The PRS (Extended Data Figure 2) were calculated after using P-value-informed clumping with an LD cutoff of r2 = 0.05 within a 500-kb window, excluding the MHC region of the genome because of its complex LD structure. The European samples of the 1000 Genomes Project were used as the LD reference panel. PRS analysis was conducted based on the GWAS summary association data using the gtx R package incorporated in PRSice v1.25 software81. For each PRS analysis, we calculated an approximate estimate of the explained variance from a multivariate regression model85. For comparison of cross-ancestry PRS (Extended Data Figure 3), we clumped summary statistics from a recent PTSD GWAS13, applying an LD cutoff of r2 = 0.3 within a 500-kb window. These clumped summary statistics were used as a base for calculating the PRS in MVP individuals of European and African ancestry, independently, using PRSice 2.0 software86.
