In UK Biobank, we used BOLT-LMM (13) v2.3.2 to conduct GWASs for each of the ten AUDIT items with the first 40 ancestry principal components, sex, age, sex-by-age interactions, and batch as covariates. In the Netherlands Twin Register, we used the fastgwa function of GCTA (14) and included the first 5 ancestry principal components, sex, birth year, and genotyping platform as covariates. In ALSPAC, we analyzed unrelated participants using PLINK v2.0 (15), including the first 10 ancestry principal components, sex, and age as covariates. Note that both BOLT-LMM and fastgwa are capable of analyzing related individuals. Further details are included in Supplementary Material 3, as well as prior work (16). We then used METAL (17) to conduct sample-size weighted meta-analyses of the cohort-level GWAS summary statistics for each AUDIT item following quality control procedures (see Supplementary Material 4). A total of 8,596,116 SNPs were included in the meta-analyses.
