Fig. 1. Accuracy of 6 polygenic prediction methods in simulations using UK Biobank genotypes.

We report results for P + T, LDpred, P + T-funct-LASSO, AnnoPred, LDpred-funct-inf, and LDpred-funct in chromosome 1 simulations with 2000 causal variants (sparse architecture) and 5000 causal variants (polygenic architecture). Results are presented mean R² values averaged across 100 simulations. Bottom dashed lines denote differences vs. LDpred; error bars represent 95% confidence intervals. The top dashed line denotes simulated SNP-heritability of 0.5. Results for other values of the number of causal variants are reported in Supplementary Fig. 1, and numerical results are reported in Supplementary Tables 1 and 2. Source data are provided as a Source Data file.