Genotyping of COGA samples were performed at (1) the Center for Inherited Disease Research (1M array37), (2) Genome Technology Access Center at Washington University School of Medicine (Illumina OmniExpress38, and (3) Rutgers University (Affymetrix Smokescreen array39). All A/T and C/G SNPs were removed and a common set of approximately 47,000 SNPs was used to detect duplicate samples and to revise the reported pedigree structure. Family structures were altered as needed, and SNP genotypes were tested for Mendelian inconsistencies40 within the revised family structure. Genotype inconsistencies were set to missing. Imputation was to 1000 Genomes (Phase 3, version 5) using SHAPEIT41 and then Minimac342 and performed separately within data from the three genotyping sites. Only SNPs with a genotype rate >75% were included in analyses. Further details on the genotyping arrays, samples, and processing are in Supplementary Information. To maximize the utility of COGA’s family-based design, participants were assigned a family-based ancestry of EA or AA, according to the majority of individual-based ancestry in that family, based on principal components (PCs) derived from GWAS data. In the <10% of cases of
