DNA samples were genotyped using the Illumina Human1 M 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)55. Data were imputed to 1000 Genomes (Phase 3) and SNPs with a minor allele frequency < .01, were genotyped at a rate < .95, or that violated Hardy-Weinberg equilibrium were excluded. Principal components (PCs) were calculated using Eigenstrat56 and 1000 Genomes (Phase 3, version 5). The first ten PCs, age, and sex were used as covariates in the polygenic score analyses (PGS). Additional details about genotyping and quality control procedures have been published elsewhere57,58. We report associations with problematic substance use (symptoms of AUD, cannabis use disorder [CUD], opioid use disorder [OUD], and other SUD as well as the Fagerstrom Test for Nicotine Dependence42).
