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Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas

A Corrigendum to this article was published on 29 May 2013

This article has been updated


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 variants associated with susceptibility, POLE p.Leu424Val and POLD1 p.Ser478Asn, have high penetrance, and POLD1 mutation was also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases ɛ and δ and are predicted to cause a defect in the correction of mispaired bases inserted during DNA replication. In agreement with this prediction, the tumors from mutation carriers 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 mutations affecting the exonuclease domain.

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Figure 1: Pedigrees of the families with POLE L424V and POLD1 S478N in the discovery phase.
Figure 2: Modeling of the germline and exonuclease domain mutations.

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  • 08 May 2013

    In the version of this article initially published, the name of author Estrella Guarino was incorrectly listed as Estrella Guarino Almeida. The error has been corrected in the HTML and PDF versions of this article.


  1. Lunter, G. & Goodson, M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 21, 936–939 (2011).

    Article  CAS  Google Scholar 

  2. Kemp, Z. et al. Evidence for a colorectal cancer susceptibility locus on chromosome 3q21-q24 from a high-density SNP genome-wide linkage scan. Hum. Mol. Genet. 15, 2903–2910 (2006).

    Article  CAS  Google Scholar 

  3. Papaemmanuil, E. et al. Deciphering the genetics of hereditary non-syndromic colorectal cancer. Eur. J. Hum. Genet. 16, 1477–1486 (2008).

    Article  CAS  Google Scholar 

  4. Laurent-Puig, P., Béroud, C. & Soussi, T. APC gene: database of germline and somatic mutations in human tumors and cell lines. Nucleic Acids Res. 26, 269–270 (1998).

    Article  CAS  Google Scholar 

  5. Pursell, Z.F., Isoz, I., Lundstrom, E.B., Johansson, E. & Kunkel, T.A. Yeast DNA polymerase ɛ participates in leading-strand DNA replication. Science 317, 127–130 (2007).

    Article  CAS  Google Scholar 

  6. Swan, M.K., Johnson, R.E., Prakash, L., Prakash, S. & Aggarwal, A.K. Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase δ. Nat. Struct. Mol. Biol. 16, 979–986 (2009).

    Article  CAS  Google Scholar 

  7. Jin, Y.H., Ayyagari, R., Resnick, M.A., Gordenin, D.A. & Burgers, P.M. Okazaki fragment maturation in yeast. II. Cooperation between the polymerase and 3′-5′-exonuclease activities of Pol δ in the creation of a ligatable nick. J. Biol. Chem. 278, 1626–1633 (2003).

    Article  CAS  Google Scholar 

  8. Murphy, K., Darmawan, H., Schultz, A., Fidalgo da Silva, E. & Reha-Krantz, L.J. A method to select for mutator DNA polymerase deltas in Saccharomyces cerevisiae. Genome 49, 403–410 (2006).

    Article  CAS  Google Scholar 

  9. Burgers, P.M. Polymerase dynamics at the eukaryotic DNA replication fork. J. Biol. Chem. 284, 4041–4045 (2009).

    Article  CAS  Google Scholar 

  10. Hindges, R. & Hubscher, U. DNA polymerase δ, an essential enzyme for DNA transactions. Biol. Chem. 378, 345–362 (1997).

    Article  CAS  Google Scholar 

  11. Bellacosa, A. Functional interactions and signaling properties of mammalian DNA mismatch repair proteins. Cell Death Differ. 8, 1076–1092 (2001).

    Article  CAS  Google Scholar 

  12. Mitra, S., Boldogh, I., Izumi, T. & Hazra, T.K. Complexities of the DNA base excision repair pathway for repair of oxidative DNA damage. Environ. Mol. Mutagen. 38, 180–190 (2001).

    Article  CAS  Google Scholar 

  13. Fleck, O., Lehmann, E., Schar, P. & Kohli, J. Involvement of nucleotide-excision repair in msh2 pms1-independent mismatch repair. Nat. Genet. 21, 314–317 (1999).

    Article  CAS  Google Scholar 

  14. da Costa, L.T. et al. Polymerase δ variants in RER colorectal tumours. Nat. Genet. 9, 10–11 (1995).

    Article  CAS  Google Scholar 

  15. Flohr, T. et al. Detection of mutations in the DNA polymerase δ gene of human sporadic colorectal cancers and colon cancer cell lines. Int. J. Cancer 80, 919–929 (1999).

    Article  CAS  Google Scholar 

  16. Yoshida, R. et al. Concurrent genetic alterations in DNA polymerase proofreading and mismatch repair in human colorectal cancer. Eur. J. Hum. Genet. 19, 320–325 (2011).

    Article  Google Scholar 

  17. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).

  18. Seshagiri, S. et al. Recurrent R-spondin fusions in colon cancer. Nature 488, 660–664 (2012).

    Article  CAS  Google Scholar 

  19. Wang, L. et al. MYH mutations in patients with attenuated and classic polyposis and with young-onset colorectal cancer without polyps. Gastroenterology 127, 9–16 (2004).

    Article  CAS  Google Scholar 

  20. Lanspa, S.J. et al. Colorectal adenomas in the Lynch syndromes. Results of a colonoscopy screening program. Gastroenterology 98, 1117–1122 (1990).

    Article  CAS  Google Scholar 

  21. Wijnen, J. et al. Familial endometrial cancer in female carriers of MSH6 germline mutations. Nat. Genet. 23, 142–144 (1999).

    Article  CAS  Google Scholar 

  22. Dunlop, M.G. et al. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nat. Genet. 44, 770–776 (2012).

    Article  CAS  Google Scholar 

  23. Albertson, T.M. et al. DNA polymerase ɛ and δ proofreading suppress discrete mutator and cancer phenotypes in mice. Proc. Natl. Acad. Sci. USA 106, 17101–17104 (2009).

    Article  CAS  Google Scholar 

  24. Preston, B.D., Albertson, T.M. & Herr, A.J. DNA replication fidelity and cancer. Semin. Cancer Biol. 20, 281–293 (2010).

    Article  CAS  Google Scholar 

  25. Goldsby, R.E. et al. Defective DNA polymerase-δ proofreading causes cancer susceptibility in mice. Nat. Med. 7, 638–639 (2001).

    Article  CAS  Google Scholar 

  26. Goldsby, R.E. et al. High incidence of epithelial cancers in mice deficient for DNA polymerase δ proofreading. Proc. Natl. Acad. Sci. USA 99, 15560–15565 (2002).

    Article  CAS  Google Scholar 

  27. Venkatesan, R.N., Hsu, J.J., Lawrence, N.A., Preston, B.D. & Loeb, L.A. Mutator phenotypes caused by substitution at a conserved motif A residue in eukaryotic DNA polymerase δ. J. Biol. Chem. 281, 4486–4494 (2006).

    Article  CAS  Google Scholar 

  28. Venkatesan, R.N. et al. Mutation at the polymerase active site of mouse DNA polymerase δ increases genomic instability and accelerates tumorigenesis. Mol. Cell. Biol. 27, 7669–7682 (2007).

    Article  CAS  Google Scholar 

  29. Jones, A.M. et al. Analysis of copy number changes suggests chromosomal instability in a minority of large colorectal adenomas. J. Pathol. 213, 249–256 (2007).

    Article  CAS  Google Scholar 

  30. Tomlinson, I. et al. A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat. Genet. 39, 984–988 (2007).

    Article  CAS  Google Scholar 

  31. Penegar, S. et al. National study of colorectal cancer genetics. Br. J. Cancer 97, 1305–1309 (2007).

    Article  CAS  Google Scholar 

  32. Drmanac, R. et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327, 78–81 (2010).

    Article  CAS  Google Scholar 

  33. Pendlebury, S., Duchesne, F., Reed, K.A., Smith, J.L. & Kerr, D.J. A trial of adjuvant therapy in colorectal cancer: the VICTOR trial. Clin. Colorectal Cancer 3, 58–60 (2003).

    Article  Google Scholar 

  34. Power, C. & Elliott, J. Cohort profile: 1958 British birth cohort (National Child Development Study). Int. J. Epidemiol. 35, 34–41 (2006).

    Article  Google Scholar 

  35. Ouwehand, W.H. Platelet genomics and the risk of atherothrombosis. J. Thromb. Haemost. 5 (suppl. 1), 188–195 (2007).

    Article  CAS  Google Scholar 

  36. Spurdle, A.B. et al. Genome-wide association study identifies a common variant associated with risk of endometrial cancer. Nat. Genet. 43, 451–454 (2011).

    Article  CAS  Google Scholar 

  37. Cuppen, E. Genotyping by Allele-Specific Amplification (KASPar). CSH Protoc. 2007, pdb.prot4841 (2007).

    Google Scholar 

  38. Moreno, S., Klar, A. & Nurse, P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 194, 795–823 (1991).

    Article  CAS  Google Scholar 

  39. Bähler, J. et al. Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe. Yeast 14, 943–951 (1998).

    Article  Google Scholar 

  40. Marti, T.M., Mansour, A.A., Lehmann, E. & Fleck, O. Different frameshift mutation spectra in non-repetitive DNA of MutSα- and MutLα-deficient fission yeast cells. DNA Repair (Amst.) 2, 571–580 (2003).

    Article  CAS  Google Scholar 

  41. Hall, B.M., Ma, C.X., Liang, P. & Singh, K.K. Fluctuation analysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis. Bioinformatics 25, 1564–1565 (2009).

    Article  CAS  Google Scholar 

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We are grateful to all the affected individuals and their relatives in the families studied and to those who have provided their medical care. We acknowledge the help of many colleagues who are part of the teams who work on the CORGI study. We acknowledge the use of DNA from the British 1958 Birth Cohort collection. This work was principally funded by Cancer Research UK (C6199/A10417) and the Oxford NIHR Comprehensive Biomedical Research Centre (to I.T.). We also acknowledge core funding to the Wellcome Trust Centre for Human Genetics from the Wellcome Trust (090532/Z/09/Z). Work in the laboratory of R.S.H. is supported by funding from Cancer Research UK (C1298/A8362, supported by the Bobby Moore Fund). Work in the laboratory of S.E.K. was supported by project grants from Cancer Research UK and the John Fell Oxford University Press (OUP) Research Fund. We thank O. Fleck (University of Copenhagen) for fission yeast strains. I.S. is supported by a fellowship from the Junta de Extremadura, Spain (Consejería de Economía, Comercio e Innovación). R.S.H. and I.T. acknowledge funding from the European Union Seventh Framework Programme (FP7/207-2013) under grant 258236, FP7 collaborative project SYSCOL.

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C. Palles, K.M.H., E.D., A.M.J., P.B., A.S., D.C., Z.K., S.L.S., C. Petridis, E.J.S., L.G.C.-C., Y.M., K.K., S.D., E.G., I.S. and S.H. performed laboratory experiments and/or analyzed the data. J.-B.C. analyzed whole-genome sequencing data, with assistance from M.B.K., and supervised other bioinformatics data analysis. J.T., S.E.K. and I.T. supervised laboratory experiments. G.M., P.D. and D.B. oversaw WGS500 analysis, and C.C.H. provided additional statistical advice. L.M., E.B., M.G., A.L., C. Petridis, R.R., E.J.S., D.J.K., S.C., H.J.W.T., R.S.H. and I.T. obtained samples. J.G. undertook structural analysis. R.S.H. and I.T. provided sequencing data and oversaw the study. I.T. wrote the manuscript.

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Correspondence to Ian Tomlinson.

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A list of contributing members is provided at the end of the manuscript

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Palles, C., Cazier, JB., Howarth, K. et al. Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat Genet 45, 136–144 (2013).

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