Exome-wide association studies discover germline mutation patterns and identify high-risk populations in human cancers

Genome-wide association studies have discovered numerous common variants associated with human cancers. However, the contribution of exome-wide rare variants to cancers remains largely unexplored, especially for the protein-coding variants. The UK Biobank provides detailed cancer follow-up information linked to whole-exome sequencing (WES) for approximately 450,000 participants, offering an unprecedented opportunity to evaluate the effect of exome variation on pan-cancer. Here, we performed exome-wide association studies (ExWAS) based on single variant levels and gene levels to detect their associations across 20 primary cancer types in the discovery set (WES-300k, N = 284,456) and replication set (WES-150k, N = 143,478), separately. The ExWAS detected 143 independent variants at variant-level and 49 genes at gene-level, while nine variants and eight genes were shared across cancers. In the cross-trait meta-analysis, we identified 239 additional independent pleiotropic variants, mapping to the genes which were functional through trans-omics analyses in transcriptomics and proteomics. Further, we developed exome-wide risk scores (ERS) to identify high-risk populations based on rare variants with minor allele frequency (MAF) < 0.05. The ERS had satisfactory performance in cancer risk stratification, especially for the extremely high-risk persons (top 5% ERS) that were frequently risk allele carriers. The ERS (median C-index (IQR): 0.655 (0.636-0.667)) outperforms the traditional polygenic risk score (PRS) (median C-index (IQR): 0.585 (0.572-0.614)) for discrimination in the replication set. Our findings offer further insight into the genetic architecture of human exomes for cancer susceptibility.