Multidimensional scaling analyses identified three distinct genetic subpopulations within the case-control sample, which corresponded to: European (EU), South African (SA) and Ashkenazi Jewish (AJ) ancestries (Supplementary materials). After QC, a total of 1,465 cases (1,279 EU, 93 SA and 93 AJ), 5,557 controls (5,139 EU, 260 AJ and 158 SA) and 400 complete trios (299 EU) remained and each had genotypes for a common set of 469,410 autosomal and 9,657 X-chromosome SNPs (Table S1). Quantile-quantile (QQ) plots of the observed versus expected log(p) values under the null hypothesis were used to calculate genomic control lambda values for the trio (λ=1.015), case-control (λ=1.002), and trio-case-control samples (λ=1.011) (Figure 1). QQ plots for EU (λ=1.009), SA (λ=0.969) and AJ (λ=0.982) case-control subpopulations were also constructed (Supplementary Figure S7). There was no evidence for significant residual stratification effects in any of the comparisons.
