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. Author manuscript; available in PMC: 2022 Oct 7.
Published in final edited form as: Nat Genet. 2022 Apr 7;54(4):450–458. doi: 10.1038/s41588-022-01036-9

Extended Data Fig. 1. Cross-population PRS results for real UK Biobank traits, using summary statistics from a meta-analysis of many cohorts.

Extended Data Fig. 1

We report average prediction accuracy (relative-R2, but computed with respect to PRS-CS instead of BOLT-LMM; see main text), meta-analyzed across 4 well-powered, approximately independent traits, for PRS trained in European Network for Genetic and Genomic Epidemiology (ENGAGE) samples (average N=61,365) and applied to 4 UK Biobank populations. Target population sample sizes are indicated in parentheses; PolyPred and its summary statistic-based analogues used 500 additional training samples from each target population to estimate mixing weights. Asterisks above each bar denote statistical significance of the difference vs. PRS-CS, with red asterisks denoting a disadvantage (*P<0.05; **P<0.001). P-values were computed using a two-sided Wald test and were not adjusted for multiple comparisons. Errors bars denote standard errors. Numerical results, results for all 4 traits analyzed, absolute prediction accuracies (R2), and P-values of relative improvements vs. PRS-CS are reported in Supplementary Table 5 and Supplementary Table 8.