Genotyping for the COGA EA participants was performed in batches using the Illumina 1 M, Illumina OmniExpress, Illumina 2.5 M, and Smokescreen arrays. Details have previously been reported38. Briefly, 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 PLINK39. Family structures were altered as needed and SNP genotypes were tested for Mendelian inconsistencies with the revised family structure40. Genotype inconsistencies were set to missing. Imputation was to 1000 Genomes (EUR and AFR, Phase 3, b37, October 2014; build hg19) using SHAPEIT241 and then Minimac342. Imputed SNPs with INFO scores <0.30 or individual genotype probability <0.90 were excluded, as were palindromic SNPs, monomorphic SNPs, SNPs with a genotyping rate of <95%, SNPs that were not in HWE, and SNPs with a minor allele frequency <0.05%. In total, 6,881,872 SNPs passed quality control and were available for analysis.
