Participants’ DNA samples were genotyped using the Illumina Human1M array (Illumina, San Diego, CA), the Illumina Human OmniExpress 12V1 array (Illumina), the Illumina 2.5M array (Illumina) or the Smokescreen genotyping array (Biorealm LLC, Walnut, CA; Baurley et al., 2016). Samples were imputed to 1000 Genomes using the cosmopolitan reference panel (Phase 3) using SHAPEIT2 (Delaneau et al., 2013) and Minimac3 (Das et al., 2016) within each array. Variants with non-A/T or C/G alleles, missing rates <5%, minor allele frequencies >3%, and Hardy-Weinberg equilibrium p-values >0.0001 were used for imputation. Imputed variants with information scores <0.30, missing rate >25%, minor allele frequency <1%, or Hardy-Weinberg equilibrium (p < 10−6) were excluded from analysis. A full description of data processing, quality control, and imputation is available elsewhere (Lai et al., 2019; Lai et al., 2022).
