As described previously [38], genotyping was performed using the Illumina 2.5 M array (Illumina, San Diego, CA, USA), the Illumina OmniExpress [39], the Illumina 1 M array, or the Affymetrix Smokescreen array [40]. Single nucleotide polymorphisms (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 removed, after which data were imputed to 1000 genomes (EUR and AFR, Phase 3, b37, October 2014; build hg19) using SHAPEIT [41] and IMPUTE2 [42]. Following imputation, genotype probabilities ≥0.90 were changed to genotypes. Mendelian errors in the imputed SNPs were reviewed and resolved as described previously [43, 44]. SNPs with an imputation information score <0.30 or MAF <0.03 were excluded from subsequent analysis.
