PRS were calculated in ancestry-stratified MVP holdout samples, based on the EA Freeze 3 PTSD GWAS. GWAS summary statistics were filtered to common (MAF > 1%), well-imputed variants (INFO > 0.8). Indels and ambiguous SNPs were removed. PRS-CS98 was used to infer posterior effect sizes of SNPs, using the KGP3 EUR based LD reference panel supplied with the program, with the global shrinkage parameter set to 0.01, 1,000 MCMC iterations with 500 burn-in iterations, and the Markov chain thinning factor set to 5. PRS were calculated using the --score option in PLINK 1.9, using the best-guess genotype data of target samples, where for each SNP the risk score was estimated as the posterior effect size multiplied by the number of copies of the risk allele. PRS was estimated as the sum of risk scores over all SNPs. PRS were used to predict PTSD status under logistic regression, adjusting for 5 PCs. The proportion of variance explained by PRS for each study was estimated as the difference in Nagelkerke’s R2 between a model containing PRS plus covariates and a model with only covariates.
