due to their complex patterns of linkage disequilibrium. All remaining SNPs were then pruned using p-value-informed clumping (i.e., grouping linked SNPs; R2 = 0.10, 500 kb window), leaving 101,202 SNPs in SAGE for analysis. For each p-value threshold, the cross-disorder log odds-ratio for each component SNP was multiplied by the number of reference alleles for that SNP. These product terms were summed and divided by the total number of contributing SNPs, thus producing a single metric for each participant representing cross-disorder genetic vulnerability. These analyses were completed using the –score method in Plink (v.1.9; Chang et al., 2015). Individual disorder risk scores for the five psychiatric disorders (ADHD, AUT, BIP, MDD, SCZ) included in the cross-disorder meta-analysis were then generated in the same manner. Subsequent to the cross-disorder meta-analysis, a much larger second-generation GWAS of schizophrenia (SCZ2; Schizophrenia Working Group of the Psychiatric Genomics Consortium, 2014) was released, and analyses were therefore repeated for schizophrenia using SCZ2 PRS. Distributions of all PRS generated are presented in Supplementary Figure S1.
