All samples were imputed to 1000 Genomes using the cosmopolitan reference panel (Phase 3, version 5, NCBI GRCh37) using SHAPEIT2 38 then Minimac3 39 within each array. Only variants with non A/T or C/G alleles, missing rates < 5%, MAF > 3%, and HWE p values > 0.0001 were used for imputation. Imputed variants with R2 < 0.30 were excluded, and genotype probabilities were converted to genotypes if probabilities >= 0.90. Pedcheck 36 was used again to detect and clean Mendelian inconsistences for imputed variants. All genotyped and imputed variants with missing rates< 25%, MAF >= 1% and HWE p values > 1E-6 were included in analyses. 8,021,023 and 6,832,792 genotyped and imputed variants passed QC and were included in COGA EA and trans-ancestral (EA+AA) meta-analysis respectively.
