Following quality control, 19,908 unambiguous Affymetrix Human Gene 1.0 ST array probe sets remained in the expression data set, of which 19,047 mapped to autosomal genes. Genotyping was completed successfully on 173 individuals. The average observed call rate per sample was 97.3%, and the minimum was 97.2%. Similarly, the average call rate per SNP was 97.3%, with 97.4% of SNPs having call rates ≥95%. Other quality control measures such as the Illumina GC score were also high. The mean GC score for all SNPs on the HumanOmniExpress platform was 0.84, and 82.9% of the SNPs had a score ≥0.8 (Supplementary Figure 2A). Respectively, the mean GC score for all SNPs on the HumanOmni2.5 BeadChips was 0.81, with 70% of SNPs having scores ≥0.8 (Supplementary Figure 2B). In total, considering all samples in the study, there were 581,633 SNPs with a call rate >95%, GC score >0.2, MAF >5%, and Hardy–Weinberg equilibrium χ2 P value >10−6.
