We tested PRS for our primary GWAS on each GWAS cohort as a target set, using a GWAS where the target cohort was left out of the meta-analysis (Supplementary Table 2). To test genetic overlaps with other psychiatric diseases, we calculated PRS for DEPR and SCZ in our GWAS cohort BD cases 73. In pairwise case subtype or psychosis analyses (Figure 2, Supplementary Table 13), we regressed outcome on the PRS adjusting for ancestry principal components and a cohort indicator using logistic regression, and visualized covariate-adjusted PRS in BD1 and BD2 subtypes (Figure 2). Outcome sample sizes were BD1 n=8,044, BD2 n=3,365, SAB n=977; BD1 cases with and without psychosis n= 2175 and 798 respectively, BD2 cases with and without psychosis n= 146 and 660.
