Genotyping of 1,564 individuals from 117 EA families was performed at the Center for Inherited Disease Research (CIDR) using the Illumina 2.5M array (Illlumina, San Diego, CA, USA). COGA’s quality control (QC) approach has been previously reported (Wetherill et al., 2015). Briefly, individuals with a genotype rate <98% were excluded from analysis, and SNPs with a genotyping rate <98% were excluded from analysis. The 795 genotyped founders were used to remove SNPs which violated Hardy-Weinberg equilibrium (HWE; p<10−6). SNPs with minor allele frequency (MAF) less than 3% in the founders were also removed from further analysis. The reported pedigree structure was assessed using a pruned set of 1,519,440 SNPs. Pairwise identity by descent estimates were computed in PLINK (http://pngu.mgh.harvard.edu/purcell/plink/) to detect pairs of individuals whose allele sharing was not consistent with the reported family relationship. Family structures were altered as needed, and then SNP genotypes were tested for Mendelian inconsistencies (Pedcheck; O’Connell & Weeks, 1998) with the revised family structure. The cleaned genotype data were imputed to 1000 genomes (EUR and AFR, Phase 3, b37, October 2014) with build hg19
