Genotyping for the COGA European American participants was performed using the Illumina 1M, Illumina OmniExpress, and Illumina 2.5 M (Illumina, San Diego, CA, USA), and Smokescreen (BioRelm, Walnut, CA, USA) 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 > 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 [46]. Family structures were altered as needed and SNP genotypes were tested for Mendelian inconsistencies with the revised family structure [47]. Genotype inconsistencies were set to missing. Imputation was to 1000 Genomes (EUR and AFR, Phase 3, b37, October 2014; build hg19) using SHAPEIT2 [48] and then Minimac3 [49]. Imputed SNPs with information (INFO) scores < 0.30 or individual genotype probability scores < 0.90 were excluded, as were palindromic SNPs (A/T or C/G), monomorphic SNPs, SNPs with a genotyping rate of <
