All discovery cohorts were genotyped using a human Exome Chip array (exact details of the chip for each study are provided in Supplementary Material, Table S15). Quality control (QC) was done according to CHARGE Exome QC guidelines, including joint variant calling with zCall (32). At the study-level, the sample-level QC consisted of excluding samples of non-European ancestry (for European-ancestry cohorts), samples with call rates <95%, samples with sex discordance or related samples with an unexpected high identical by descent estimate. It was recommended that principal components (PCs) be obtained using variants with MAF ≥ 1%. The variant QC consisted of exclusion of SNVs with call rate < 95%, with Hardy–Weinberg equilibrium values of P < 1 × 10−6, and of variants that were strongly associated with plate assignment.
