Genotyping of 3,654 individuals of AA and 7,382 individuals of EA was performed using the Illumina 2.5M array (Illumina, San Diego, CA, USA), the Illumina OmniExpress39, the Illumina 1M array, or the Affymetrix Smokescreen array40. SNPs with a genotyping rate <98%, or that violated Hardy-Weinberg equilibrium (p<10−6), or with minor allele frequency (MAF) less than 3% were excluded from analyses. Mendelian inconsistencies were removed38, after which data were imputed to 1000 genomes (EUR and AFR, Phase 3, b37, October 2014; build hg19) using SHAPEIT41 and IMPUTE242. Following imputation, genotype probabilities ≥ 0.90 were changed to genotypes. Mendelian errors in the imputed SNPs were reviewed and resolved as described previously7,43. SNPs with an imputation information score < 0.30 or MAF < 0.03 were excluded from subsequent analysis. Further details are in Supplemental Information.
