Genome-wide polygenic risk scores (PRS) of alcohol use in the COGA sample were constructed based on GWAS summary statistics of alcohol consumption, measured in grams of alcohol per day, from the Alcohol Genome-Wide Association (AlcGen) and Cohorts for Heart and Aging Research in Genomic Epidemiology Plus (CHARGE+) consortia (Schumann et al., 2016). After removing palindromic SNPs (which can be ambiguous with respect to the reference allele when going across samples), we used the clump and score procedures in PLINK (Purcell et al., 2007) to sum each individual’s total number of minor alleles from the score SNPs, with each SNP weighted by the negative log of the GWAS association p-value and sign of the association coefficient (beta). Clumping was done with respect to the linkage disequilibrium (LD) pattern in the 1000 Genome Phase 3 sample using a 500kb physical distance and an LD threshold of r2 >= 0.25. Thus, PRS were constructed of SNPs that capture independent genetic association signals from the AlcGen and CHARGE+ GWAS. Following conventions for polygenic scoring using the pruning and thresholding approach (Bogdan et al., 2018),
