To verify and correct the misclassification of self-reported race, we compared the GWAS data from all subjects with genotypes from the HapMap 3 (http://hapmap.ncbi.nlm.nih.gov/) reference CEU (CEPH collection), YRI (Yoruba in Ibadan, Nigeria), and CHB (Han Chinese in Beijing, China) populations. Principal components (PC) analysis was conducted in the entire GWAS sample using Eigensoft (19,20) and 145,472 SNPs that were common to the GWAS dataset and HapMap panel (after pruning the GWAS SNPs for linkage disequilibrium [R2] >80%) to characterize the underlying genetic architecture of the samples. The first 10 PC scores were used in a k-means cluster analysis to distinguish AAs and EAs; these groups were subsequently analyzed separately. We then conducted PC analyses within the two groups and the first three PCs were used in all subsequent analyses to correct for residual population stratification.
