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). A full description of data processing, quality control, and imputation is available elsewhere (Lai et al., 2019). Briefly, data were imputed to Haplotype Reference Consortium (HRC). Single nucleotide polymorphisms (SNPs) with a genotyping rate < 0.95, that violated Hardy-Weinberg equilibrium (p < 10−6), or had minor allele frequency (MAF) < 0.01 were excluded from analysis. SNPrelate (Zheng et al., 2012) was used to estimate principal components from GWAS data. These principal components are distinct from the phenotypic principal components and are referred to as ancestry PCs throughout the rest of the manuscript.
