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 CL, Cheng I, Assimes TL, Dumitrescu L, Hindorff LA, Mitchell S, Ambite JL, Boerwinkle E, Buzkova P, Carlson CS, Cochran B, Duggan D, Eaton CB, Fesinmeyer MD, Franceschini N, Haessler J, Jenny N, Kang HM, Kooperberg C, Lin Y, Le Marchand L, Matise TC, Robinson JG, Rodriguez C, Schumacher FR, Voight BF, Young A, Manolio TA, Mohlke KL, Haiman CA, Peters U, Crawford DC, North KE
PLoS One. 2012 7 (4): e35651

PMID: 22539988 · PMCID: PMC3335090 · DOI:10.1371/journal.pone.0035651

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.

MeSH Terms (14)

African Americans Cardiovascular Diseases Cholesterol, HDL Cholesterol, LDL Cholesterol Ester Transfer Proteins Chromosomes, Human Cohort Studies Gene Frequency Genome-Wide Association Study Genotype Humans Metabolic Diseases Polymorphism, Single Nucleotide Quantitative Trait Loci

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