Evaluation of the Metabochip Genotyping Array in African Americans and Implications for Fine Mapping of GWAS-Identified Loci: The PAGE Study

PLOS ONE, April 2012

22539988

Steven Buyske, Ying Wu, Cara L. Carty, Iona Cheng, Themistocles L. Assimes, Logan Dumitrescu, Lucia A. Hindorff, Sabrina Mitchell, Jose Luis Ambite, Eric Boerwinkle, Petra Buzkova, Chris S. Carlson, Barbara Cochran, David Duggan, Charles B. Eaton, Megan D. Fesinmeyer, Nora Franceschini, Jeffrey Haessler, Nancy Jenny, Hyun Min Kang, Charles Kooperberg, Yi Lin, Loic Le Marchand, Tara C. Matise, Jennifer G. Robinson, Carlos Rodriguez, Fredrick R. Schumacher, Benjamin F. Voight, Alicia Young, Teri A. Manolio, Karen L. Mohlke, Christopher A. Haiman, Ulrike Peters, Dana C. Crawford, Kari E. North

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.