Summary association statistics used to create the polygenic scores for alcohol problems come from a previously reported GWAS of an alcohol problems factor score conducted in 4,304 Caucasian young adults from the Avon Longitudinal Study of Parents and Children (Edwards et al., 2015); this is the largest GWAS to date of alcohol problems in European young adults. Genotypes in this discovery sample were also imputed to the 1000 Genomes Phase I (v3) reference panel. From this discovery sample, we selected a list of 4,415,289 SNPs also available in FinnTwin12 and with a minor allele frequency > 5% and imputation quality R2 > .90 in both samples, and pruned this SNP set to obtain 212,718 autosomal SNPs (4.8% of the common SNPs) in approximate linkage equilibrium (R2 < .25). This list was further filtered to create two sets of score SNPs with nominal GWAS association p values in the discovery GWAS (thresholds of p < .05 and p < .01, NSNPs = 10,693 and 2,221, respectively), based on preliminary analyses as well as previous work showing these thresholds have the best signal-to-noise ratio/predictive power for polygenic scores (Yang et al., 2014).
