For the design of the genome-wide scoring routines, autosomal GWAS data (n = 1,003,800) was pruned of SNPs in strong linkage disequilibrium (LD) with other markers (pairwise r2 threshold of 0.25, within a 200-SNP sliding window), ensuring that the scores computed in our target samples represent the aggregate effect of a large number of predominantly independent markers. The retained genotype data for EA (n = 193,979) and AA samples (n = 332,687) were further trimmed for minor allele frequency (MAF ≥ 0.05), call rate (≥ 0.98) and deviation from Hardy-Weinberg (HW) equilibrium (p ≥ 1×10−3), leaving 124,291 and 256,549 SNPs in the two respective population samples available for developing the scoring routines.
