Germline mutations in the proofreading domains of POLE and POLD 1 predispose to colorectal adenomas and carcinomas

Many individuals with multiple or large colorectal adenomas, or early-onset colorectal cancer (CRC), have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple adenoma and/or CRC cases, but in no controls. The susceptibility variants appear to have high penetrance. POLD1 is also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proof-reading (exonuclease) domain of DNA polymerases ε and δ, and are predicted to impair correction of mispaired bases inserted during DNA replication. In agreement with this prediction, mutation carriers’ tumours were microsatellite-stable, but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently-described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE exonuclease domain mutations. Europe PMC Funders Group Author Manuscript Nat Genet. Author manuscript; available in PMC 2013 September 27. Published in final edited form as: Nat Genet. 2013 February ; 45(2): 136–144. doi:10.1038/ng.2503. E uope PM C Fuders A uhor M ancripts E uope PM C Fuders A uhor M ancripts Mutations in at least 10 genes are responsible for Mendelian syndromes associated with colorectal cancer. For some of these genes (APC and MUTYH), the primary predisposition is to multiple adenomas, the benign precursors of many colorectal cancers (CRCs). For other genes (STK11/LKB1, SMAD4, BMPR1A and GREM1), CRC risk is mediated through the development of hamartomas or mixed polyps; and for yet other genes (MSH2, MLH1, MSH6 and PMS2), there is usually no great number of polyps and early-onset CRC or endometrial cancer is the usual presentation. The functions of these 10 genes vary, although it is notable that four encode (MSH2, MLH1, MSH6 and PMS2) encode DNA mismatch repair proteins and a fifth (MUTYH) codes for a glycolsylase that effects base excision repair (MUTYH). There exists a set of patients who appear a priori to have a strong chance of carrying a high-penetrance CRC predisposition allele, but who have no mutations in these genes. One such group of patients is characterised by multiple adenomas, typically 10-100 in number, often presenting before the age of 60 and frequently progressing to CRC unless treated. Some of these individuals come from extensive CRC pedigrees, but many have no significant family history of colorectal tumours. As part of the Oxford-Illumina WGS500 project, we undertook whole-genome sequencing (WGS) of 15 probands who had been diagnosed with at least 10 colorectal adenomas by 60 years of age (Supplementary Table 1). For three probands, a relative with more than 5 adenomas was also sequenced, and for one proband two additional affected relatives were sequenced. Eight of the 20 sequenced individuals had developed colorectal carcinoma (CRC) and all of the remainder had a first-degree relative with CRC. Known Mendelian cancer syndromes had reportedly been excluded previously in the clinical diagnostic setting, by mutation screening for APC, MUTYH and the mismatch repair genes, together with microsatellite instability (MSI) testing and immunohistochemistry for mismatch repair proteins in some cases. The pedigrees of the 15 families showed a degree of heterogeneity in their phenotypes and patterns of inheritance, and we anticipated that this might reflect underlying genetic heterogeneity.