We develop a new method, SBayesRC, that integrates GWAS summary statistics with functional genomic annotations to improve polygenic prediction of complex traits. Our method is scalable to whole-genome variant analysis and refines signals from functional annotations by allowing them to affect both causal variant probability and causal effect distribution. We analyse 28 traits in the UK Biobank using ~7 million common SNPs and 96 annotations. SBayesRC improves prediction accuracy by 14% in European ancestry and by up to 33% in trans-ancestry prediction, compared to the baseline method SBayesR which does not use annotations, and outperforms state-of-the-art methods LDpred-funct, PolyPred-S and PRS-CSx by 12-15%. Investigation of factors affecting prediction accuracy identified a significant interaction between SNP density and annotation information, encouraging future use of whole-genome sequence variants for prediction. Functional partitioning analysis highlights a major contribution of evolutionary constrained regions to prediction accuracy and the largest per-SNP contribution from non-synonymous SNPs.

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