@article{Verma2023,
abstract = {Rationale: Standardized dosing of anti-tubercular (TB) drugs leads to variable plasma drug levels, which are associated with adverse drug reactions, delayed treatment response, and relapse. Mutations in genes affecting drug metabolism explain considerable interindividual pharmacokinetic variability; however, pharmacogenomic (PGx) assays that predict metabolism of anti-TB drugs have been lacking. Objectives: To develop a Nanopore sequencing panel and validate its performance in active TB patients to personalize treatment dosing. Measurements and Main Results: We developed a Nanopore sequencing panel targeting 15 single nucleotide polymorphisms (SNP) in 5 genes affecting the metabolism of isoniazid (INH), rifampin (RIF), linezolid and bedaquiline. For validation, we sequenced DNA samples (n=48) from the 1000 genomes project and compared variant calling accuracy with Illumina genome sequencing. We then sequenced DNA samples from patients with active TB (n=100) from South Africa on a MinION Mk1C and evaluated the relationship between genotypes and pharmacokinetic parameters for INH and RIF. Results: The PGx panel achieved 100{\%} concordance with Illumina sequencing in variant identification for the samples from the 1000 Genomes Project. In the clinical cohort, coverage was {\textgreater}100x for 1498/1500 (99.8{\%}) amplicons across the 100 samples. One third (33{\%}) of participants were identified as slow, 47{\%} were intermediate and 20{\%} were rapid isoniazid acetylators. Isoniazid clearance was significantly impacted by acetylator status (p{\textless}0.0001) with median (IQR) clearances of 11.2 L/h (9.3-13.4), 27.2 L/h (22.0-31.7), and 45.1 L/h (34.1-51.1) in slow, intermediate, and rapid acetylators. Rifampin clearance was 17.3{\%} (2.50-29.9) lower in individuals with homozygous AADAC rs1803155 G{\textgreater}A substitutions (p=0.0015). Conclusion: Targeted sequencing can enable detection of polymorphisms influencing TB drug metabolism on a low-cost, portable instrument to personalize dosing for TB treatment or prevention. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest. {\#}{\#}{\#} Funding Statement This study was supported by the National Institutes of Health (R21 AI172182). RJW receives funding from Wellcome (203135) and from the Francis Crick Institute which is supported by Cancer Research UK (FC2112), UK Research and Innovation-Medical Research Council (CC2112) and Wellcome (CC2112). For the purposes of open access, a CC-BY public copyright has been applied to any author-accepted manuscript arising from this submission. {\#}{\#}{\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Patients with GeneXpert MTB/RIF-confirmed RIF-susceptible pulmonary TB were recruited at the Ubuntu HIV/TB Clinic, Site B, Khayelitsha, South Africa (University of Cape Town Faculty of Health Sciences Human Research Ethics Committee approval 568/2012) as a part of a larger study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data supporting the findings of this manuscript are available in the Supplementary Information files or from the corresponding author upon request.},
author = {Verma, Renu and da Silva, Kesia and Rockwood, Neesha and Wasmann, Roeland E and Yende, Nombuso and Song, Taeksun and Kim, Eugene and Denti, Paolo and Wilkinson, Robert J and Andrews, Jason R},
doi = {10.1101/2023.09.08.23295248},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Verma et al. - 2023 - A Nanopore sequencing-based pharmacogenomic panel to personalize tuberculosis drug dosing.pdf:pdf},
journal = {medRxiv},
keywords = {OA,fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,original},
month = {sep},
pages = {2023.09.08.23295248},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{A Nanopore sequencing-based pharmacogenomic panel to personalize tuberculosis drug dosing}},
url = {https://www.medrxiv.org/content/10.1101/2023.09.08.23295248v1 https://www.medrxiv.org/content/10.1101/2023.09.08.23295248v1.abstract},
year = {2023}
}

{"_id":"fk2zp7uEipWQedsvm","bibbaseid":"verma-dasilva-rockwood-wasmann-yende-song-kim-denti-etal-ananoporesequencingbasedpharmacogenomicpaneltopersonalizetuberculosisdrugdosing-2023","author_short":["Verma, R.","da Silva, K.","Rockwood, N.","Wasmann, R. E","Yende, N.","Song, T.","Kim, E.","Denti, P.","Wilkinson, R. J","Andrews, J. R"],"bibdata":{"bibtype":"article","type":"article","abstract":"Rationale: Standardized dosing of anti-tubercular (TB) drugs leads to variable plasma drug levels, which are associated with adverse drug reactions, delayed treatment response, and relapse. Mutations in genes affecting drug metabolism explain considerable interindividual pharmacokinetic variability; however, pharmacogenomic (PGx) assays that predict metabolism of anti-TB drugs have been lacking. Objectives: To develop a Nanopore sequencing panel and validate its performance in active TB patients to personalize treatment dosing. Measurements and Main Results: We developed a Nanopore sequencing panel targeting 15 single nucleotide polymorphisms (SNP) in 5 genes affecting the metabolism of isoniazid (INH), rifampin (RIF), linezolid and bedaquiline. For validation, we sequenced DNA samples (n=48) from the 1000 genomes project and compared variant calling accuracy with Illumina genome sequencing. We then sequenced DNA samples from patients with active TB (n=100) from South Africa on a MinION Mk1C and evaluated the relationship between genotypes and pharmacokinetic parameters for INH and RIF. Results: The PGx panel achieved 100% concordance with Illumina sequencing in variant identification for the samples from the 1000 Genomes Project. In the clinical cohort, coverage was \\textgreater100x for 1498/1500 (99.8%) amplicons across the 100 samples. One third (33%) of participants were identified as slow, 47% were intermediate and 20% were rapid isoniazid acetylators. Isoniazid clearance was significantly impacted by acetylator status (p\\textless0.0001) with median (IQR) clearances of 11.2 L/h (9.3-13.4), 27.2 L/h (22.0-31.7), and 45.1 L/h (34.1-51.1) in slow, intermediate, and rapid acetylators. Rifampin clearance was 17.3% (2.50-29.9) lower in individuals with homozygous AADAC rs1803155 G\\textgreaterA substitutions (p=0.0015). Conclusion: Targeted sequencing can enable detection of polymorphisms influencing TB drug metabolism on a low-cost, portable instrument to personalize dosing for TB treatment or prevention. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was supported by the National Institutes of Health (R21 AI172182). RJW receives funding from Wellcome (203135) and from the Francis Crick Institute which is supported by Cancer Research UK (FC2112), UK Research and Innovation-Medical Research Council (CC2112) and Wellcome (CC2112). For the purposes of open access, a CC-BY public copyright has been applied to any author-accepted manuscript arising from this submission. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Patients with GeneXpert MTB/RIF-confirmed RIF-susceptible pulmonary TB were recruited at the Ubuntu HIV/TB Clinic, Site B, Khayelitsha, South Africa (University of Cape Town Faculty of Health Sciences Human Research Ethics Committee approval 568/2012) as a part of a larger study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data supporting the findings of this manuscript are available in the Supplementary Information files or from the corresponding author upon request.","author":[{"propositions":[],"lastnames":["Verma"],"firstnames":["Renu"],"suffixes":[]},{"propositions":["da"],"lastnames":["Silva"],"firstnames":["Kesia"],"suffixes":[]},{"propositions":[],"lastnames":["Rockwood"],"firstnames":["Neesha"],"suffixes":[]},{"propositions":[],"lastnames":["Wasmann"],"firstnames":["Roeland","E"],"suffixes":[]},{"propositions":[],"lastnames":["Yende"],"firstnames":["Nombuso"],"suffixes":[]},{"propositions":[],"lastnames":["Song"],"firstnames":["Taeksun"],"suffixes":[]},{"propositions":[],"lastnames":["Kim"],"firstnames":["Eugene"],"suffixes":[]},{"propositions":[],"lastnames":["Denti"],"firstnames":["Paolo"],"suffixes":[]},{"propositions":[],"lastnames":["Wilkinson"],"firstnames":["Robert","J"],"suffixes":[]},{"propositions":[],"lastnames":["Andrews"],"firstnames":["Jason","R"],"suffixes":[]}],"doi":"10.1101/2023.09.08.23295248","file":":C$\\$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Verma et al. - 2023 - A Nanopore sequencing-based pharmacogenomic panel to personalize tuberculosis drug dosing.pdf:pdf","journal":"medRxiv","keywords":"OA,fund_ack,original","mendeley-tags":"OA,fund_ack,original","month":"sep","pages":"2023.09.08.23295248","publisher":"Cold Spring Harbor Laboratory Press","title":"A Nanopore sequencing-based pharmacogenomic panel to personalize tuberculosis drug dosing","url":"https://www.medrxiv.org/content/10.1101/2023.09.08.23295248v1 https://www.medrxiv.org/content/10.1101/2023.09.08.23295248v1.abstract","year":"2023","bibtex":"@article{Verma2023,\r\nabstract = {Rationale: Standardized dosing of anti-tubercular (TB) drugs leads to variable plasma drug levels, which are associated with adverse drug reactions, delayed treatment response, and relapse. Mutations in genes affecting drug metabolism explain considerable interindividual pharmacokinetic variability; however, pharmacogenomic (PGx) assays that predict metabolism of anti-TB drugs have been lacking. Objectives: To develop a Nanopore sequencing panel and validate its performance in active TB patients to personalize treatment dosing. Measurements and Main Results: We developed a Nanopore sequencing panel targeting 15 single nucleotide polymorphisms (SNP) in 5 genes affecting the metabolism of isoniazid (INH), rifampin (RIF), linezolid and bedaquiline. For validation, we sequenced DNA samples (n=48) from the 1000 genomes project and compared variant calling accuracy with Illumina genome sequencing. We then sequenced DNA samples from patients with active TB (n=100) from South Africa on a MinION Mk1C and evaluated the relationship between genotypes and pharmacokinetic parameters for INH and RIF. Results: The PGx panel achieved 100{\\%} concordance with Illumina sequencing in variant identification for the samples from the 1000 Genomes Project. In the clinical cohort, coverage was {\\textgreater}100x for 1498/1500 (99.8{\\%}) amplicons across the 100 samples. One third (33{\\%}) of participants were identified as slow, 47{\\%} were intermediate and 20{\\%} were rapid isoniazid acetylators. Isoniazid clearance was significantly impacted by acetylator status (p{\\textless}0.0001) with median (IQR) clearances of 11.2 L/h (9.3-13.4), 27.2 L/h (22.0-31.7), and 45.1 L/h (34.1-51.1) in slow, intermediate, and rapid acetylators. Rifampin clearance was 17.3{\\%} (2.50-29.9) lower in individuals with homozygous AADAC rs1803155 G{\\textgreater}A substitutions (p=0.0015). Conclusion: Targeted sequencing can enable detection of polymorphisms influencing TB drug metabolism on a low-cost, portable instrument to personalize dosing for TB treatment or prevention. {\\#}{\\#}{\\#} Competing Interest Statement The authors have declared no competing interest. {\\#}{\\#}{\\#} Funding Statement This study was supported by the National Institutes of Health (R21 AI172182). RJW receives funding from Wellcome (203135) and from the Francis Crick Institute which is supported by Cancer Research UK (FC2112), UK Research and Innovation-Medical Research Council (CC2112) and Wellcome (CC2112). For the purposes of open access, a CC-BY public copyright has been applied to any author-accepted manuscript arising from this submission. {\\#}{\\#}{\\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Patients with GeneXpert MTB/RIF-confirmed RIF-susceptible pulmonary TB were recruited at the Ubuntu HIV/TB Clinic, Site B, Khayelitsha, South Africa (University of Cape Town Faculty of Health Sciences Human Research Ethics Committee approval 568/2012) as a part of a larger study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data supporting the findings of this manuscript are available in the Supplementary Information files or from the corresponding author upon request.},\r\nauthor = {Verma, Renu and da Silva, Kesia and Rockwood, Neesha and Wasmann, Roeland E and Yende, Nombuso and Song, Taeksun and Kim, Eugene and Denti, Paolo and Wilkinson, Robert J and Andrews, Jason R},\r\ndoi = {10.1101/2023.09.08.23295248},\r\nfile = {:C$\\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Verma et al. - 2023 - A Nanopore sequencing-based pharmacogenomic panel to personalize tuberculosis drug dosing.pdf:pdf},\r\njournal = {medRxiv},\r\nkeywords = {OA,fund{\\_}ack,original},\r\nmendeley-tags = {OA,fund{\\_}ack,original},\r\nmonth = {sep},\r\npages = {2023.09.08.23295248},\r\npublisher = {Cold Spring Harbor Laboratory Press},\r\ntitle = {{A Nanopore sequencing-based pharmacogenomic panel to personalize tuberculosis drug dosing}},\r\nurl = {https://www.medrxiv.org/content/10.1101/2023.09.08.23295248v1 https://www.medrxiv.org/content/10.1101/2023.09.08.23295248v1.abstract},\r\nyear = {2023}\r\n}\r\n","author_short":["Verma, R.","da Silva, K.","Rockwood, N.","Wasmann, R. 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