Evaluation of the Metabochip genotyping array in African Americans and implications for fine mapping of GWAS-identified loci: the PAGE study. Buyske, S., Wu, Y., Carty, C. L., Cheng, I., Assimes, T. L., Dumitrescu, L., Hindorff, L. A., Mitchell, S., Ambite, J. L., Boerwinkle, E., Buzkova, P., Carlson, C. S., Cochran, B., Duggan, D., Eaton, C. B., Fesinmeyer, M. D., Franceschini, N., Haessler, J., Jenny, N., Kang, H. M., Kooperberg, C., Lin, Y., Le Marchand, L., Matise, T. C., Robinson, J. G., Rodriguez, C., Schumacher, F. R., Voight, B. F., Young, A., Manolio, T. A., Mohlke, K. L., Haiman, C. A., Peters, U., Crawford, D. C., & North, K. E. PloS one, 7:e35651, 2012.
Evaluation of the Metabochip genotyping array in African Americans and implications for fine mapping of GWAS-identified loci: the PAGE study. [link]Paper  doi  abstract   bibtex   
The Metabochip is a custom genotyping array designed for replication and fine mapping of metabolic, cardiovascular, and anthropometric trait loci and includes low frequency variation content identified from the 1000 Genomes Project. It has 196,725 SNPs concentrated in 257 genomic regions. We evaluated the Metabochip in 5,863 African Americans; 89% of all SNPs passed rigorous quality control with a call rate of 99.9%. Two examples illustrate the value of fine mapping with the Metabochip in African-ancestry populations. At CELSR2/PSRC1/SORT1, we found the strongest associated SNP for LDL-C to be rs12740374 (p = 3.5 × 10(-11)), a SNP indistinguishable from multiple SNPs in European ancestry samples due to high correlation. Its distinct signal supports functional studies elsewhere suggesting a causal role in LDL-C. At CETP we found rs17231520, with risk allele frequency 0.07 in African Americans, to be associated with HDL-C (p = 7.2 × 10(-36)). This variant is very rare in Europeans and not tagged in common GWAS arrays, but was identified as associated with HDL-C in African Americans in a single-gene study. Our results, one narrowing the risk interval and the other revealing an associated variant not found in Europeans, demonstrate the advantages of high-density genotyping of common and rare variation for fine mapping of trait loci in African American samples.
@article{BuyskeWuCartyEtAl2012,
	abstract = {The Metabochip is a custom genotyping array designed for replication and fine mapping of metabolic, cardiovascular, and anthropometric trait loci and includes low frequency variation content identified from the 1000 Genomes Project. It has 196,725 SNPs concentrated in 257 genomic regions. We evaluated the Metabochip in 5,863 African Americans; 89% of all SNPs passed rigorous quality control with a call rate of 99.9%. Two examples illustrate the value of fine mapping with the Metabochip in African-ancestry populations. At CELSR2/PSRC1/SORT1, we found the strongest associated {SNP} for LDL-C to be rs12740374 (p = 3.5 × 10(-11)), a {SNP} indistinguishable from multiple SNPs in European ancestry samples due to high correlation. Its distinct signal supports functional studies elsewhere suggesting a causal role in LDL-C. At CETP we found rs17231520, with risk allele frequency 0.07 in African Americans, to be associated with HDL-C (p = 7.2 × 10(-36)). This variant is very rare in Europeans and not tagged in common {GWAS} arrays, but was identified as associated with HDL-C in African Americans in a single-gene study. Our results, one narrowing the risk interval and the other revealing an associated variant not found in Europeans, demonstrate the advantages of high-density genotyping of common and rare variation for fine mapping of trait loci in African American samples.},
	author = {Buyske, Steven and Wu, Ying and Carty, Cara L. and Cheng, Iona and Assimes, Themistocles L. and Dumitrescu, Logan and Hindorff, Lucia A. and Mitchell, Sabrina and Ambite, Jose Luis and Boerwinkle, Eric and Buzkova, Petra and Carlson, Chris S. and Cochran, Barbara and Duggan, David and Eaton, Charles B. and Fesinmeyer, Megan D. and Franceschini, Nora and Haessler, Jeffrey and Jenny, Nancy and Kang, Hyun Min and Kooperberg, Charles and Lin, Yi and Le Marchand, Loic and Matise, Tara C. and Robinson, Jennifer G. and Rodriguez, Carlos and Schumacher, Fredrick R. and Voight, Benjamin F. and Young, Alicia and Manolio, Teri A. and Mohlke, Karen L. and Haiman, Christopher A. and Peters, Ulrike and Crawford, Dana C. and North, Kari E.},
	chemicals = {CETP protein, human, Cholesterol Ester Transfer Proteins, Cholesterol, HDL, Cholesterol, LDL},
	citation-subset = {IM},
	completed = {2012-09-10},
	country = {United States},
	doi = {10.1371/journal.pone.0035651},
	issn = {1932-6203},
	issn-linking = {1932-6203},
	issue = {4},
	journal = {PloS one},
	keywords = {African Americans, genetics; Cardiovascular Diseases, ethnology, genetics; Cholesterol Ester Transfer Proteins, genetics; Cholesterol, HDL, blood; Cholesterol, LDL, blood; Chromosomes, Human, genetics; Cohort Studies; Gene Frequency; Genome-Wide Association Study; Genotype; Humans; Metabolic Diseases, ethnology, genetics; Polymorphism, Single Nucleotide; Quantitative Trait Loci},
	nlm-id = {101285081},
	owner = {NLM},
	pages = {e35651},
	pii = {PONE-D-12-01108},
	pmc = {PMC3335090},
	pmid = {22539988},
	url = {https://pubmed.ncbi.nlm.nih.gov/22539988/},

	pubmodel = {Print-Electronic},
	pubstate = {ppublish},
	revised = {2019-12-10},
	title = {Evaluation of the {Metabochip} genotyping array in {African Americans} and implications for fine mapping of {GWAS}-identified loci: the {PAGE} study.},
	volume = {7},
	year = {2012},
	bdsk-url-1 = {https://pubmed.ncbi.nlm.nih.gov/22539988/},
	bdsk-url-2 = {https://doi.org/10.1371/journal.pone.0035651}}
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