SNP dosages were imputed in each study using MaCH (Li et al., 2010). The imputation reference was HapMap3 CEU (Utah residents with Northern and Western European ancestry) for subjects of European ancestry. Unobserved population admixture due to ancestry is a well-known confound in GWAS (Patterson et al., 2006). To protect against false-positives due to ancestry, we extracted five principal components from each sample to capture population stratification. To improve the efficiency of population stratification principal components analysis (PCA), a subset of independent SNPs was selected using PLINK, with 77155–79517 SNPs analyzed in each study. PCA was applied to the selected SNPs using the “smartpca” module of EIGENSOFT.
