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Chunk #13 — Methods — LD clumping, P value thresholding, and computing PRS

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Polygenic risk associated with post-traumatic stress disorder onset and severity.
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performance (PT = 0.2) was chosen for the final PRS calculation. For schizophrenia–PRS, a threshold of 0.05 had been shown to be the most predictive in the original publication27. Thus, this threshold was used to avoid multiple testing burden. The first five principal components were added as covariates to correct for population stratification in both analyses. Standardization was done by converting raw scores to z scores (centering by mean and scaling by standard deviation). This part of the analyses was done with a wrapper function around the R code of PRSice v1.2528.