Genotyping for the COGA European American participants was performed using the Illumina 1M, Illumina OmniExpress, and Illumina 2.5M (Illumina, San Diego, CA), and Smokescreen (BioRelm, Walnut, CA) arrays. Array type was included as a covariate in all analyses. A pruned set of 47,000 variants that were genotyped on all platforms and had minor allele frequencies (MAF) > 10% in the combined samples, Hardy-Weinberg Equilibrium (HWE) p-values > 0.001, missing rates < 2%, and were not in linkage disequilibrium (LD, defined as R2 < 0.5) were used to assess reported pedigree structure using identity-by-descent calculations in PLINK (Purcell et al., 2007). Family structures were altered as needed and SNP genotypes were tested for Mendelian inconsistencies with the revised family structure (O’Connell & Weeks, 1998). Genotype inconsistencies were set to missing. Imputation was to 1000 Genomes (EUR and AFR, Phase 3, b37, October 2014; build hg19) using SHAPEIT2 (Delaneau et al., 2012) and then Minimac3 (Das et al., 2016). Only non-palindromic variants, with missing rates < 5%, MAF > 3%, and HWE p values > 0.0001 were used for imputation. Imputed SNPs
