Figure 3: Relative prediction accuracy for quantitative traits within each target population.

Relative prediction performance for single-discovery and multi-discovery PRS construction methods using discovery GWAS summary statistics a, from UKBB and BBJ, across 33 traits, in different UKBB target populations (EUR, EAS and AFR); b, from UKBB and BBJ, across 21 traits, in the Taiwan Biobank (TWB); c, from UKBB, BBJ and PAGE, across 14 traits, in different UKBB target populations (EUR, EAS and AFR). Each data point shows the relative increase of prediction performance, defined as R²/R²_{PRS-CS (UKBB)} - 1, in which R²_{PRS-CS (UKBB)} is the R² of the trait in the same target population using PRS-CS trained on the UKBB GWAS summary statistics. In UKBB target populations (panels a and c), R² was averaged across 100 random splits of the target samples into validation and testing datasets. The crossbar indicates the median of the relative increase of predictive performance across the traits examined. “median N” indicates the median sample size across the respective discovery GWAS. The trait MCHC was not included in the AFR panel because its R² from PRS-CS (UKBB) was almost 0, which inflated relative increase of prediction performance for other methods.