Participants’ DNA samples were genotyped using the Illumina Human1M array (Illumina, San Diego, CA), the Illumina Human OmniExpress 12V1 array, the Illumina 2.5M array, or the Smokescreen genotyping array (Biorealm LLC, Walnut, CA; Baurley et al., 2016). Data processing, quality control and imputation have been described elsewhere (Lai et al., 2019). Genotypes were imputed to 1000 Genomes using the cosmopolitan reference panel (Phase 3, Version 5, NCBI GRCh37) using SHAPPEIT2 and Minimac 3. Single nucleotide polymorphisms (SNPs) with a genotyping rate < 0.95, that violated Hardy-Weinberg equilibrium (p < 10−6) or had a minor allele frequency < 0.01, were excluded from analysis. More details on genotyping, quality control, and imputation for the COGA sample has been reported elsewhere (Wetherill et al., 2019).
