To calculate the externalizing polygenic score, we obtained a list of reference alleles and effect sizes for 587,378 SNPs from the investigators of the discovery externalizing disorders GWAS (Salvatore et al., 2015) that reflect polygenic associations with externalizing disorders (e.g., alcohol use disorder, substance use disorder, antisocial personality disorder). We confirmed this list had been pruned of SNPs with ambiguous coding (i.e. A/T and G/C SNPs) in our data. Of the SNPS, 480,856 were genotyped on the Illumina OMNI 2.5–8 array in our sample and available for externalizing risk-score calculations (after removal of SNPs with missing rates >0.01 and Hardy–Weinberg equilibrium p-values <0.000001). Polygenic scores were calculated by PLINK1 (Purcell et al., 2007) using the --score option, which computes a linear function of the additively coded number of reference alleles weighted by the betas from the discovery externalizing GWAS sample.
