All participants were genotyped on the Affymetrix 6.0 platform (Affymetrix, Inc., Santa Clara CA), with a total of 696,388 autosomal SNPs available for analysis after quality control. Full details on processing and cleaning genotypes for the CADD GWAS sample is provided in the Supplement. Population stratification was examined by performing multidimensional scaling in PLINK (Purcell et al. 2007), in which ten ancestry dimensions were estimated. The first three dimensions notably captured genetic variation among individuals of self-reported African, Hispanic, and Asian ancestry, compared to a central (majority) node of individuals of self-reported European ancestry. Supplemental Figure S2 illustrates the first three ancestry dimensions within the CADD GWAS sample (along with individuals’ self-reported ancestry).
