PT-meta applies PT to the meta-GWAS that combines all discovery summary statistics through an inverse-variance-weighted fixed-effect meta-analysis. We used the same clumping parameters and screened the same list of p-value thresholds as the PT method. The 1KG LD reference panel (EUR, EAS, AFR or AMR) that had matched ancestry with each of the discovery samples was in turn used for clumping, producing multiple sets of clumped variants. The best combination of the LD reference panel and the p-value threshold that maximized the R2 in the validation dataset was selected, and used in the independent testing dataset to calculate the final PRS and its performance metrics.
