Polygenic risk scores (PRS) were calculated in hold out target samples based on SNP effect sizes from PTSD GWAS in non-overlapping discovery/training samples. GWAS summary statistics were filtered to common (MAF > 5%), well imputed variants (INFO > 0.9). Indels, ambiguous SNPs, and variants in the extended MHC region (chr6:25-34 Mb) were removed. LD pruning was performed using the --clump procedure in PLINK1.9, where variants were pruned if they were nearby (within 500 kb) and in LD (r2 > 0.3) with the leading variant (lowest P-value) in a given region. PRS were calculated in PRSice v2.1.2 using the best-guess genotype data of target samples, where for each SNP the risk score was estimated as the natural log of the odds ratio multiplied by number of copies of the risk allele. PRS was estimated as the sum of risk scores overall SNPs. PRS were generated at multiple P-value thresholds (PT) (at intervals of 0.01 ranging from P = 0.0001 to P = 1). Best-fit PRS (at PT = 0.3 for PTSD and PT = 0.3 for re-experiencing symptoms, respectively) were used
