreds, respectively. A noteworthy similarity in class II disease association was observed among southern African Caucasoid and their European parental populations. Unique HLA class II disease associations observed in southern Africa are consistent with the notion that unique environmental and natural selective factors have resulted in certain ethnic-specific HLA class II disease associations, while common HLA class II disease associations found across different populations support the notion that common diseases are caused by common, ancient alleles present in indigenous African populations.

@article{warren_differentiation_2006,
	title = {Differentiation of {Mycobacterium} tuberculosis complex by {PCR} amplification of genomic regions of difference},
	volume = {10},
	issn = {1027-3719},
	abstract = {Differentiation of members of the Mycobacterium tuberculosis complex by conventional mycobacteriological methods is time consuming, making surveillance of species-specific disease difficult. A two-step, multiplex polymerase chain reaction (PCR) method based on genomic regions of difference (RD1, RD1(mic), RD2(seal), RD4, RD9 and RD12) was developed for the differentiation of M. canettii, M. tuberculosis, M. africanum, M. microti, M. pinnipedii, M. caprae, M. bovis and M. bovis BCG. The size of the respective multiplex PCR amplification products corresponded to the presence of the different M. tuberculosis complex members. This method allows for rapid differentiation, making it suitable for routine laboratories and surveillance purposes.},
	language = {eng},
	number = {7},
	journal = {The International Journal of Tuberculosis and Lung Disease: The Official Journal of the International Union Against Tuberculosis and Lung Disease},
	author = {Warren, R. M. and Gey van Pittius, N. C. and Barnard, M. and Hesseling, A. and Engelke, E. and de Kock, M. and Gutierrez, M. C. and Chege, G. K. and Victor, T. C. and Hoal, E. G. and van Helden, P. D.},
	month = jul,
	year = {2006},
	pmid = {16850559},
	note = {00118 },
	keywords = {Electrophoresis, Polyacrylamide Gel, Genes, Bacterial, Mycobacterium tuberculosis, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Species Specificity},
	pages = {818--822},
}

Differentiation of members of the Mycobacterium tuberculosis complex by conventional mycobacteriological methods is time consuming, making surveillance of species-specific disease difficult. A two-step, multiplex polymerase chain reaction (PCR) method based on genomic regions of difference (RD1, RD1(mic), RD2(seal), RD4, RD9 and RD12) was developed for the differentiation of M. canettii, M. tuberculosis, M. africanum, M. microti, M. pinnipedii, M. caprae, M. bovis and M. bovis BCG. The size of the respective multiplex PCR amplification products corresponded to the presence of the different M. tuberculosis complex members. This method allows for rapid differentiation, making it suitable for routine laboratories and surveillance purposes.

@article{van_helden_antimicrobial_2006,
	title = {Antimicrobial resistance in tuberculosis: an international perspective},
	volume = {4},
	issn = {1744-8336},
	shorttitle = {Antimicrobial resistance in tuberculosis},
	doi = {10.1586/14787210.4.5.759},
	abstract = {Drug-resistant tuberculosis is a threat to tuberculosis control programs and community health. This growing problem mirrors the increasing incidence of tuberculosis in general. Public health problems include the absence of early diagnosis and effective treatment. The real need is to identify tuberculosis patients far earlier, particularly those with drug-resistant strains, and to begin appropriate therapy, which is of the shortest possible duration with minimal risk of acquiring further drug resistance or permitting further transmission. This article will address the epidemic of drug resistance and discuss some of the inherent difficulties in the treatment of drug-resistant tuberculosis. We highlight some of the controversies and new findings in this area, as well as future perspectives requiring more active interventions, in addition to new technology and developments.},
	language = {eng},
	number = {5},
	journal = {Expert Review of Anti-Infective Therapy},
	author = {van Helden, Paul D. and Donald, Peter R. and Victor, Thomas C. and Schaaf, H. Simon and Hoal, Eileen G. and Walzl, Gerhard and Warren, Robin M.},
	month = oct,
	year = {2006},
	pmid = {17140353},
	note = {00029 },
	keywords = {Antitubercular Agents, Drug Resistance, Multiple, Bacterial, Global Health, Humans, Internationality, Tuberculosis, Tuberculosis, Multidrug-Resistant, World Health Organization},
	pages = {759--766},
}

Drug-resistant tuberculosis is a threat to tuberculosis control programs and community health. This growing problem mirrors the increasing incidence of tuberculosis in general. Public health problems include the absence of early diagnosis and effective treatment. The real need is to identify tuberculosis patients far earlier, particularly those with drug-resistant strains, and to begin appropriate therapy, which is of the shortest possible duration with minimal risk of acquiring further drug resistance or permitting further transmission. This article will address the epidemic of drug resistance and discuss some of the inherent difficulties in the treatment of drug-resistant tuberculosis. We highlight some of the controversies and new findings in this area, as well as future perspectives requiring more active interventions, in addition to new technology and developments.

@article{lochner_cluster_2005,
	title = {Cluster analysis of obsessive-compulsive spectrum disorders in patients with obsessive-compulsive disorder: clinical and genetic correlates},
	volume = {46},
	issn = {0010-440X},
	shorttitle = {Cluster analysis of obsessive-compulsive spectrum disorders in patients with obsessive-compulsive disorder},
	doi = {10.1016/j.comppsych.2004.07.020},
	abstract = {BACKGROUND: Comorbidity of certain obsessive-compulsive spectrum disorders (OCSDs; such as Tourette's disorder) in obsessive-compulsive disorder (OCD) may serve to define important OCD subtypes characterized by differing phenomenology and neurobiological mechanisms. Comorbidity of the putative OCSDs in OCD has, however, not often been systematically investigated.
METHODS: The Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition , Axis I Disorders-Patient Version as well as a Structured Clinical Interview for Putative OCSDs (SCID-OCSD) were administered to 210 adult patients with OCD (N = 210, 102 men and 108 women; mean age, 35.7 +/- 13.3). A subset of Caucasian subjects (with OCD, n = 171; control subjects, n = 168), including subjects from the genetically homogeneous Afrikaner population (with OCD, n = 77; control subjects, n = 144), was genotyped for polymorphisms in genes involved in monoamine function. Because the items of the SCID-OCSD are binary (present/absent), a cluster analysis (Ward's method) using the items of SCID-OCSD was conducted. The association of identified clusters with demographic variables (age, gender), clinical variables (age of onset, obsessive-compulsive symptom severity and dimensions, level of insight, temperament/character, treatment response), and monoaminergic genotypes was examined.
RESULTS: Cluster analysis of the OCSDs in our sample of patients with OCD identified 3 separate clusters at a 1.1 linkage distance level. The 3 clusters were named as follows: (1) "reward deficiency" (including trichotillomania, Tourette's disorder, pathological gambling, and hypersexual disorder), (2) "impulsivity" (including compulsive shopping, kleptomania, eating disorders, self-injury, and intermittent explosive disorder), and (3) "somatic" (including body dysmorphic disorder and hypochondriasis). Several significant associations were found between cluster scores and other variables; for example, cluster I scores were associated with earlier age of onset of OCD and the presence of tics, cluster II scores were associated with female gender and childhood emotional abuse, and cluster III scores were associated with less insight and with somatic obsessions and compulsions. However, none of these clusters were associated with any particular genetic variant.
CONCLUSION: Analysis of comorbid OCSDs in OCD suggested that these lie on a number of different dimensions. These dimensions are partially consistent with previous theoretical approaches taken toward classifying OCD spectrum disorders. The lack of genetic validation of these clusters in the present study may indicate the involvement of other, as yet untested, genes. Further genetic and cluster analyses of comorbid OCSDs in OCD may ultimately contribute to a better delineation of OCD endophenotypes.},
	language = {eng},
	number = {1},
	journal = {Comprehensive Psychiatry},
	author = {Lochner, Christine and Hemmings, Sian M. J. and Kinnear, Craig J. and Niehaus, Dana J. H. and Nel, Daniel G. and Corfield, Valerie A. and Moolman-Smook, Johanna C. and Seedat, Soraya and Stein, Dan J.},
	month = feb,
	year = {2005},
	pmid = {15714189},
	note = {00101 },
	keywords = {Adolescent, Adult, Aged, Cluster Analysis, Comorbidity, Female, Gambling, Genotype, Humans, Impulse Control Disorders, Interview, Psychological, Male, Middle Aged, Monoamine Oxidase, Obsessive-Compulsive Disorder, Polymorphism, Genetic, Questionnaires, Self-Injurious Behavior, Serotonin, Severity of Illness Index, Tourette Syndrome, Trichotillomania},
	pages = {14--19},
}

BACKGROUND: Comorbidity of certain obsessive-compulsive spectrum disorders (OCSDs; such as Tourette's disorder) in obsessive-compulsive disorder (OCD) may serve to define important OCD subtypes characterized by differing phenomenology and neurobiological mechanisms. Comorbidity of the putative OCSDs in OCD has, however, not often been systematically investigated. METHODS: The Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition , Axis I Disorders-Patient Version as well as a Structured Clinical Interview for Putative OCSDs (SCID-OCSD) were administered to 210 adult patients with OCD (N = 210, 102 men and 108 women; mean age, 35.7 +/- 13.3). A subset of Caucasian subjects (with OCD, n = 171; control subjects, n = 168), including subjects from the genetically homogeneous Afrikaner population (with OCD, n = 77; control subjects, n = 144), was genotyped for polymorphisms in genes involved in monoamine function. Because the items of the SCID-OCSD are binary (present/absent), a cluster analysis (Ward's method) using the items of SCID-OCSD was conducted. The association of identified clusters with demographic variables (age, gender), clinical variables (age of onset, obsessive-compulsive symptom severity and dimensions, level of insight, temperament/character, treatment response), and monoaminergic genotypes was examined. RESULTS: Cluster analysis of the OCSDs in our sample of patients with OCD identified 3 separate clusters at a 1.1 linkage distance level. The 3 clusters were named as follows: (1) "reward deficiency" (including trichotillomania, Tourette's disorder, pathological gambling, and hypersexual disorder), (2) "impulsivity" (including compulsive shopping, kleptomania, eating disorders, self-injury, and intermittent explosive disorder), and (3) "somatic" (including body dysmorphic disorder and hypochondriasis). Several significant associations were found between cluster scores and other variables; for example, cluster I scores were associated with earlier age of onset of OCD and the presence of tics, cluster II scores were associated with female gender and childhood emotional abuse, and cluster III scores were associated with less insight and with somatic obsessions and compulsions. However, none of these clusters were associated with any particular genetic variant. CONCLUSION: Analysis of comorbid OCSDs in OCD suggested that these lie on a number of different dimensions. These dimensions are partially consistent with previous theoretical approaches taken toward classifying OCD spectrum disorders. The lack of genetic validation of these clusters in the present study may indicate the involvement of other, as yet untested, genes. Further genetic and cluster analyses of comorbid OCSDs in OCD may ultimately contribute to a better delineation of OCD endophenotypes.

@article{lochner_hoarding_2005,
	title = {Hoarding in obsessive-compulsive disorder: clinical and genetic correlates},
	volume = {66},
	issn = {0160-6689},
	shorttitle = {Hoarding in obsessive-compulsive disorder},
	abstract = {OBJECTIVE: Hoarding may be an important symptom dimension in obsessive-compulsive disorder (OCD). Hoarding in OCD has been associated with poor insight, poorer response to selective serotonin reuptake inhibitors than other OCD symptom dimensions, and a distinctive psychobiological profile. The clinical and genetic correlates of hoarding in OCD therefore deserve additional investigation.
METHOD: Adult OCD patients (N = 315) underwent a comprehensive clinical assessment that included the Structured Clinical Interview for DSM-IV Axis I Disorders (Patient Edition) and for Diagnosis of Obsessive-Compulsive Spectrum Disorders. DNA extracted from venous blood (10-30 mL) in a Caucasian subset of the interviewed OCD patients (N = 204) and Caucasian controls (N = 169), including patients (N = 94) and controls (N = 138) of Afrikaner descent, was genotyped to investigate polymorphisms in genes involved in monoamine function and previously hypothesized to be relevant to OCD. Data were collected from 1998 through 2004.
RESULTS: OCD patients with hoarding made up 18.1\% of the total sample. Compared with nonhoarding OCD, OCD with hoarding was associated with a number of comorbid Axis I disorders, obsessive-compulsive personality disorder, significantly higher OCD severity scores, and more functional impairment. In subjects of Afrikaner descent, the L/L genotype of the COMT Val158Met polymorphism was significantly more common in the OCD hoarding group, with a preponderance of low activity alleles, compared with nonhoarding patients and controls.
CONCLUSIONS: These data are consistent with the hypothesis that hoarding represents a unique symptom subtype in OCD with a distinctive clinical and psychobiological profile. Further work is needed to determine the psychobiological mechanisms responsible for hoarding and to replicate the genetic findings noted here.},
	language = {eng},
	number = {9},
	journal = {The Journal of Clinical Psychiatry},
	author = {Lochner, Christine and Kinnear, Craig J. and Hemmings, Sian M. J. and Seller, Cathlene and Niehaus, Dana J. H. and Knowles, James A. and Daniels, Willie and Moolman-Smook, Johanna C. and Seedat, Soraya and Stein, Dan J.},
	month = sep,
	year = {2005},
	pmid = {16187774},
	note = {00108 },
	keywords = {Adult, Catechol O-Methyltransferase, Child, Child Abuse, Comorbidity, Diagnostic and Statistical Manual of Mental Disorders, Disability Evaluation, Ethnic Groups, European Continental Ancestry Group, Female, Genotype, Humans, Male, Mental Disorders, Obsessive-Compulsive Disorder, Personality Inventory, Polymorphism, Genetic, Psychiatric Status Rating Scales, Severity of Illness Index, South Africa},
	pages = {1155--1160},
}

OBJECTIVE: Hoarding may be an important symptom dimension in obsessive-compulsive disorder (OCD). Hoarding in OCD has been associated with poor insight, poorer response to selective serotonin reuptake inhibitors than other OCD symptom dimensions, and a distinctive psychobiological profile. The clinical and genetic correlates of hoarding in OCD therefore deserve additional investigation. METHOD: Adult OCD patients (N = 315) underwent a comprehensive clinical assessment that included the Structured Clinical Interview for DSM-IV Axis I Disorders (Patient Edition) and for Diagnosis of Obsessive-Compulsive Spectrum Disorders. DNA extracted from venous blood (10-30 mL) in a Caucasian subset of the interviewed OCD patients (N = 204) and Caucasian controls (N = 169), including patients (N = 94) and controls (N = 138) of Afrikaner descent, was genotyped to investigate polymorphisms in genes involved in monoamine function and previously hypothesized to be relevant to OCD. Data were collected from 1998 through 2004. RESULTS: OCD patients with hoarding made up 18.1% of the total sample. Compared with nonhoarding OCD, OCD with hoarding was associated with a number of comorbid Axis I disorders, obsessive-compulsive personality disorder, significantly higher OCD severity scores, and more functional impairment. In subjects of Afrikaner descent, the L/L genotype of the COMT Val158Met polymorphism was significantly more common in the OCD hoarding group, with a preponderance of low activity alleles, compared with nonhoarding patients and controls. CONCLUSIONS: These data are consistent with the hypothesis that hoarding represents a unique symptom subtype in OCD with a distinctive clinical and psychobiological profile. Further work is needed to determine the psychobiological mechanisms responsible for hoarding and to replicate the genetic findings noted here.

@article{lochner_gender_2004,
	title = {Gender in obsessive-compulsive disorder: clinical and genetic findings},
	volume = {14},
	issn = {0924-977X},
	shorttitle = {Gender in obsessive-compulsive disorder},
	doi = {10.1016/S0924-977X(03)00063-4},
	abstract = {BACKGROUND: There is increasing recognition that obsessive-compulsive disorder (OCD) is not a homogeneous entity. It has been suggested that gender may contribute to the clinical and biological heterogeneity of OCD.
METHODS: Two hundred and twenty patients (n=220; 107 male, 113 female) with DSM-IV OCD (age: 36.40+/-13.46) underwent structured interviews. A subset of Caucasian subjects (n=178), including subjects from the genetically homogeneous Afrikaner population (n=81), and of matched control subjects (n=161), was genotyped for polymorphisms in genes involved in monoamine function. Clinical and genetic data were statistically analyzed across gender.
RESULTS: Compared with females, males with OCD (1) had an earlier age of onset, and a trend toward having more tics and worse outcome, (2) had somewhat differing patterns of OCD symptomatology and axis I comorbidity, and (3) in the Caucasian group, were more likely to have the high activity T allele of the EcoRV variant of the monoamine oxidase A (MAO-A) gene compared to controls, and (4) in the Afrikaner subgroup, were more frequently homozygous for the C allele at the G861C variant of the 5HT(1D beta) gene than controls. Females with OCD (1) reported more sexual abuse during childhood than males, (2) often noted changes in obsessive-compulsive symptoms in the premenstrual/menstrual period as well as during/shortly after pregnancy, and with menopause, and (3) in the Caucasian subgroup, were more frequently homozygous for the low activity C allele of the EcoRV variant of the MAO-A gene compared to controls, with this allele also more frequent in female patients than controls.
CONCLUSION: This study supports the hypothesis that gender contributes to the clinical and biological heterogeneity of OCD. A sexually dimorphic pattern of genetic susceptibility to OCD may be present. Further work is, however, needed to delineate the mechanisms that are responsible for mediating the effects of gender.},
	language = {eng},
	number = {2},
	journal = {European Neuropsychopharmacology: The Journal of the European College of Neuropsychopharmacology},
	author = {Lochner, Christine and Hemmings, Sian M. J. and Kinnear, Craig J. and Moolman-Smook, Johanna C. and Corfield, Valerie A. and Knowles, James A. and Niehaus, Dana J. H. and Stein, Dan J.},
	month = mar,
	year = {2004},
	pmid = {15013025},
	note = {00137 },
	keywords = {Adolescent, Adult, Age of Onset, Aged, Case-Control Studies, Comorbidity, Cysteine, Female, Gene Frequency, Genetic Predisposition to Disease, Genetic Variation, Genotype, Glycine, Humans, Interviews as Topic, Male, Middle Aged, Monoamine Oxidase, Obsessive-Compulsive Disorder, Polymorphism, Genetic, Pregnancy, Psychiatric Status Rating Scales, Quality of Life, Receptor, Serotonin, 5-HT1D, Serotonin, Sex Characteristics, South Africa},
	pages = {105--113},
}

BACKGROUND: There is increasing recognition that obsessive-compulsive disorder (OCD) is not a homogeneous entity. It has been suggested that gender may contribute to the clinical and biological heterogeneity of OCD. METHODS: Two hundred and twenty patients (n=220; 107 male, 113 female) with DSM-IV OCD (age: 36.40+/-13.46) underwent structured interviews. A subset of Caucasian subjects (n=178), including subjects from the genetically homogeneous Afrikaner population (n=81), and of matched control subjects (n=161), was genotyped for polymorphisms in genes involved in monoamine function. Clinical and genetic data were statistically analyzed across gender. RESULTS: Compared with females, males with OCD (1) had an earlier age of onset, and a trend toward having more tics and worse outcome, (2) had somewhat differing patterns of OCD symptomatology and axis I comorbidity, and (3) in the Caucasian group, were more likely to have the high activity T allele of the EcoRV variant of the monoamine oxidase A (MAO-A) gene compared to controls, and (4) in the Afrikaner subgroup, were more frequently homozygous for the C allele at the G861C variant of the 5HT(1D beta) gene than controls. Females with OCD (1) reported more sexual abuse during childhood than males, (2) often noted changes in obsessive-compulsive symptoms in the premenstrual/menstrual period as well as during/shortly after pregnancy, and with menopause, and (3) in the Caucasian subgroup, were more frequently homozygous for the low activity C allele of the EcoRV variant of the MAO-A gene compared to controls, with this allele also more frequent in female patients than controls. CONCLUSION: This study supports the hypothesis that gender contributes to the clinical and biological heterogeneity of OCD. A sexually dimorphic pattern of genetic susceptibility to OCD may be present. Further work is, however, needed to delineate the mechanisms that are responsible for mediating the effects of gender.

@article{koen_violence_2004,
	title = {Violence in male patients with schizophrenia: risk markers in a {South} {African} population},
	volume = {38},
	issn = {0004-8674},
	shorttitle = {Violence in male patients with schizophrenia},
	doi = {10.1111/j.1440-1614.2004.01338.x},
	abstract = {OBJECTIVE: We investigate the role of functional variants in the catecholamine-O-methyl transferase gene (COMT) and the monoamine oxidase-A gene (MOA-A), as well as previously identified non-genetic risk factors in the manifestation of violent behaviour in South African male schizophrenia patients.
METHOD: A cohort of 70 acutely relapsed male schizophrenia patients was stratified into violent and non-violent subsets, based on the presence or absence of previous or current violent behaviour. Standardized violence rating scales were also applied and the COMT/NlaIII and MAO-A promoter region variable number of tandem repeats (VNTR) polymorphisms were genotyped.
RESULTS: A multiple logistic regression model based on the clinical, genetic and socio-demographic variables indicated that delusions of control (OR = 3.7, 95\% CI = 1.21-11.61) and the combined use of cannabis and alcohol (OR = 6.89, 95\% CI = 1.28-37.05) were two significant predictors of violent behaviour in this schizophrenia population. No association was found between the tested polymorphisms and violent behaviour.
CONCLUSIONS: Although the sample size may have limited power to exclude a minor role for these specific gene variants, such a small contribution would have limited clinical relevance given the strong significance of the non-genetic markers. These findings suggest that currently proactive management of violent behaviour in this schizophrenia population should continue to be based on clinical predictors of violence.},
	language = {eng},
	number = {4},
	journal = {The Australian and New Zealand Journal of Psychiatry},
	author = {Koen, L. and Kinnear, C. J. and Corfield, V. A. and Emsley, R. A. and Jordaan, E. and Keyter, N. and Moolman-Smook, J. C. and Stein, D. J. and Niehaus, D. J. H.},
	month = apr,
	year = {2004},
	pmid = {15038805},
	note = {00040 },
	keywords = {Adult, Cohort Studies, Demography, Diagnostic and Statistical Manual of Mental Disorders, Ethnic Groups, Genetic Markers, Humans, Male, Minisatellite Repeats, Monoamine Oxidase, Polymorphism, Genetic, Promoter Regions, Genetic, Risk Factors, Schizophrenia, Schizophrenic Psychology, South Africa, Substance-Related Disorders, Tandem Repeat Sequences, Violence},
	pages = {254--259},
}

OBJECTIVE: We investigate the role of functional variants in the catecholamine-O-methyl transferase gene (COMT) and the monoamine oxidase-A gene (MOA-A), as well as previously identified non-genetic risk factors in the manifestation of violent behaviour in South African male schizophrenia patients. METHOD: A cohort of 70 acutely relapsed male schizophrenia patients was stratified into violent and non-violent subsets, based on the presence or absence of previous or current violent behaviour. Standardized violence rating scales were also applied and the COMT/NlaIII and MAO-A promoter region variable number of tandem repeats (VNTR) polymorphisms were genotyped. RESULTS: A multiple logistic regression model based on the clinical, genetic and socio-demographic variables indicated that delusions of control (OR = 3.7, 95% CI = 1.21-11.61) and the combined use of cannabis and alcohol (OR = 6.89, 95% CI = 1.28-37.05) were two significant predictors of violent behaviour in this schizophrenia population. No association was found between the tested polymorphisms and violent behaviour. CONCLUSIONS: Although the sample size may have limited power to exclude a minor role for these specific gene variants, such a small contribution would have limited clinical relevance given the strong significance of the non-genetic markers. These findings suggest that currently proactive management of violent behaviour in this schizophrenia population should continue to be based on clinical predictors of violence.

@article{lochner_dissociative_2004,
	title = {Dissociative experiences in obsessive-compulsive disorder and trichotillomania: clinical and genetic findings},
	volume = {45},
	issn = {0010-440X},
	shorttitle = {Dissociative experiences in obsessive-compulsive disorder and trichotillomania},
	doi = {10.1016/j.comppsych.2004.03.010},
	abstract = {A link between dissociation proneness in adulthood and self-reports of childhood traumatic events (including familial loss in childhood, sexual/physical abuse and neglect) has been documented. Several studies have also provided evidence for an association between dissociative experiences and trauma in patients with various psychiatric disorders, including post-traumatic stress disorder, borderline personality, dissociative identity and eating disorders. Based on the relative paucity of data on dissociation and trauma in obsessive-compulsive disorder (OCD) and trichotillomania (TTM), the primary objective of this study was to examine the relationship between trauma and dissociative experiences (DE) in these two diagnostic groups. Furthermore, the availability of clinical and genetic data on this sample allowed us to explore clinical and genetic factors relevant to this association. A total of 110 OCD and 32 TTM patients were compared with respect to the degree of dissociation (using the Dissociative Experiences Scale [DES]) and childhood trauma (using the Childhood Trauma Questionnaire [CTQ]). Patients were classified on the DES as either "high" (mean DES score {\textgreater}/= 30) or "low" (mean DES score {\textless} 30) dissociators. Additional clinical and genetic factors were also explored with chi-square and t tests as appropriate. A total of 15.8\% of OCD patients and 18.8\% of TTM patients were high dissociators. OCD and TTM groups were comparable on DES and CTQ total scores, and in both OCD and TTM groups, significant positive correlations were found between mean DES scores and mean CTQ subscores of emotional abuse, physical abuse, sexual abuse, and physical neglect. In the OCD group, high dissociators were significantly younger than low dissociators, and significantly more high dissociators than low dissociators reported a lifetime (current and past) history of tics (P {\textless}.001), Tourette's syndrome (P =.019), bulimia nervosa (P =.003), and borderline personality disorder (P =.027). In the TTM group, significantly more high dissociators than low dissociators reported (lifetime) kleptomania (P =.005) and depersonalisation disorder (P =.005). In the Caucasian OCD patients (n = 114), investigation of genetic polymorphisms involved in monoamine function revealed no significant differences between high and low dissociator groups. This study demonstrates a link between childhood trauma and DE in patients with OCD and TTM. High dissociative symptomatology may be present in a substantial proportion of patients diagnosed with these disorders. High dissociators may also be differentiated from low dissociators on some demographic features (e.g., lower age) and comorbidity profile (e.g., increased incidence of impulse dyscontrol disorders). Additional work is necessary before conclusions about the role of monoaminergic systems in mediating such dissociation can be drawn.},
	language = {eng},
	number = {5},
	journal = {Comprehensive Psychiatry},
	author = {Lochner, Christine and Seedat, Soraya and Hemmings, Sian M. J. and Kinnear, Craig J. and Corfield, Valerie A. and Niehaus, Dana J. H. and Moolman-Smook, Johanna C. and Stein, Dan J.},
	month = oct,
	year = {2004},
	pmid = {15332202},
	note = {00074 },
	keywords = {Adult, Dissociative Disorders, Female, Genotype, Humans, Male, Monoamine Oxidase, Obsessive-Compulsive Disorder, Polymorphism, Genetic, Prevalence, Questionnaires, Trichotillomania},
	pages = {384--391},
}

A link between dissociation proneness in adulthood and self-reports of childhood traumatic events (including familial loss in childhood, sexual/physical abuse and neglect) has been documented. Several studies have also provided evidence for an association between dissociative experiences and trauma in patients with various psychiatric disorders, including post-traumatic stress disorder, borderline personality, dissociative identity and eating disorders. Based on the relative paucity of data on dissociation and trauma in obsessive-compulsive disorder (OCD) and trichotillomania (TTM), the primary objective of this study was to examine the relationship between trauma and dissociative experiences (DE) in these two diagnostic groups. Furthermore, the availability of clinical and genetic data on this sample allowed us to explore clinical and genetic factors relevant to this association. A total of 110 OCD and 32 TTM patients were compared with respect to the degree of dissociation (using the Dissociative Experiences Scale [DES]) and childhood trauma (using the Childhood Trauma Questionnaire [CTQ]). Patients were classified on the DES as either "high" (mean DES score \textgreater/= 30) or "low" (mean DES score \textless 30) dissociators. Additional clinical and genetic factors were also explored with chi-square and t tests as appropriate. A total of 15.8% of OCD patients and 18.8% of TTM patients were high dissociators. OCD and TTM groups were comparable on DES and CTQ total scores, and in both OCD and TTM groups, significant positive correlations were found between mean DES scores and mean CTQ subscores of emotional abuse, physical abuse, sexual abuse, and physical neglect. In the OCD group, high dissociators were significantly younger than low dissociators, and significantly more high dissociators than low dissociators reported a lifetime (current and past) history of tics (P \textless.001), Tourette's syndrome (P =.019), bulimia nervosa (P =.003), and borderline personality disorder (P =.027). In the TTM group, significantly more high dissociators than low dissociators reported (lifetime) kleptomania (P =.005) and depersonalisation disorder (P =.005). In the Caucasian OCD patients (n = 114), investigation of genetic polymorphisms involved in monoamine function revealed no significant differences between high and low dissociator groups. This study demonstrates a link between childhood trauma and DE in patients with OCD and TTM. High dissociative symptomatology may be present in a substantial proportion of patients diagnosed with these disorders. High dissociators may also be differentiated from low dissociators on some demographic features (e.g., lower age) and comorbidity profile (e.g., increased incidence of impulse dyscontrol disorders). Additional work is necessary before conclusions about the role of monoaminergic systems in mediating such dissociation can be drawn.

@article{lochner_corrigendum_2004,
	title = {Corrigendum to "gender in obsessive-compulsive disorder: clinical and genetic findings" [{Eur}. {Neuropsychopharmacol}. 14 (2004) 105-113]},
	volume = {14},
	issn = {0924-977X},
	shorttitle = {Corrigendum to "gender in obsessive-compulsive disorder},
	abstract = {BACKGROUND: There is increasing recognition that obsessive-compulsive disorder (OCD) is not a homogeneous entity. It has been suggested that gender may contribute to the clinical and biological heterogeneity of OCD.
METHODS: Two hundred and twenty patients (n=220; 107 male, 113 female) with DSM-IV OCD (age: 36.40 +/- 13.46) underwent structured interviews. A subset of Caucasian subjects (n=178), including subjects from the genetically homogeneous Afrikaner population (n=81), and of matched control subjects (n=161), was genotyped for polymorphisms in genes involved in monoamine function. Clinical and genetic data were statistically analyzed across gender.
RESULTS: Compared with females, males with OCD (1) had an earlier age of onset, and a trend toward having more tics and worse outcome, (2) had somewhat differing patterns of OCD symptomatology and axis I comorbidity, and (3) in the Caucasian group, were more likely to have the high activity T allele of the EcoRV variant of the monoamine oxidase A (MAO-A) gene compared to controls, and (4) in the Afrikaner subgroup, were more frequently homozygous for the G allele at the G861C variant of the 5HT1Dbeta gene than controls. Females with OCD (1) reported more sexual abuse during childhood than males, (2) often noted changes in obsessive-compulsive symptoms in the premenstrual/menstrual period as well as during/shortly after pregnancy, and with menopause, and (3) in the Caucasian subgroup, were more frequently homozygous for the low activity C allele of the EcoRV variant of the MAO-A gene compared to controls, with this allele also more frequent in female patients than controls.
CONCLUSION: This study supports the hypothesis that gender contributes to the clinical and biological heterogeneity of OCD. A sexually dimorphic pattern of genetic susceptibility to OCD may be present. Further work is, however, needed to delineate the mechanisms that are responsible for mediating the effects of gender.},
	language = {eng},
	number = {5},
	journal = {European Neuropsychopharmacology: The Journal of the European College of Neuropsychopharmacology},
	author = {Lochner, Christine and Hemmings, Sian M. J. and Kinnear, Craig J. and Moolman-Smook, Johanna C. and Corfield, Valerie A. and Knowles, James A. and Niehaus, Dana J. H. and Stein, Dan J.},
	month = oct,
	year = {2004},
	pmid = {15468463},
	note = {00000 },
	keywords = {Adolescent, Adult, Aged, Case-Control Studies, Chi-Square Distribution, Demography, Female, Gene Frequency, Genotype, Humans, Interviews as Topic, Male, Middle Aged, Monoamine Oxidase, Obsessive-Compulsive Disorder, Polymorphism, Genetic, Psychiatric Status Rating Scales, Questionnaires, Receptor, Serotonin, 5-HT1D, Sex Characteristics},
	pages = {437--445},
}

BACKGROUND: There is increasing recognition that obsessive-compulsive disorder (OCD) is not a homogeneous entity. It has been suggested that gender may contribute to the clinical and biological heterogeneity of OCD. METHODS: Two hundred and twenty patients (n=220; 107 male, 113 female) with DSM-IV OCD (age: 36.40 +/- 13.46) underwent structured interviews. A subset of Caucasian subjects (n=178), including subjects from the genetically homogeneous Afrikaner population (n=81), and of matched control subjects (n=161), was genotyped for polymorphisms in genes involved in monoamine function. Clinical and genetic data were statistically analyzed across gender. RESULTS: Compared with females, males with OCD (1) had an earlier age of onset, and a trend toward having more tics and worse outcome, (2) had somewhat differing patterns of OCD symptomatology and axis I comorbidity, and (3) in the Caucasian group, were more likely to have the high activity T allele of the EcoRV variant of the monoamine oxidase A (MAO-A) gene compared to controls, and (4) in the Afrikaner subgroup, were more frequently homozygous for the G allele at the G861C variant of the 5HT1Dbeta gene than controls. Females with OCD (1) reported more sexual abuse during childhood than males, (2) often noted changes in obsessive-compulsive symptoms in the premenstrual/menstrual period as well as during/shortly after pregnancy, and with menopause, and (3) in the Caucasian subgroup, were more frequently homozygous for the low activity C allele of the EcoRV variant of the MAO-A gene compared to controls, with this allele also more frequent in female patients than controls. CONCLUSION: This study supports the hypothesis that gender contributes to the clinical and biological heterogeneity of OCD. A sexually dimorphic pattern of genetic susceptibility to OCD may be present. Further work is, however, needed to delineate the mechanisms that are responsible for mediating the effects of gender.

@article{hemmings_early-_2004,
	title = {Early- versus late-onset obsessive-compulsive disorder: investigating genetic and clinical correlates},
	volume = {128},
	issn = {0165-1781},
	shorttitle = {Early- versus late-onset obsessive-compulsive disorder},
	doi = {10.1016/j.psychres.2004.05.007},
	abstract = {There is increasing evidence that obsessive-compulsive disorder (OCD) is mediated by genetic factors. Although the precise mechanism of inheritance is unclear, recent evidence has pointed towards the involvement of the serotonergic and dopaminergic systems in the disorder's development. Furthermore, early-onset OCD appears to be a subtype that exhibits distinct clinical features and that is associated with greater familial loading. In the present investigation, South African OCD patients (n=252) were stratified according to age of onset and were clinically assessed. Additionally, selected variants in genes encoding serotonergic and dopaminergic components were investigated in a Caucasian OCD subset (n=180). This subgroup was further stratified to evaluate the role that these candidate genes may play in the genetically homogeneous Afrikaner subset (n=80). Analysis of the clinical data revealed an association between early age of onset and an increased frequency of tics, Tourette's disorder, and trichotillomania (TTM). The genetic studies yielded statistically significant results when the allelic distributions of genetic variants in the dopamine receptor type 4 gene (DRD4) were analysed in the Caucasian OCD cohort. These data support a role for the dopaminergic system, which may be relevant to the development of early-onset OCD.},
	language = {eng},
	number = {2},
	journal = {Psychiatry Research},
	author = {Hemmings, Sîan M. J. and Kinnear, Craig J. and Lochner, Christine and Niehaus, Dana J. H. and Knowles, James A. and Moolman-Smook, Johanna C. and Corfield, Valerie A. and Stein, Dan J.},
	month = sep,
	year = {2004},
	pmid = {15488960},
	note = {00110 },
	keywords = {Adult, Age of Onset, Alleles, Cohort Studies, Comorbidity, Gene Frequency, Genetic Load, Genetic Predisposition to Disease, Genetic Variation, Genetics, Population, Genotype, Humans, Male, Obsessive-Compulsive Disorder, Phenotype, Receptors, Dopamine, Receptors, Dopamine D2, Receptors, Dopamine D4, Receptors, Serotonin, South Africa, Tics, Tourette Syndrome, Trichotillomania},
	pages = {175--182},
}

There is increasing evidence that obsessive-compulsive disorder (OCD) is mediated by genetic factors. Although the precise mechanism of inheritance is unclear, recent evidence has pointed towards the involvement of the serotonergic and dopaminergic systems in the disorder's development. Furthermore, early-onset OCD appears to be a subtype that exhibits distinct clinical features and that is associated with greater familial loading. In the present investigation, South African OCD patients (n=252) were stratified according to age of onset and were clinically assessed. Additionally, selected variants in genes encoding serotonergic and dopaminergic components were investigated in a Caucasian OCD subset (n=180). This subgroup was further stratified to evaluate the role that these candidate genes may play in the genetically homogeneous Afrikaner subset (n=80). Analysis of the clinical data revealed an association between early age of onset and an increased frequency of tics, Tourette's disorder, and trichotillomania (TTM). The genetic studies yielded statistically significant results when the allelic distributions of genetic variants in the dopamine receptor type 4 gene (DRD4) were analysed in the Caucasian OCD cohort. These data support a role for the dopaminergic system, which may be relevant to the development of early-onset OCD.

@article{wiid_total_2004,
	title = {Total antioxidant levels are low during active {TB} and rise with anti-tuberculosis therapy},
	volume = {56},
	issn = {1521-6543},
	doi = {10.1080/15216540410001671259},
	abstract = {In tuberculosis, oxidative stress is a result of tissue inflammation, poor dietary intake of micronutrients due to illness, free radical burst from activated macrophages, and anti-tuberculosis drugs. These free radicals may in turn contribute towards pulmonary inflammation if not neutralized by antioxidants. The total antioxidant status (TAS) of individuals is a function of dietary, enzymatic, and other systemic antioxidants and is therefore an indicator of the free radical load. Our aim was to evaluate the TAS of healthy and M. tuberculosis-infected persons from a high TB incidence community, as well as tuberculosis patients at various stages of antituberculosis drug treatment and to correlate results with plasma micronutrient levels. Blood plasma samples from TB infected patients and following antituberculosis drug treatment were assayed for TAS, vitamins A, E and Zinc. Statistical analysis of results was by one-way ANOVA and the Tukey multiple comparison post test. Active TB patients showed a significantly lower TAS (P {\textless} 0.001) compared to the community controls. We also show that TAS values increase during therapy. Results correlated with micronutrients vitamin A and zinc but vitamin E remained unaffected. We suggest that total antioxidant status of TB patients should be considered for more effective disease control and that diets low in antioxidants may render individuals susceptible to tuberculosis.},
	language = {eng},
	number = {2},
	journal = {IUBMB life},
	author = {Wiid, I. and Seaman, T. and Hoal, E. G. and Benade, A. J. S. and Van Helden, Paul D.},
	month = feb,
	year = {2004},
	pmid = {15085934},
	note = {00034 },
	keywords = {Antioxidants, Antitubercular Agents, Humans, Oxidative Stress, Tuberculosis, Pulmonary},
	pages = {101--106},
}

In tuberculosis, oxidative stress is a result of tissue inflammation, poor dietary intake of micronutrients due to illness, free radical burst from activated macrophages, and anti-tuberculosis drugs. These free radicals may in turn contribute towards pulmonary inflammation if not neutralized by antioxidants. The total antioxidant status (TAS) of individuals is a function of dietary, enzymatic, and other systemic antioxidants and is therefore an indicator of the free radical load. Our aim was to evaluate the TAS of healthy and M. tuberculosis-infected persons from a high TB incidence community, as well as tuberculosis patients at various stages of antituberculosis drug treatment and to correlate results with plasma micronutrient levels. Blood plasma samples from TB infected patients and following antituberculosis drug treatment were assayed for TAS, vitamins A, E and Zinc. Statistical analysis of results was by one-way ANOVA and the Tukey multiple comparison post test. Active TB patients showed a significantly lower TAS (P \textless 0.001) compared to the community controls. We also show that TAS values increase during therapy. Results correlated with micronutrients vitamin A and zinc but vitamin E remained unaffected. We suggest that total antioxidant status of TB patients should be considered for more effective disease control and that diets low in antioxidants may render individuals susceptible to tuberculosis.

@article{hoal_slc11a1_2004,
	title = {{SLC11A1} ({NRAMP1}) but not {SLC11A2} ({NRAMP2}) polymorphisms are associated with susceptibility to tuberculosis in a high-incidence community in {South} {Africa}},
	volume = {8},
	issn = {1027-3719},
	abstract = {SETTING: Stellenbosch University Faculty of Health Sciences, and metropolitan Cape Town, Western Cape, South Africa.
OBJECTIVE: To investigate whether the reported association between SLC11A1 (also NRAMP1) polymorphisms and susceptibility to tuberculosis (TB) can be confirmed in a different population, and whether polymorphisms in SLC11A2 (also NRAMP2, DCT1, DMT1) are associated with TB.
DESIGN: A case-control study design was used to compare the frequencies of five polymorphisms in SLC11A1 and three in SLC11A2 between a group of bacteriologically confirmed TB patients and healthy community controls.
RESULTS: The 5' (GT)9 allele in the promoter of SLC1A1 was found at significantly higher frequencies among 265 controls than in 224 pulmonary TB (PTB) patients (P = 0.002; OR 0.6; 95\% CI 0.43-0.83). Homozygotes for the TGTG deletion (1729+55del4) in the 3'UTR of SLC11A1 were over-represented among PTB patients (P = 0.013; OR 5.19; 95\% CI 1.42-18.94). Stepwise logistic regression analysis indicated that the 5' and 3' polymorphisms contribute separate main effects. Tuberculous meningitis patients (n = 22) showed the same allele and genotype frequency as PTB patients. No SLC11A2 polymorphisms tested were associated with TB.
CONCLUSION: The 5' (GT)n allele driving the highest rate of transcription of SLC11A1 appears to be associated with protection against TB in the majority of the populations studied.},
	language = {eng},
	number = {12},
	journal = {The International Journal of Tuberculosis and Lung Disease: The Official Journal of the International Union Against Tuberculosis and Lung Disease},
	author = {Hoal, E. G. and Lewis, L. A. and Jamieson, S. E. and Tanzer, F. and Rossouw, M. and Victor, T. and Hillerman, R. and Beyers, N. and Blackwell, J. M. and Van Helden, P. D.},
	month = dec,
	year = {2004},
	pmid = {15636493},
	note = {00070 },
	keywords = {Adult, Case-Control Studies, Cation Transport Proteins, Female, Genetic Predisposition to Disease, Humans, Incidence, Iron-Binding Proteins, Male, Polymorphism, Genetic, South Africa, Tuberculosis, Pulmonary},
	pages = {1464--1471},
}

SETTING: Stellenbosch University Faculty of Health Sciences, and metropolitan Cape Town, Western Cape, South Africa. OBJECTIVE: To investigate whether the reported association between SLC11A1 (also NRAMP1) polymorphisms and susceptibility to tuberculosis (TB) can be confirmed in a different population, and whether polymorphisms in SLC11A2 (also NRAMP2, DCT1, DMT1) are associated with TB. DESIGN: A case-control study design was used to compare the frequencies of five polymorphisms in SLC11A1 and three in SLC11A2 between a group of bacteriologically confirmed TB patients and healthy community controls. RESULTS: The 5' (GT)9 allele in the promoter of SLC1A1 was found at significantly higher frequencies among 265 controls than in 224 pulmonary TB (PTB) patients (P = 0.002; OR 0.6; 95% CI 0.43-0.83). Homozygotes for the TGTG deletion (1729+55del4) in the 3'UTR of SLC11A1 were over-represented among PTB patients (P = 0.013; OR 5.19; 95% CI 1.42-18.94). Stepwise logistic regression analysis indicated that the 5' and 3' polymorphisms contribute separate main effects. Tuberculous meningitis patients (n = 22) showed the same allele and genotype frequency as PTB patients. No SLC11A2 polymorphisms tested were associated with TB. CONCLUSION: The 5' (GT)n allele driving the highest rate of transcription of SLC11A1 appears to be associated with protection against TB in the majority of the populations studied.

@article{hemmings_investigating_2003,
	title = {Investigating the role of dopaminergic and serotonergic candidate genes in obsessive-compulsive disorder},
	volume = {13},
	issn = {0924-977X},
	abstract = {There is increasing evidence that the aetiology of obsessive-compulsive disorder (OCD) has a marked genetic component, although the precise mechanism of inheritance is unclear. Clinical and pharmacological studies have implicated the serotonergic and dopaminergic systems in disease pathogenesis. This study investigated the role of attractive candidate genes in the serotonergic and dopaminergic pathways in the development of OCD. The distribution of selected polymorphic variants in the serotonin receptor type 2A and 1Dbeta (5-HT(2A), 5-HT(1Dbeta)), dopamine transporter (DAT), dopamine receptor type 4 (DRD4) and monoamine-oxidase A (MAO-A) genes were analysed in 71 OCD cases and 129 control individuals in the genetically homogeneous Afrikaner population, by means of case-control association studies. Although no statistically significant genotypic or allelic associations were detected, the data yielded interesting preliminary results that warrant further discussion and investigation.},
	language = {eng},
	number = {2},
	journal = {European Neuropsychopharmacology: The Journal of the European College of Neuropsychopharmacology},
	author = {Hemmings, Sîan M. J. and Kinnear, Craig J. and Niehaus, Dana J. H. and Moolman-Smook, Johanna C. and Lochner, Christine and Knowles, James A. and Corfield, Valerie A. and Stein, Dan J.},
	month = mar,
	year = {2003},
	pmid = {12650952},
	note = {00000 },
	keywords = {Case-Control Studies, Chi-Square Distribution, Dopamine, Dopamine Plasma Membrane Transport Proteins, Gene Frequency, Humans, Membrane Glycoproteins, Membrane Transport Proteins, Monoamine Oxidase, Nerve Tissue Proteins, Obsessive-Compulsive Disorder, Polymorphism, Genetic, Receptor, Serotonin, 5-HT1B, Receptor, Serotonin, 5-HT2A, Receptors, Dopamine D2, Receptors, Dopamine D4, Receptors, Serotonin, Serotonin},
	pages = {93--98},
}

There is increasing evidence that the aetiology of obsessive-compulsive disorder (OCD) has a marked genetic component, although the precise mechanism of inheritance is unclear. Clinical and pharmacological studies have implicated the serotonergic and dopaminergic systems in disease pathogenesis. This study investigated the role of attractive candidate genes in the serotonergic and dopaminergic pathways in the development of OCD. The distribution of selected polymorphic variants in the serotonin receptor type 2A and 1Dbeta (5-HT(2A), 5-HT(1Dbeta)), dopamine transporter (DAT), dopamine receptor type 4 (DRD4) and monoamine-oxidase A (MAO-A) genes were analysed in 71 OCD cases and 129 control individuals in the genetically homogeneous Afrikaner population, by means of case-control association studies. Although no statistically significant genotypic or allelic associations were detected, the data yielded interesting preliminary results that warrant further discussion and investigation.

@article{adams_allele_2003,
	title = {Allele frequencies for glutathione {S}-transferase and {N}-acetyltransferase 2 differ in {African} population groups and may be associated with oesophageal cancer or tuberculosis incidence},
	volume = {41},
	issn = {1434-6621},
	doi = {10.1515/CCLM.2003.090},
	abstract = {Glutathione S-transferase (GST) and arylamine N-acetyltransferase 2 (NAT2) metabolise many environmental and chemotherapeutic agents, which influence susceptibility to disease. Polymorphisms in these enzymes result in different host phenotypes and contribute to different disease profiles or responses to toxic or chemotherapeutic agents, depending on their frequency in different populations. GST and NAT2 polymorphisms were investigated in different population groups, including African populations, and a range of allelic frequencies have been observed. The GSTM1 null genotype frequency, reported in this paper in two South African ethnic groups, is the lowest reported (0.19-0.21). In contrast, these same groups have a high GSTT1 null frequency (0.41-0.54), which is considerably higher than in African-Americans, or other Africans. The GSTT1 null frequency is comparable to the Chinese, a population with a very high oesophageal cancer incidence, similar to that in the African group. The frequency of the GSTPi Val105 variant in the South African Xhosas was also high (0.53), differing significantly from the low frequency in other Africans. These variants could therefore be associated with high cancer susceptibility. In addition, the high proportion of NAT2 "fast" alleles may partially explain the high tuberculosis prevalence in South Africans, due to reduced isoniazid efficacy in the presence of rapid acetylation.},
	language = {eng},
	number = {4},
	journal = {Clinical chemistry and laboratory medicine: CCLM / FESCC},
	author = {Adams, Craig H. and Werely, Cedric J. and Victor, Thomas C. and Hoal, Eileen G. and Rossouw, Gawie and van Helden, Paul D.},
	month = apr,
	year = {2003},
	pmid = {12747608},
	note = {00039 },
	keywords = {African Continental Ancestry Group, Arylamine N-Acetyltransferase, Cohort Studies, DNA Primers, Esophageal Neoplasms, Gene Frequency, Genetic Predisposition to Disease, Genotype, Glutathione S-Transferase pi, Glutathione Transferase, Humans, Incidence, Isoenzymes, Polymerase Chain Reaction, Polymorphism, Genetic, Tuberculosis},
	pages = {600--605},
}

Glutathione S-transferase (GST) and arylamine N-acetyltransferase 2 (NAT2) metabolise many environmental and chemotherapeutic agents, which influence susceptibility to disease. Polymorphisms in these enzymes result in different host phenotypes and contribute to different disease profiles or responses to toxic or chemotherapeutic agents, depending on their frequency in different populations. GST and NAT2 polymorphisms were investigated in different population groups, including African populations, and a range of allelic frequencies have been observed. The GSTM1 null genotype frequency, reported in this paper in two South African ethnic groups, is the lowest reported (0.19-0.21). In contrast, these same groups have a high GSTT1 null frequency (0.41-0.54), which is considerably higher than in African-Americans, or other Africans. The GSTT1 null frequency is comparable to the Chinese, a population with a very high oesophageal cancer incidence, similar to that in the African group. The frequency of the GSTPi Val105 variant in the South African Xhosas was also high (0.53), differing significantly from the low frequency in other Africans. These variants could therefore be associated with high cancer susceptibility. In addition, the high proportion of NAT2 "fast" alleles may partially explain the high tuberculosis prevalence in South Africans, due to reduced isoniazid efficacy in the presence of rapid acetylation.

@article{rossouw_association_2003,
	title = {Association between tuberculosis and a polymorphic {NFkappaB} binding site in the interferon gamma gene},
	volume = {361},
	issn = {0140-6736},
	doi = {10.1016/S0140-6736(03)13491-5},
	abstract = {Interferon gamma is believed to be crucial for host defence against many infections. To test the hypothesis that a polymorphism in the gene for interferon gamma (IFNG) is associated with susceptibility to tuberculosis, we did two independent investigations. In a case-control study of 313 tuberculosis cases, we noted a significant association between a polymorphism (+874A--{\textgreater}T) in IFNG and tuberculosis in a South African population (p=0.0055). This finding was replicated in a family-based study, in which the transmission disequilibrium test was used in 131 families (p=0.005). The transcription factor NFkappaB binds preferentially to the +874T allele, which is over-represented in controls. This preferential binding suggests that genetically determined variability in interferon gamma and expression might be important for the development of tuberculosis.},
	language = {eng},
	number = {9372},
	journal = {Lancet (London, England)},
	author = {Rossouw, Manda and Nel, Hendrik J. and Cooke, Graham S. and van Helden, Paul D. and Hoal, Eileen G.},
	month = may,
	year = {2003},
	pmid = {12788577},
	note = {00000 },
	keywords = {Alleles, Case-Control Studies, Genetic Predisposition to Disease, Humans, Interferon-alpha, NF-kappa B, Polymorphism, Single Nucleotide, South Africa, Tuberculosis},
	pages = {1871--1872},
}

Interferon gamma is believed to be crucial for host defence against many infections. To test the hypothesis that a polymorphism in the gene for interferon gamma (IFNG) is associated with susceptibility to tuberculosis, we did two independent investigations. In a case-control study of 313 tuberculosis cases, we noted a significant association between a polymorphism (+874A–\textgreaterT) in IFNG and tuberculosis in a South African population (p=0.0055). This finding was replicated in a family-based study, in which the transmission disequilibrium test was used in 131 families (p=0.005). The transcription factor NFkappaB binds preferentially to the +874T allele, which is over-represented in controls. This preferential binding suggests that genetically determined variability in interferon gamma and expression might be important for the development of tuberculosis.

@article{barnard_spectrum_2003,
	title = {The spectrum of mutations in {TP53} in laryngeal cancer patients from a high-incidence population shows similarities to many of the known mutational hotspots},
	volume = {145},
	issn = {0165-4608},
	abstract = {Laryngeal cancer (LC) is the sixth most common cancer in the world and the second most common respiratory cancer, with approximately 500000 new cases worldwide, annually. The mechanisms of tumorigenesis in LC remain unknown, although smoking and alcohol consumption are considered to be major risk factors. Mutations within TP53 have been strongly implicated as frequent events in several cancers. We screened exons 5-8 of TP53 for mutations in DNA from tumor biopsies (n = 44) and blood samples (n = 42) from the same LC patients, and blood samples from a healthy, matched control group (n = 40), using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) analysis and direct sequencing. Significant positive correlations were found between the occurrence of LC and age and smoking, whereas daily meat consumption was a possible protective factor. In tumor-derived samples, mutations were found in three of the exons under investigation, representing 25\% of the samples. The mutations were unique to the tumor biopsies, indicating a somatic origin for mutations. The data confirm that the region between codons 175 and 273 of TP53 is a mutational hotspot region for cancers in general; six novel mutations were found within this same region.},
	language = {eng},
	number = {2},
	journal = {Cancer Genetics and Cytogenetics},
	author = {Barnard, Desiré and Lehmann, Karen and Hoal, Eileen G. and van Helden, Paul D. and Victor, Thomas C.},
	month = sep,
	year = {2003},
	pmid = {12935924},
	note = {00006 },
	keywords = {Adult, Aged, Female, Humans, Laryngeal Neoplasms, Male, Middle Aged, Mutation, Polymorphism, Single-Stranded Conformational, Risk Factors, Sequence Analysis, DNA, Tumor Suppressor Protein p53},
	pages = {126--132},
}

Laryngeal cancer (LC) is the sixth most common cancer in the world and the second most common respiratory cancer, with approximately 500000 new cases worldwide, annually. The mechanisms of tumorigenesis in LC remain unknown, although smoking and alcohol consumption are considered to be major risk factors. Mutations within TP53 have been strongly implicated as frequent events in several cancers. We screened exons 5-8 of TP53 for mutations in DNA from tumor biopsies (n = 44) and blood samples (n = 42) from the same LC patients, and blood samples from a healthy, matched control group (n = 40), using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) analysis and direct sequencing. Significant positive correlations were found between the occurrence of LC and age and smoking, whereas daily meat consumption was a possible protective factor. In tumor-derived samples, mutations were found in three of the exons under investigation, representing 25% of the samples. The mutations were unique to the tumor biopsies, indicating a somatic origin for mutations. The data confirm that the region between codons 175 and 273 of TP53 is a mutational hotspot region for cancers in general; six novel mutations were found within this same region.

@article{wiid_o6-alkylguanine-dna_2002,
	title = {O(6)-alkylguanine-{DNA} alkyltransferase {DNA} repair in mycobacteria: pathogenic and non-pathogenic species differ},
	volume = {82},
	issn = {1472-9792},
	shorttitle = {O(6)-alkylguanine-{DNA} alkyltransferase {DNA} repair in mycobacteria},
	abstract = {SETTING: DNA repair genes assist the organism in maintaining DNA integrity in the face of environmental (mutagenic) stress. The genome sequences of M. tuberculosis and M. bovis demonstrate sequences suggestive of an O(6)-alkylguanine-DNA alkyltransferase DNA repair activity similar to that seen in almost all other bacterial and eukaryotic organisms. The near ubiquitousness of this gene implies an important function.
OBJECTIVE: Our aim was to ascertain whether mycobacteria exert an alkyltransferase response to mutagen (streptozotocin) stimulation and whether alkyltransferase activity is essential for mycobacterial survival.
DESIGN: Alkyltransferase activity in slow- and fast-growing mycobacterial species was determined in the presence and absence of sublethal concentrations of an alkylating agent streptozotocin. The intracellular survival and response to anti-tuberculosis drugs of an alkyltransferase knockout strain of M. bovis BCG was also determined.
RESULTS: We demonstrate the presence of O(6)-alkylguanine alkyltransferase (cellular methyltransferase activity) in mycobacterial species and that there is an inducible and constitutive form in fast-growing mycobacteria (M. smegmatis), whereas only the constitutive form exists in the pathogenic or slow-growing species (M. bovis BCG) under the conditions tested. The overall activity of the constitutive form is high. We also show that intracellular growth of M. bovis BCG in macrophages is reduced when the alkyltransferase gene is absent. The presence of alkyltransferase activity appears to assist the organism in reducing the effects of isoniazid, since interruption of the gene confers sensitivity to the drug.
CONCLUSIONS: We conclude that for the slow-growing mycobacteria, an inducible response is not essential as their ecological niche is stable and protected, but that the presence of the alkyltransferase activity confers a growth advantage in macrophages and offers some protection against antibiotics.},
	language = {eng},
	number = {2-3},
	journal = {Tuberculosis (Edinburgh, Scotland)},
	author = {Wiid, I. and Grundlingh, R. and Bourn, W. and Bradley, G. and Harington, A. and Hoal-van Helden, E. G. and van Helden, P.},
	year = {2002},
	pmid = {12356454},
	keywords = {Base Sequence, Blotting, Southern, DNA Repair, Enzyme Activation, Humans, Macrophages, Methyltransferases, Mycobacterium bovis, Mycobacterium smegmatis, Mycobacterium tuberculosis, O(6)-Methylguanine-DNA Methyltransferase, Species Specificity},
	pages = {45--53},
}

SETTING: DNA repair genes assist the organism in maintaining DNA integrity in the face of environmental (mutagenic) stress. The genome sequences of M. tuberculosis and M. bovis demonstrate sequences suggestive of an O(6)-alkylguanine-DNA alkyltransferase DNA repair activity similar to that seen in almost all other bacterial and eukaryotic organisms. The near ubiquitousness of this gene implies an important function. OBJECTIVE: Our aim was to ascertain whether mycobacteria exert an alkyltransferase response to mutagen (streptozotocin) stimulation and whether alkyltransferase activity is essential for mycobacterial survival. DESIGN: Alkyltransferase activity in slow- and fast-growing mycobacterial species was determined in the presence and absence of sublethal concentrations of an alkylating agent streptozotocin. The intracellular survival and response to anti-tuberculosis drugs of an alkyltransferase knockout strain of M. bovis BCG was also determined. RESULTS: We demonstrate the presence of O(6)-alkylguanine alkyltransferase (cellular methyltransferase activity) in mycobacterial species and that there is an inducible and constitutive form in fast-growing mycobacteria (M. smegmatis), whereas only the constitutive form exists in the pathogenic or slow-growing species (M. bovis BCG) under the conditions tested. The overall activity of the constitutive form is high. We also show that intracellular growth of M. bovis BCG in macrophages is reduced when the alkyltransferase gene is absent. The presence of alkyltransferase activity appears to assist the organism in reducing the effects of isoniazid, since interruption of the gene confers sensitivity to the drug. CONCLUSIONS: We conclude that for the slow-growing mycobacteria, an inducible response is not essential as their ecological niche is stable and protected, but that the presence of the alkyltransferase activity confers a growth advantage in macrophages and offers some protection against antibiotics.

@article{hoal_human_2002,
	title = {Human genetic susceptibility to tuberculosis and other mycobacterial diseases},
	volume = {53},
	issn = {1521-6543},
	doi = {10.1080/15216540212644},
	abstract = {The existence of a genetic component in mycobacterial disease susceptibility is no longer in doubt and the investigations now being conducted aim to determine which genes are involved, to what extent, and in which disease phenotype they are relevant. In certain rare instances of susceptibility to poorly pathogenic mycobacteria, the genetic component is clear. The approaches employed to elucidate common disease susceptibility include linkage studies, particularly genome-wide linkage analysis of both tuberculosis and leprosy, and association studies. A number of candidate genes have shown association with tuberculosis, and in many cases, on replication of the study, association has been confirmed in a disparate population, indicating the wider importance of the gene in the disease process. In other instances, associations appear to be particular to a population or a subtype of disease.},
	language = {eng},
	number = {4-5},
	journal = {IUBMB life},
	author = {Hoal, Eileen G.},
	month = may,
	year = {2002},
	pmid = {12121000},
	note = {00000 },
	keywords = {Genetic Linkage, Genetic Predisposition to Disease, Genotype, Humans, Mycobacterium tuberculosis, Phenotype, Tuberculosis},
	pages = {225--229},
}

The existence of a genetic component in mycobacterial disease susceptibility is no longer in doubt and the investigations now being conducted aim to determine which genes are involved, to what extent, and in which disease phenotype they are relevant. In certain rare instances of susceptibility to poorly pathogenic mycobacteria, the genetic component is clear. The approaches employed to elucidate common disease susceptibility include linkage studies, particularly genome-wide linkage analysis of both tuberculosis and leprosy, and association studies. A number of candidate genes have shown association with tuberculosis, and in many cases, on replication of the study, association has been confirmed in a disparate population, indicating the wider importance of the gene in the disease process. In other instances, associations appear to be particular to a population or a subtype of disease.

@article{rossouw_accurate_2002,
	title = {Accurate microsatellite typing and inter-study comparison: pitfalls and solutions using interferon-gamma ({IFNG}) and natural resistance-associated macrophage protein 2 ({NRAMP2}) genes as examples},
	volume = {40},
	issn = {1434-6621},
	shorttitle = {Accurate microsatellite typing and inter-study comparison},
	doi = {10.1515/CCLM.2002.162},
	abstract = {Microsatellite typing is frequently used in disease diagnosis and in genetic association studies. Inter-study consistency and comparability is essential in both applications. In this study, we show that the interlaboratory comparison of microsatellite sizes is often discrepant and misleading. This is a matter of great concern in the recent literature. However, accurate allele designation is easily attainable by the simple procedures we report, which are applicable to all gel-based genotyping methods. These involve: 1) the creation of dedicated standards for a specific microsatellite by PCR-amplifying representative alleles to generate an allelic ladder with comparable electrophoretic characteristics; 2) including both internal and external standards during electrophoresis to facilitate alignment. In addition, we recommend procedures that will improve inter-study comparability of all microsatellite analyses regardless of genotyping method. These involve: 1) cloning and sequencing representative microsatellite alleles to obtain accurate size designation; 2) sharing alleles of known sequence between laboratories to use as standards. We report on the typing of natural resistance-associated macrophage protein (NRAMP2) and interferon-y (IFNG) gene microsatellites as examples, the latter of which is crucial to many pathogenic processes. We describe in detail the varying allele sizes obtained by different methods, which prevent meaningful inter-study comparisons.},
	language = {eng},
	number = {9},
	journal = {Clinical chemistry and laboratory medicine: CCLM / FESCC},
	author = {Rossouw, Manda and Warren, Robin and Hoal, Eileen G.},
	month = sep,
	year = {2002},
	pmid = {12435110},
	note = {00000 },
	keywords = {Alleles, Cation Transport Proteins, Clinical Laboratory Techniques, Cloning, Molecular, Databases, Nucleic Acid, Electrophoresis, Polyacrylamide Gel, Genotype, Humans, Interferon-gamma, Iron-Binding Proteins, Microsatellite Repeats, Polymerase Chain Reaction, Reproducibility of Results, Sequence Analysis, DNA},
	pages = {926--929},
}

Microsatellite typing is frequently used in disease diagnosis and in genetic association studies. Inter-study consistency and comparability is essential in both applications. In this study, we show that the interlaboratory comparison of microsatellite sizes is often discrepant and misleading. This is a matter of great concern in the recent literature. However, accurate allele designation is easily attainable by the simple procedures we report, which are applicable to all gel-based genotyping methods. These involve: 1) the creation of dedicated standards for a specific microsatellite by PCR-amplifying representative alleles to generate an allelic ladder with comparable electrophoretic characteristics; 2) including both internal and external standards during electrophoresis to facilitate alignment. In addition, we recommend procedures that will improve inter-study comparability of all microsatellite analyses regardless of genotyping method. These involve: 1) cloning and sequencing representative microsatellite alleles to obtain accurate size designation; 2) sharing alleles of known sequence between laboratories to use as standards. We report on the typing of natural resistance-associated macrophage protein (NRAMP2) and interferon-y (IFNG) gene microsatellites as examples, the latter of which is crucial to many pathogenic processes. We describe in detail the varying allele sizes obtained by different methods, which prevent meaningful inter-study comparisons.

@article{niehaus_association_2001,
	title = {Association between a catechol-o-methyltransferase polymorphism and obsessive-compulsive disorder in the {Afrikaner} population},
	volume = {65},
	issn = {0165-0327},
	abstract = {BACKGROUND: It has been proposed that the catechol-o-methyl transferase gene (COMT) may play a role in the pathogenesis of obsessive-compulsive disorder (OCD). Whereas studies in a North American population showed that the low activity (L) allele of a functional polymorphism in COMT was associated with OCD in male patients, this result was not supported by studies in a Japanese population. The present association study assessed the risk for OCD conferred by this COMT polymorphism in a geographically different patient group, namely, the relatively genetically homogeneous Afrikaner population of South Africa.
METHODS: Fifty-four unrelated OCD patients and fifty-four sex-matched controls were recruited from the same Afrikaner community. Patients and controls were phenotyped (DSM-IV) and genotyped for a NlaIII polymorphism with H (high activity) or L (low activity) alleles in the COMT gene.
RESULTS: The H/L genotype was significantly more common than expected in the OCD patient group (P = 0.0017).
LIMITATIONS: Replication studies with related individuals may be useful in discovering factors underpinning the H/L genotype abundance in the Afrikaner population.
CONCLUSIONS: These results emphasise the need for further studies in genetically homogeneous populations to help define the complex etiology of this disease.},
	language = {eng},
	number = {1},
	journal = {Journal of Affective Disorders},
	author = {Niehaus, D. J. and Kinnear, C. J. and Corfield, V. A. and du Toit, P. L. and van Kradenburg, J. and Moolman-Smook, J. C. and Weyers, J. B. and Potgieter, A. and Seedat, S. and Emsley, R. A. and Knowles, J. A. and Brink, P. A. and Stein, D. J.},
	month = jun,
	year = {2001},
	pmid = {11426511},
	note = {00063 },
	keywords = {Adult, Alleles, Catechol O-Methyltransferase, Cross-Cultural Comparison, Female, Genetics, Population, Genotype, Humans, Male, Obsessive-Compulsive Disorder, Polymorphism, Genetic, South Africa},
	pages = {61--65},
}

BACKGROUND: It has been proposed that the catechol-o-methyl transferase gene (COMT) may play a role in the pathogenesis of obsessive-compulsive disorder (OCD). Whereas studies in a North American population showed that the low activity (L) allele of a functional polymorphism in COMT was associated with OCD in male patients, this result was not supported by studies in a Japanese population. The present association study assessed the risk for OCD conferred by this COMT polymorphism in a geographically different patient group, namely, the relatively genetically homogeneous Afrikaner population of South Africa. METHODS: Fifty-four unrelated OCD patients and fifty-four sex-matched controls were recruited from the same Afrikaner community. Patients and controls were phenotyped (DSM-IV) and genotyped for a NlaIII polymorphism with H (high activity) or L (low activity) alleles in the COMT gene. RESULTS: The H/L genotype was significantly more common than expected in the OCD patient group (P = 0.0017). LIMITATIONS: Replication studies with related individuals may be useful in discovering factors underpinning the H/L genotype abundance in the Afrikaner population. CONCLUSIONS: These results emphasise the need for further studies in genetically homogeneous populations to help define the complex etiology of this disease.

@article{van_helden_factors_2001,
	title = {Factors influencing peak expiratory flow in teenage boys},
	volume = {91},
	issn = {0256-9574},
	abstract = {BACKGROUND: Peak expiratory flow (PEF) is a useful measure of pulmonary health status and is frequently utilised in asthma management. Reduction in PEF is usually indicative of onset of asthma symptoms. However, use can be made of PEF values only if normal values are known. The definition of normal range is always difficult and may vary between regions and be affected by a variety of factors.
OBJECTIVE: To establish PEF values for teenage boys in a Cape Town suburb and examine factors that possibly influence this measurement.
SETTING: A high school for boys in the southern suburbs of Cape Town.
METHODS: Measurements of PEF were taken for 124 boys. Subjects were approximately 16 years old and apparently healthy at the time of survey. Further details were provided by means of a questionnaire.
RESULTS: PEF ranged from 350 to 760 l/min, with a mean (+/- standard deviation (SD)) of 539 +/- 68 l/min. Factors expected to influence PEF included height and mass, whereas unexpected factors included sport intensity and academic grade. A trend to reduced peak flow was already evident in boys who smoked and boys from homes where a parent smoked. Regression analysis suggested peak flow differences in our population compared with the standard reference.
CONCLUSION: Interpretation of results obtained from peak-flow instruments should take into account additional knowledge concerning the individual. Further surveys of the South African population and of different groups should be done to establish local standards and factors influencing PEF.},
	language = {eng},
	number = {11},
	journal = {South African Medical Journal = Suid-Afrikaanse Tydskrif Vir Geneeskunde},
	author = {van Helden, S. N. and Hoal van Helden, E. G. and van Helden, P. D.},
	month = nov,
	year = {2001},
	pmid = {11847925},
	keywords = {Adolescent, Asthma, Body Composition, Environment, Exercise, Health Status Indicators, Humans, Life Style, Male, Peak Expiratory Flow Rate, Reference Values, Regression Analysis, Risk Factors, Smoking, South Africa},
	pages = {996--1000},
}

BACKGROUND: Peak expiratory flow (PEF) is a useful measure of pulmonary health status and is frequently utilised in asthma management. Reduction in PEF is usually indicative of onset of asthma symptoms. However, use can be made of PEF values only if normal values are known. The definition of normal range is always difficult and may vary between regions and be affected by a variety of factors. OBJECTIVE: To establish PEF values for teenage boys in a Cape Town suburb and examine factors that possibly influence this measurement. SETTING: A high school for boys in the southern suburbs of Cape Town. METHODS: Measurements of PEF were taken for 124 boys. Subjects were approximately 16 years old and apparently healthy at the time of survey. Further details were provided by means of a questionnaire. RESULTS: PEF ranged from 350 to 760 l/min, with a mean (+/- standard deviation (SD)) of 539 +/- 68 l/min. Factors expected to influence PEF included height and mass, whereas unexpected factors included sport intensity and academic grade. A trend to reduced peak flow was already evident in boys who smoked and boys from homes where a parent smoked. Regression analysis suggested peak flow differences in our population compared with the standard reference. CONCLUSION: Interpretation of results obtained from peak-flow instruments should take into account additional knowledge concerning the individual. Further surveys of the South African population and of different groups should be done to establish local standards and factors influencing PEF.

@article{hoal_van_helden_mycobacterial_2001,
	title = {Mycobacterial growth in human macrophages: variation according to donor, inoculum and bacterial strain},
	volume = {25},
	issn = {1065-6995},
	shorttitle = {Mycobacterial growth in human macrophages},
	doi = {10.1006/cbir.2000.0679},
	abstract = {The microbicidal capacity of the macrophage is frequently evaded by mycobacteria, leading to tuberculosis (TB). We investigated a number of parameters affecting the rate of growth of mycobacteria in human monocyte-derived macrophages (MDM). The results show a great deal of variation in the growth of both Mycobacterium bovis BCG and M. tuberculosis H37Rv, using a large number of human macrophage donors, (132 and 40, respectively), but no correlation was seen with the TB status of the MDM donor. Clumping of the mycobacteria resulted in more vigorous growth in MDM, suggesting that inoculum size could affect disease progression. The growth rates of 17 clinical isolates of M. tuberculosis were measured in macrophages derived from three donors and no consistent or marked differences between isolates were observed over the 5-day period of growth measurement. However, all 17 clinical strains grew consistently faster than H37Rv in the same experiments.},
	language = {eng},
	number = {1},
	journal = {Cell Biology International},
	author = {Hoal van Helden, E. G. and Hon, D. and Lewis, L. A. and Beyers, N. and van Helden, P. D.},
	year = {2001},
	pmid = {11237410},
	keywords = {Adolescent, Adult, Aged, Cell Division, Disease Progression, Humans, Macrophages, Middle Aged, Mycobacterium bovis, Mycobacterium tuberculosis, Species Specificity, Time Factors, Tuberculosis},
	pages = {71--81},
}

The microbicidal capacity of the macrophage is frequently evaded by mycobacteria, leading to tuberculosis (TB). We investigated a number of parameters affecting the rate of growth of mycobacteria in human monocyte-derived macrophages (MDM). The results show a great deal of variation in the growth of both Mycobacterium bovis BCG and M. tuberculosis H37Rv, using a large number of human macrophage donors, (132 and 40, respectively), but no correlation was seen with the TB status of the MDM donor. Clumping of the mycobacteria resulted in more vigorous growth in MDM, suggesting that inoculum size could affect disease progression. The growth rates of 17 clinical isolates of M. tuberculosis were measured in macrophages derived from three donors and no consistent or marked differences between isolates were observed over the 5-day period of growth measurement. However, all 17 clinical strains grew consistently faster than H37Rv in the same experiments.

@article{hoal_van_helden_diversity_2001,
	title = {Diversity of in vitro cytokine responses by human macrophages to infection by mycobacterium tuberculosis strains},
	volume = {25},
	issn = {1065-6995},
	doi = {10.1006/cbir.2000.0680},
	abstract = {Macrophages are an important component in the first line of defence of the innate immune system. They are capable of producing cytokines in response to bacterial challenge, as well as in response to cytokine stimuli from other cells in the immune system. The microbicidal response of human monocyte-derived macrophages in vitro, induced by exogenously added cytokines, is highly variable. We found that tumour necrosis factor-alpha (TNF-alpha) and granulocyte-macrophage colony-stimulating factor (GM-CSF) could have either stimulatory or inhibitory effects on intracellular BCG killing, depending on the macrophage donor. Macrophages infected in vitro by various clinical isolates of Mycobacterium tuberculosis or the laboratory strain H37Rv, produced varying levels of both TNF-alpha and IFN-gamma. Certain M. tuberculosis strains tended to be associated with high cytokine production in each of three independent experiments, indicating that strains may differ in the host response elicited to infection.},
	language = {eng},
	number = {1},
	journal = {Cell Biology International},
	author = {Hoal van Helden, E. G. and Stanton, L. A. and Warren, R. and Richardson, M. and van Helden, P. D.},
	year = {2001},
	pmid = {11237411},
	keywords = {Adolescent, Adult, Aged, Cytokines, Granulocyte-Macrophage Colony-Stimulating Factor, Humans, Infection, Macrophages, Male, Middle Aged, Mycobacterium tuberculosis, Species Specificity, Tumor Necrosis Factor-alpha},
	pages = {83--90},
}

Macrophages are an important component in the first line of defence of the innate immune system. They are capable of producing cytokines in response to bacterial challenge, as well as in response to cytokine stimuli from other cells in the immune system. The microbicidal response of human monocyte-derived macrophages in vitro, induced by exogenously added cytokines, is highly variable. We found that tumour necrosis factor-alpha (TNF-alpha) and granulocyte-macrophage colony-stimulating factor (GM-CSF) could have either stimulatory or inhibitory effects on intracellular BCG killing, depending on the macrophage donor. Macrophages infected in vitro by various clinical isolates of Mycobacterium tuberculosis or the laboratory strain H37Rv, produced varying levels of both TNF-alpha and IFN-gamma. Certain M. tuberculosis strains tended to be associated with high cytokine production in each of three independent experiments, indicating that strains may differ in the host response elicited to infection.

@article{kinnear_obsessive-compulsive_2000,
	title = {Obsessive-compulsive disorder and the promoter region polymorphism (5-{HTTLPR}) in the serotonin transporter gene ({SLC6A4}): a negative association study in the {Afrikaner} population},
	volume = {3},
	issn = {1469-5111},
	shorttitle = {Obsessive-compulsive disorder and the promoter region polymorphism (5-{HTTLPR}) in the serotonin transporter gene ({SLC6A4})},
	doi = {10.1017/S1461145700002054},
	abstract = {A polymorphism (5-HTTLPR) in the promoter region of the serotonin transporter gene (SLC6A4) has been reported to have functional significance and to be associated with obsessive-compulsive disorder (OCD). However, other studies have generated confounding results. A study was undertaken to re-evaluate this association in subjects drawn from the relatively genetically homogeneous Afrikaner population of South Africa. Fifty-four OCD patients of Afrikaner descent and 82 ethnically matched control individuals were phenotyped and genotyped. No significant association was found between the distribution of the 5-HTTLPR genotypes at the SLC6A4 locus and OCD. A similar result (p = 0.108) was generated when a meta-analysis of the 5-HTTLPR polymorphism, combining the current study with a previously reported Caucasian group, was performed; the meta-study comprised 129 OCD patients and 479 control individuals. However, both studies lacked power. Therefore, evidence that variation in SLC6A4 plays a significant role in the development of OCD in the population groups studied is inconclusive. Future association studies in Caucasian populations may extend the power of such meta-analyses and assist in delineating the role of SLC6A4 in OCD.},
	language = {ENG},
	number = {4},
	journal = {The international journal of neuropsychopharmacology / official scientific journal of the Collegium Internationale Neuropsychopharmacologicum (CINP)},
	author = {Kinnear, Craig J. and Niehaus, Dana J. H. and Moolman-Smook, Johanna C. and du Toit, Pieter L. and van Kradenberg, Jeanine and Weyers, Jakobus B. and Potgieter, Annemarie and Marais, Vanessa and Emsley, Robin A. and Knowles, James A. and Corfield, Valerie A. and Brink, Paul A. and Stein, Dan J.},
	month = dec,
	year = {2000},
	pmid = {11343612},
	note = {00053 },
	pages = {327--331},
}

A polymorphism (5-HTTLPR) in the promoter region of the serotonin transporter gene (SLC6A4) has been reported to have functional significance and to be associated with obsessive-compulsive disorder (OCD). However, other studies have generated confounding results. A study was undertaken to re-evaluate this association in subjects drawn from the relatively genetically homogeneous Afrikaner population of South Africa. Fifty-four OCD patients of Afrikaner descent and 82 ethnically matched control individuals were phenotyped and genotyped. No significant association was found between the distribution of the 5-HTTLPR genotypes at the SLC6A4 locus and OCD. A similar result (p = 0.108) was generated when a meta-analysis of the 5-HTTLPR polymorphism, combining the current study with a previously reported Caucasian group, was performed; the meta-study comprised 129 OCD patients and 479 control individuals. However, both studies lacked power. Therefore, evidence that variation in SLC6A4 plays a significant role in the development of OCD in the population groups studied is inconclusive. Future association studies in Caucasian populations may extend the power of such meta-analyses and assist in delineating the role of SLC6A4 in OCD.

@article{van_helden_molecular_2000,
	title = {Molecular answers to tuberculous questions},
	volume = {356 Suppl},
	issn = {0140-6736},
	language = {eng},
	journal = {Lancet (London, England)},
	author = {van Helden, P. D. and Hoal van Helden, E. G.},
	month = dec,
	year = {2000},
	pmid = {11191521},
	keywords = {Developing Countries, Humans, Molecular Epidemiology, Tuberculosis},
	pages = {s61},
}

@article{hoal_van_helden_mannose-binding_1999,
	title = {Mannose-binding protein {B} allele confers protection against tuberculous meningitis},
	volume = {45},
	issn = {0031-3998},
	doi = {10.1203/00006450-199904010-00002},
	abstract = {Inhalation is the principal mode of entry for Mycobacterium tuberculosis in humans. Primary infection is usually restricted to the lungs and contiguous lymph nodes. In a subset of infected individuals, predominantly children, the infection is spread hematogenously to the meninges. The host factors that influence the development of tuberculous meningitis have not been well elucidated. The mannose-binding protein (MBP), a serum protein, is considered as an "ante-antibody." MBP has been shown to bind mycobacteria and acts as an opsonin in vitro. Although MBP plays a role in first-line host defense, it may under certain circumstances be deleterious to the host. In tuberculosis (TB), MBP may assist the spread of this intracellular pathogen. Therefore, we hypothesized that MBP genotypes that result in a phenotype of low MBP levels might be protective. We studied a well-defined South African population in which TB has reached epidemic levels. We found that the MBP B allele (G54D), which disrupts the collagen region of the protein and results in low MBP levels, was found in 22 of 79 (28\%) of the TB-negative controls from the same community, compared with 12 of 91 (13\%) of the patients with pulmonary TB (p {\textless} 0.017), and 5 of 64 (8\%) of patients with tuberculous meningitis (p {\textless} 0.002). In addition, we found significantly lower serum MBP concentrations in TB-negative controls compared with postacute phase, fully recovered TB patients (p {\textless} 0.004). These findings suggest that the MBP B allele affords protection against tuberculous meningitis.},
	language = {eng},
	number = {4 Pt 1},
	journal = {Pediatric Research},
	author = {Hoal van Helden, E. G. and Epstein, J. and Victor, T. C. and Hon, D. and Lewis, L. A. and Beyers, N. and Zurakowski, D. and Ezekowitz, A. B. and Van Helden, P. D.},
	month = apr,
	year = {1999},
	pmid = {10203135},
	keywords = {Adult, African Continental Ancestry Group, Alleles, Carrier Proteins, Child, Ethnic Groups, Female, Humans, Immunity, Innate, Incidence, Male, Mannose-Binding Lectins, Mycobacterium tuberculosis, South Africa, Tuberculosis, Meningeal},
	pages = {459--464},
}

Inhalation is the principal mode of entry for Mycobacterium tuberculosis in humans. Primary infection is usually restricted to the lungs and contiguous lymph nodes. In a subset of infected individuals, predominantly children, the infection is spread hematogenously to the meninges. The host factors that influence the development of tuberculous meningitis have not been well elucidated. The mannose-binding protein (MBP), a serum protein, is considered as an "ante-antibody." MBP has been shown to bind mycobacteria and acts as an opsonin in vitro. Although MBP plays a role in first-line host defense, it may under certain circumstances be deleterious to the host. In tuberculosis (TB), MBP may assist the spread of this intracellular pathogen. Therefore, we hypothesized that MBP genotypes that result in a phenotype of low MBP levels might be protective. We studied a well-defined South African population in which TB has reached epidemic levels. We found that the MBP B allele (G54D), which disrupts the collagen region of the protein and results in low MBP levels, was found in 22 of 79 (28%) of the TB-negative controls from the same community, compared with 12 of 91 (13%) of the patients with pulmonary TB (p \textless 0.017), and 5 of 64 (8%) of patients with tuberculous meningitis (p \textless 0.002). In addition, we found significantly lower serum MBP concentrations in TB-negative controls compared with postacute phase, fully recovered TB patients (p \textless 0.004). These findings suggest that the MBP B allele affords protection against tuberculous meningitis.

@article{van_wyk_growth_1995,
	title = {Growth of oral and skin fibroblasts from patients with oral submucous fibrosis},
	volume = {24},
	issn = {0904-2512},
	abstract = {The purpose of the investigation was to evaluate and compare the proliferation (growth) of mouth fibroblasts and skin fibroblasts from patients with oral submucous fibrosis (OSF). Material comprised fibroblasts from fibrous bands situated in the buccal mucosa and from the inner aspect of the forearm of 8 patients with classic features of OSF as well as fibroblasts from 6 buccal mucosa and 8 skin biopsy specimens from healthy non-areca nut chewing individuals. Cells were cultured for 8 days according to standard techniques. Their growth was monitored daily, under optimal conditions as well as exposure to concentrations of arecoline. The data were analyzed using regression analysis, analysis of variance and the Kruskal-Wallis test. We found no statistically significant differences between the proliferation patterns of oral and skin fibroblasts from patients or between those from patients and controls. The reaction of the cells exposed to concentrations of arecoline was similar; at low concentrations (0.1-10 micrograms/ml) normal growth was maintained, while 100 micrograms/ml inhibited growth. It is concluded that fibroblasts from mouths affected by OSF have proliferation patterns which fall within normal parameters, that the excessive collagen formation in established OSF is not due to increased fibroblast proliferation and that arecoline does not stimulate fibroblast proliferation.},
	language = {eng},
	number = {8},
	journal = {Journal of Oral Pathology \& Medicine: Official Publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
	author = {van Wyk, C. W. and Olivier, A. and Hoal-van Helden, E. G. and Grobler-Rabie, A. F.},
	month = sep,
	year = {1995},
	pmid = {7500290},
	keywords = {Adolescent, Adult, Analysis of Variance, Areca, Arecoline, Cell Division, Cells, Cultured, Collagen, Female, Fibroblasts, Forearm, Humans, Male, Middle Aged, Mouth Mucosa, Muscarinic Agonists, Nicotinic Agonists, Oral Submucous Fibrosis, Plants, Medicinal, Regression Analysis, Skin},
	pages = {349--353},
}

The purpose of the investigation was to evaluate and compare the proliferation (growth) of mouth fibroblasts and skin fibroblasts from patients with oral submucous fibrosis (OSF). Material comprised fibroblasts from fibrous bands situated in the buccal mucosa and from the inner aspect of the forearm of 8 patients with classic features of OSF as well as fibroblasts from 6 buccal mucosa and 8 skin biopsy specimens from healthy non-areca nut chewing individuals. Cells were cultured for 8 days according to standard techniques. Their growth was monitored daily, under optimal conditions as well as exposure to concentrations of arecoline. The data were analyzed using regression analysis, analysis of variance and the Kruskal-Wallis test. We found no statistically significant differences between the proliferation patterns of oral and skin fibroblasts from patients or between those from patients and controls. The reaction of the cells exposed to concentrations of arecoline was similar; at low concentrations (0.1-10 micrograms/ml) normal growth was maintained, while 100 micrograms/ml inhibited growth. It is concluded that fibroblasts from mouths affected by OSF have proliferation patterns which fall within normal parameters, that the excessive collagen formation in established OSF is not due to increased fibroblast proliferation and that arecoline does not stimulate fibroblast proliferation.

@article{van_helden_detection_1994,
	title = {Detection by {DNA} fingerprinting of somatic changes during the establishment of a new prostate cell line},
	volume = {70},
	issn = {0007-0920},
	abstract = {The establishment of a new prostate cell line (BM1604) from a human prostatic adenocarcinoma is reported. The line was rapidly established by culture of tissue on an extracellular matrix, previously laid down by culture of non-related cells. The method has been shown to work well, and other prostate lines have recently been cultured in this way. The cells have a doubling time of 28 h. DNA fingerprinting comparison of the genome from the tumour, the germline and the cells shows that somatic mutations have occurred in the tumour and that clonal selection has clearly occurred in establishment of the line. Many somatic mutations are apparent in the selected cells, which are now stable in culture. This method and the cells may be a useful addition to the limited material available for the in vitro study of prostate cells.},
	language = {eng},
	number = {2},
	journal = {British Journal of Cancer},
	author = {van Helden, P. D. and Wiid, I. J. and Hoal-van Helden, E. G. and Bey, E. and Cohen, R.},
	month = aug,
	year = {1994},
	pmid = {8054265},
	pmcid = {PMC2033493},
	keywords = {Adenocarcinoma, Aged, DNA, DNA Fingerprinting, DNA, Neoplasm, Humans, Immunohistochemistry, Leukocytes, Male, Prostatic Neoplasms, Tumor Cells, Cultured},
	pages = {195--198},
}

The establishment of a new prostate cell line (BM1604) from a human prostatic adenocarcinoma is reported. The line was rapidly established by culture of tissue on an extracellular matrix, previously laid down by culture of non-related cells. The method has been shown to work well, and other prostate lines have recently been cultured in this way. The cells have a doubling time of 28 h. DNA fingerprinting comparison of the genome from the tumour, the germline and the cells shows that somatic mutations have occurred in the tumour and that clonal selection has clearly occurred in establishment of the line. Many somatic mutations are apparent in the selected cells, which are now stable in culture. This method and the cells may be a useful addition to the limited material available for the in vitro study of prostate cells.

@article{wilson_assay_1994,
	title = {An assay for {O6}-alkylguanine-{DNA} alkyltransferase based on restriction endonuclease inhibition and magnetic bead separation of products},
	volume = {15},
	issn = {0143-3334},
	abstract = {We describe an improved, rapid and cost effective assay for measuring O6-alkylguanine-DNA alkyltransferase (AGT) levels in large numbers of small biological samples. The assay is based on the use of a synthetic O6-methylguanine oligonucleotide bound to magnetic beads via a biotin-streptavidin linkage and bound to its complement. A 35S label is incorporated into the free end of the duplex. The basis of the assay lies in the observation that the restriction enzyme PvuII will not cleave the bead-bound duplex oligonucleotide having an O6-methylguanine within the restriction sequence. However, on removal of the methyl group by AGT present in cell extracts prior to incubation with PvuII, the 35S-labelled oligonucleotide is cleaved by the restriction enzyme, releasing a 35S-labelled 8 bp fragment. Due to the stoichiometric nature of the AGT reaction, quantitation of AGT is easily achieved by counting an aliquot of the supernatant after pelleting the unrestricted bead complexes with a magnet. AGT levels measured in certain cell lines and human lymphocytes by the reported assay are comparable to other methods. The assay can be performed in basic laboratories and allows for the rapid processing of many samples simultaneously, which could prove useful in clinical and epidemiological studies.},
	language = {eng},
	number = {10},
	journal = {Carcinogenesis},
	author = {Wilson, B. D. and Strauss, M. and Stickells, B. J. and Hoal-van Helden, E. G. and van Helden, P.},
	month = oct,
	year = {1994},
	pmid = {7955046},
	keywords = {Base Sequence, DNA, Deoxyribonucleases, Type II Site-Specific, Escherichia coli, Feasibility Studies, Humans, Hydrolysis, Immunomagnetic Separation, Lymphocytes, Methyltransferases, Molecular Sequence Data, O(6)-Methylguanine-DNA Methyltransferase, Oligonucleotides, Phenotype, Sensitivity and Specificity},
	pages = {2143--2148},
}

We describe an improved, rapid and cost effective assay for measuring O6-alkylguanine-DNA alkyltransferase (AGT) levels in large numbers of small biological samples. The assay is based on the use of a synthetic O6-methylguanine oligonucleotide bound to magnetic beads via a biotin-streptavidin linkage and bound to its complement. A 35S label is incorporated into the free end of the duplex. The basis of the assay lies in the observation that the restriction enzyme PvuII will not cleave the bead-bound duplex oligonucleotide having an O6-methylguanine within the restriction sequence. However, on removal of the methyl group by AGT present in cell extracts prior to incubation with PvuII, the 35S-labelled oligonucleotide is cleaved by the restriction enzyme, releasing a 35S-labelled 8 bp fragment. Due to the stoichiometric nature of the AGT reaction, quantitation of AGT is easily achieved by counting an aliquot of the supernatant after pelleting the unrestricted bead complexes with a magnet. AGT levels measured in certain cell lines and human lymphocytes by the reported assay are comparable to other methods. The assay can be performed in basic laboratories and allows for the rapid processing of many samples simultaneously, which could prove useful in clinical and epidemiological studies.

@article{hoal_van_helden_age-related_1989,
	title = {Age-related methylation changes in {DNA} may reflect the proliferative potential of organs},
	volume = {219},
	issn = {0027-5107},
	abstract = {The percentage of 5-methylcytosine in DNA was measured in brain, liver, heart and skeletal muscle of the rat at various ages. Age-related hypomethylation occurred rapidly shortly after birth and then declined to eventually stabilize in brain, heart and skeletal muscle. Hypomethylation in liver DNA continued throughout the period studied (6 months). Our hypothesis that the age-related decline of 5-methylcytosine content in DNA is related to the proliferative potential of organs is discussed.},
	language = {eng},
	number = {5-6},
	journal = {Mutation Research},
	author = {Hoal van Helden, E. G. and van Helden, P. D.},
	month = nov,
	year = {1989},
	pmid = {2615776},
	keywords = {5-Methylcytosine, Aging, Animals, Animals, Newborn, Brain, Cell Division, Cytosine, DNA, Heart, Liver, Muscle Development, Rats, Rats, Inbred Strains, Reference Values},
	pages = {263--266},
}

The percentage of 5-methylcytosine in DNA was measured in brain, liver, heart and skeletal muscle of the rat at various ages. Age-related hypomethylation occurred rapidly shortly after birth and then declined to eventually stabilize in brain, heart and skeletal muscle. Hypomethylation in liver DNA continued throughout the period studied (6 months). Our hypothesis that the age-related decline of 5-methylcytosine content in DNA is related to the proliferative potential of organs is discussed.

@article{van_helden_cross-contamination_1988,
	title = {Cross-contamination of human esophageal squamous carcinoma cell lines detected by {DNA} fingerprint analysis},
	volume = {48},
	issn = {0008-5472},
	abstract = {DNA "fingerprint" analysis has recently become known as a valuable technique for positive identification of any given individual. The chances for mistaken identity have been estimated to be 10(-6) for close siblings or as little as 10(-23) for randomly selected individuals. This methodology thus represents a significant improvement over previously established identification tests using protein or enzyme analysis techniques and has already found application in forensic medicine. One of the chief problems in tissue culture studies is the question of the unequivocal identity of the cultured cells used and the very real possibility of their being contaminated by cells of a similar morphological appearance. We report here the application of the DNA "fingerprint" technique to the genotypic analysis of cultured human squamous carcinoma cells. The results show that a number of lines, designation HCu, have become cross-contaminated. Lines SNO, HCu 10, and HCu 13 are genetically distinct, however lines HCu 10, 18, 33, 37, and 39 are genetically identical and are in fact subcultures of the same cells. In addition, a myocardial line known as Girardi is shown to be identical to HeLa cells. The introduction of this technique to tissue culture laboratories could therefore prevent contaminated cultures from being disseminated or used in research studies.},
	language = {eng},
	number = {20},
	journal = {Cancer Research},
	author = {van Helden, P. D. and Wiid, I. J. and Albrecht, C. F. and Theron, E. and Thornley, A. L. and Hoal-van Helden, E. G.},
	month = oct,
	year = {1988},
	pmid = {3167823},
	keywords = {Carcinoma, Squamous Cell, Cell Line, DNA, Neoplasm, Esophageal Neoplasms, HeLa Cells, Humans, Nucleotide Mapping},
	pages = {5660--5662},
}

DNA "fingerprint" analysis has recently become known as a valuable technique for positive identification of any given individual. The chances for mistaken identity have been estimated to be 10(-6) for close siblings or as little as 10(-23) for randomly selected individuals. This methodology thus represents a significant improvement over previously established identification tests using protein or enzyme analysis techniques and has already found application in forensic medicine. One of the chief problems in tissue culture studies is the question of the unequivocal identity of the cultured cells used and the very real possibility of their being contaminated by cells of a similar morphological appearance. We report here the application of the DNA "fingerprint" technique to the genotypic analysis of cultured human squamous carcinoma cells. The results show that a number of lines, designation HCu, have become cross-contaminated. Lines SNO, HCu 10, and HCu 13 are genetically distinct, however lines HCu 10, 18, 33, 37, and 39 are genetically identical and are in fact subcultures of the same cells. In addition, a myocardial line known as Girardi is shown to be identical to HeLa cells. The introduction of this technique to tissue culture laboratories could therefore prevent contaminated cultures from being disseminated or used in research studies.

@article{van_helden_plasmid_1988,
	title = {Plasmid preparation on sephacryl s1000},
	volume = {4},
	issn = {1064-3745},
	doi = {10.1385/0-89603-127-6:69},
	abstract = {Production of pure plasmid DNA is a prerequisite for most laboratories engaged in recombinant DNA research. There are a number of procedures available for plasmid purification, all of which have common features; namely, (1) growth of plasmid-containing bacteria, (2) lysis of bacteria, (3) low-speed centrifugation to remove the majority of bacterial DNA and protein, (4) an ultracentrifugation step in cesium chloride and ethidium bromide to separate plasmid DNA from RNA and chromosomal DNA, and (5) recovery of plasmid DNA band (extraction of ethidium bromide and cesium chloride). Steps (4) and (5) of this procedure are expensive, time-consuming, and require expensive machinery [ultracentrifuge, rotor(s)]. In addition, incomplete extraction of ethidium bromide can result in plasmid DNA that is not manipulable by many enzymes commonly used in DNA research.},
	language = {eng},
	journal = {Methods in Molecular Biology (Clifton, N.J.)},
	author = {Van Helden, P. D. and Hoal, E. G.},
	year = {1988},
	pmid = {21424627},
	note = {00000 },
	pages = {69--74},
}

Production of pure plasmid DNA is a prerequisite for most laboratories engaged in recombinant DNA research. There are a number of procedures available for plasmid purification, all of which have common features; namely, (1) growth of plasmid-containing bacteria, (2) lysis of bacteria, (3) low-speed centrifugation to remove the majority of bacterial DNA and protein, (4) an ultracentrifugation step in cesium chloride and ethidium bromide to separate plasmid DNA from RNA and chromosomal DNA, and (5) recovery of plasmid DNA band (extraction of ethidium bromide and cesium chloride). Steps (4) and (5) of this procedure are expensive, time-consuming, and require expensive machinery [ultracentrifuge, rotor(s)]. In addition, incomplete extraction of ethidium bromide can result in plasmid DNA that is not manipulable by many enzymes commonly used in DNA research.

@article{van_helden_new_1987,
	title = {A new assay for anti-{DNA} antibodies in serum which includes the measurement of anti-{Z}-{DNA}},
	volume = {69},
	issn = {0009-9104},
	abstract = {A simple, rapid assay for measuring anti-DNA titre of serum which includes anti-Z-DNA is described. The assay involves solution binding of antibody to labelled DNA under conditions such that the DNA is altered to form a left-handed or Z-DNA structure in the presence of cobalt ions. The absence or presence of cobalt determines a B or Z form structure in DNA and antibodies to these forms are detectable. The majority of SLE and RA patients (88\%) have a higher anti-DNA titre in the presence of cobalt ions. An additional 25\% of SLE patients and 22/23 RA patients who had normal anti-DNA levels according to the Crithidea assay, reacted with abnormal titres in our assay. Patients experiencing a relapse in SLE also showed a large increase in anti-DNA in the presence of antigenic Z-DNA. These results suggest that monitoring anti-DNA levels in SLE and RA to detect anti-Z DNA antibodies, provides significant advantages over methods currently in use to measure anti-DNA antibodies.},
	language = {eng},
	number = {2},
	journal = {Clinical and Experimental Immunology},
	author = {Van Helden, P. D. and Van Lill, L. and Bester, A. J. and De Waal, L. and Hoal-van Helden, E. G.},
	month = aug,
	year = {1987},
	pmid = {3498594},
	pmcid = {PMC1542401},
	keywords = {Antibodies, Antinuclear, Arthritis, Rheumatoid, Cobalt, DNA, DNA, Single-Stranded, Humans, Lupus Erythematosus, Systemic, Polydeoxyribonucleotides, Radioimmunoassay},
	pages = {394--402},
}

A simple, rapid assay for measuring anti-DNA titre of serum which includes anti-Z-DNA is described. The assay involves solution binding of antibody to labelled DNA under conditions such that the DNA is altered to form a left-handed or Z-DNA structure in the presence of cobalt ions. The absence or presence of cobalt determines a B or Z form structure in DNA and antibodies to these forms are detectable. The majority of SLE and RA patients (88%) have a higher anti-DNA titre in the presence of cobalt ions. An additional 25% of SLE patients and 22/23 RA patients who had normal anti-DNA levels according to the Crithidea assay, reacted with abnormal titres in our assay. Patients experiencing a relapse in SLE also showed a large increase in anti-DNA in the presence of antigenic Z-DNA. These results suggest that monitoring anti-DNA levels in SLE and RA to detect anti-Z DNA antibodies, provides significant advantages over methods currently in use to measure anti-DNA antibodies.

@article{hoal_van_helden_characterization_1986,
	title = {Characterization of seven human melanoma cell lines: melanogenesis and secretion of plasminogen activators},
	volume = {54},
	issn = {0007-0920},
	shorttitle = {Characterization of seven human melanoma cell lines},
	abstract = {Permanent cell lines (UCT-Mel 1 through 7) were established from biopsies of metastatic tissue taken from seven patients with malignant melanoma. Cells from these lines were all aneuploid and all grew as non-contact-inhibited, adherent monolayers. All of the lines, with the remarkable exception of UCT-Mel 6, formed tumours in nude mice, expressed the melanoma M-18 antigen and synthesized plasminogen activators exclusively of the tissue-type. UCT-Mel 6 cells were non tumourigenic, they lacked the M-18 antigen and they synthesized plasminogen activators exclusively of the urokinase type. UCT-Mel 1 and UCT-Mel 2 formed pigment in vitro and both of these lines showed an increase in pigment content and tyrosinase synthesis with increasing cell density. The rate of plasminogen activator released by UCT-Mel 1 and UCT-Mel 3 declined strikingly as the cells became confluent. Assuming that proteolytic activity is required for cell migration in vivo; that tyrosinase synthesis reflects expression of the differentiated phenotype and that melanoma cells retain some of the characteristics of neural crest cells, we suggest that the effects of confluence and close cell-cell contact provide a useful experimental counterpart for the study of normal neural crest all behaviour that is characterized by an inverse relationship between migration and a protease secretion on the one hand and pigmentation on the other.},
	language = {eng},
	number = {2},
	journal = {British Journal of Cancer},
	author = {Hoal van Helden, E. G. and Wilson, E. L. and Dowdle, E. B.},
	month = aug,
	year = {1986},
	pmid = {3091056},
	pmcid = {PMC2001511},
	keywords = {Cell Count, Cell Line, Electrophoresis, Polyacrylamide Gel, Humans, Melanins, Melanoma, Monophenol Monooxygenase, Plasminogen Activators},
	pages = {287--295},
}

Permanent cell lines (UCT-Mel 1 through 7) were established from biopsies of metastatic tissue taken from seven patients with malignant melanoma. Cells from these lines were all aneuploid and all grew as non-contact-inhibited, adherent monolayers. All of the lines, with the remarkable exception of UCT-Mel 6, formed tumours in nude mice, expressed the melanoma M-18 antigen and synthesized plasminogen activators exclusively of the tissue-type. UCT-Mel 6 cells were non tumourigenic, they lacked the M-18 antigen and they synthesized plasminogen activators exclusively of the urokinase type. UCT-Mel 1 and UCT-Mel 2 formed pigment in vitro and both of these lines showed an increase in pigment content and tyrosinase synthesis with increasing cell density. The rate of plasminogen activator released by UCT-Mel 1 and UCT-Mel 3 declined strikingly as the cells became confluent. Assuming that proteolytic activity is required for cell migration in vivo; that tyrosinase synthesis reflects expression of the differentiated phenotype and that melanoma cells retain some of the characteristics of neural crest cells, we suggest that the effects of confluence and close cell-cell contact provide a useful experimental counterpart for the study of normal neural crest all behaviour that is characterized by an inverse relationship between migration and a protease secretion on the one hand and pigmentation on the other.

@article{hoal_regulation_1983,
	title = {The regulation of tissue plasminogen activator activity by human fibroblasts},
	volume = {34},
	issn = {0092-8674},
	abstract = {We have found that live and ethanol-fixed fibroblasts, when covered with conditioned medium containing tissue plasminogen activator, associate with the enzyme and remove it from the medium. Binding of tissue plasminogen activator to fixed cells showed equilibrium kinetics with maximal uptake corresponding to 2.4 units of enzyme per 10(6) fixed cells. Enzyme bound to fixed cells could activate plasminogen and produce plaques of caseinolysis in casein-plasminogen-agar overlays. Electrophoretic analysis showed it covalently attached to a fibroblast component with a molecular weight of 40,000-50,000. Sequestration of tissue plasminogen activator by live fibroblasts showed nonsaturable first order kinetics with a rate constant of 0.465/hr. We conclude that active enzyme is bound to a surface receptor, then internalized and degraded. Fibroblasts did not release the binding molecule into the medium; binding of tissue plasminogen activator from the medium was unaffected by heparin or thrombin. This phenomenon differs from that described by Baker et al. and ascribed to "proteasenexin."},
	language = {eng},
	number = {1},
	journal = {Cell},
	author = {Hoal, E. G. and Wilson, E. L. and Dowdle, E. B.},
	month = aug,
	year = {1983},
	pmid = {6683996},
	note = {00000 },
	keywords = {Cell Count, Cells, Cultured, Culture Media, Fibroblasts, Heparin, Humans, Melanoma, Plasminogen Activators, Protein Biosynthesis, Thrombin, Urokinase-Type Plasminogen Activator},
	pages = {273--279},
}

We have found that live and ethanol-fixed fibroblasts, when covered with conditioned medium containing tissue plasminogen activator, associate with the enzyme and remove it from the medium. Binding of tissue plasminogen activator to fixed cells showed equilibrium kinetics with maximal uptake corresponding to 2.4 units of enzyme per 10(6) fixed cells. Enzyme bound to fixed cells could activate plasminogen and produce plaques of caseinolysis in casein-plasminogen-agar overlays. Electrophoretic analysis showed it covalently attached to a fibroblast component with a molecular weight of 40,000-50,000. Sequestration of tissue plasminogen activator by live fibroblasts showed nonsaturable first order kinetics with a rate constant of 0.465/hr. We conclude that active enzyme is bound to a surface receptor, then internalized and degraded. Fibroblasts did not release the binding molecule into the medium; binding of tissue plasminogen activator from the medium was unaffected by heparin or thrombin. This phenomenon differs from that described by Baker et al. and ascribed to "proteasenexin."

@article{rehberg_specific_1982,
	title = {Specific molecular activities of recombinant and hybrid leukocyte interferons},
	volume = {257},
	issn = {0021-9258},
	abstract = {Hybrid interferon DNA recombinants were constructed from the IFLrA and IFLrD leukocyte interferon-coding sequences. Each of the hybrid interferons was purified with the use of a monoclonal antibody to human leukocyte interferon. Three amino acid residues were identified, one or all of which function to potentiate antiviral activity on feline cells and reduce activity on human cells. Because at sufficiently high concentrations human interferons can interact with mouse and rat receptors, it is apparent that the species barrier is only relative and that interferons can be forced into heterologous receptors by mass action. In addition, the specific molecular antiviral and antiproliferative activities (molecules of interferon/cell required for a specific effect) for each of these interferons were determined. The specific molecular activities permit an accurate comparison of the efficacy of different interferons for a specific effect. Because the ratios of antiproliferative/antiviral activity of these interferons vary over a 12-fold range, it appears that the antiviral and antiproliferative activities are promulgated through different mechanisms. To account for these results, it is proposed that there are at least two distinct interferon receptors on cells.},
	language = {eng},
	number = {19},
	journal = {The Journal of Biological Chemistry},
	author = {Rehberg, E. and Kelder, B. and Hoal, E. G. and Pestka, S.},
	month = oct,
	year = {1982},
	pmid = {6288687},
	note = {00000 },
	keywords = {Amino Acid Sequence, Animals, Cats, Cattle, Cell Line, DNA Restriction Enzymes, DNA, Recombinant, Escherichia coli, Humans, Interferon Type I, Kidney, Lung, Molecular Weight, Nucleic Acid Hybridization, Plasmids, Viruses},
	pages = {11497--11502},
}

Hybrid interferon DNA recombinants were constructed from the IFLrA and IFLrD leukocyte interferon-coding sequences. Each of the hybrid interferons was purified with the use of a monoclonal antibody to human leukocyte interferon. Three amino acid residues were identified, one or all of which function to potentiate antiviral activity on feline cells and reduce activity on human cells. Because at sufficiently high concentrations human interferons can interact with mouse and rat receptors, it is apparent that the species barrier is only relative and that interferons can be forced into heterologous receptors by mass action. In addition, the specific molecular antiviral and antiproliferative activities (molecules of interferon/cell required for a specific effect) for each of these interferons were determined. The specific molecular activities permit an accurate comparison of the efficacy of different interferons for a specific effect. Because the ratios of antiproliferative/antiviral activity of these interferons vary over a 12-fold range, it appears that the antiviral and antiproliferative activities are promulgated through different mechanisms. To account for these results, it is proposed that there are at least two distinct interferon receptors on cells.

@article{wilson_molecular_1980,
	title = {Molecular species of plasminogen activators secreted by normal and neoplastic human cells},
	volume = {40},
	issn = {0008-5472},
	abstract = {A survey of 56 normal and neoplastic tissues has shown that plasminogen activators were released by cultured human cells in several molecular weights and their susceptibility to inhibition by antibodies to the normal urinary enzyme, urokinase. Melanoma cells characteristically secreted plasminogen activators which were immunochemically distinct from urokinase and which migrated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis as a prominent, closely spaced doublet with an apparent molecular weight of approximately 70,000 and a minor molecular weight component of approximately 60,000. Enzymes with similar characteristics have been observed in serum-free harvest fluids collected from other neoplastic tissue (a breast carcinoma, a glioblastoma, a malignant teratoma, a uterine sarcoma, and a carcinoma of the renal pelvis) and from normal tissue (8-week embryo fibroblasts, normal esophageal fibroblasts, and one culture of normal adult bladder epithelium). Plasminogen activators released by cells derived from most normal adult tissues, or from a 26-week-old embryo, and from other tumors of ectodermal or mesenchymal origin were inhibited by anti-urokinase antibody and showed a closely spaced doublet with a molecular weight of 60,000 as the most abundant molecular species with no evidence of the enzyme with a molecular weight of 70,000.},
	language = {eng},
	number = {3},
	journal = {Cancer Research},
	author = {Wilson, E. L. and Becker, M. L. and Hoal, E. G. and Dowdle, E. B.},
	month = mar,
	year = {1980},
	pmid = {7193517},
	keywords = {Antigen-Antibody Reactions, Cross Reactions, Female, Humans, Male, Melanoma, Molecular Weight, Neoplasms, Plasminogen Activators, Urokinase-Type Plasminogen Activator},
	pages = {933--938},
}

A survey of 56 normal and neoplastic tissues has shown that plasminogen activators were released by cultured human cells in several molecular weights and their susceptibility to inhibition by antibodies to the normal urinary enzyme, urokinase. Melanoma cells characteristically secreted plasminogen activators which were immunochemically distinct from urokinase and which migrated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis as a prominent, closely spaced doublet with an apparent molecular weight of approximately 70,000 and a minor molecular weight component of approximately 60,000. Enzymes with similar characteristics have been observed in serum-free harvest fluids collected from other neoplastic tissue (a breast carcinoma, a glioblastoma, a malignant teratoma, a uterine sarcoma, and a carcinoma of the renal pelvis) and from normal tissue (8-week embryo fibroblasts, normal esophageal fibroblasts, and one culture of normal adult bladder epithelium). Plasminogen activators released by cells derived from most normal adult tissues, or from a 26-week-old embryo, and from other tumors of ectodermal or mesenchymal origin were inhibited by anti-urokinase antibody and showed a closely spaced doublet with a molecular weight of 60,000 as the most abundant molecular species with no evidence of the enzyme with a molecular weight of 70,000.

@misc{noauthor_challenges_nodate,
	title = {Challenges of {Diagnosing} {Mendelian} {Susceptibility} to {Mycobacterial} {Diseases} in {South} {Africa} - {PubMed}},
	url = {https://pubmed.ncbi.nlm.nih.gov/37569495/},
	urldate = {2024-01-17},
}