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CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer


Aberrant DNA methylation of CpG islands has been widely observed in human colorectal tumors and is associated with gene silencing when it occurs in promoter areas. A subset of colorectal tumors has an exceptionally high frequency of methylation of some CpG islands, leading to the suggestion of a distinct trait referred to as 'CpG island methylator phenotype', or 'CIMP'1,2. However, the existence of CIMP has been challenged3,4. To resolve this continuing controversy, we conducted a systematic, stepwise screen of 195 CpG island methylation markers using MethyLight technology, involving 295 primary human colorectal tumors and 16,785 separate quantitative analyses. We found that CIMP-positive (CIMP+) tumors convincingly represent a distinct subset, encompassing almost all cases of tumors with BRAFmutation (odds ratio = 203). Sporadic cases of mismatch repair deficiency occur almost exclusively as a consequence of CIMP-associated methylation of MLH1. We propose a robust new marker panel to classify CIMP+ tumors.

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Figure 1: Identification of Type C methylation markers.
Figure 2: Identification of tumor clusters.
Figure 3: Independent test of 14 methylation markers.
Figure 4: Comparison of CIMP panel performance.
Figure 5: Final independent test of CIMP panels.


  1. 1

    Toyota, M. et al. CpG island methylator phenotype in colorectal cancer. Proc. Natl. Acad. Sci. USA 96, 8681–8686 (1999).

    CAS  Article  Google Scholar 

  2. 2

    Issa, J.P. CpG island methylator phenotype in cancer. Nat. Rev. Cancer 4, 988–993 (2004).

    CAS  Article  Google Scholar 

  3. 3

    Yamashita, K., Dai, T., Dai, Y., Yamamoto, F. & Perucho, M. Genetics supersedes epigenetics in colon cancer phenotype. Cancer Cell 4, 121–131 (2003).

    CAS  Article  Google Scholar 

  4. 4

    Anacleto, C. et al. Colorectal cancer “methylator phenotype”: fact or artifact? Neoplasia 7, 331–335 (2005).

    CAS  Article  Google Scholar 

  5. 5

    Samowitz, W.S. et al. Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer. Gastroenterology 129, 837–845 (2005).

    CAS  Article  Google Scholar 

  6. 6

    Laird, P.W. Cancer epigenetics. Hum. Mol. Genet. 14 Spec No 1, R65–76 (2005).

    CAS  Article  Google Scholar 

  7. 7

    Kaufman, L. & Rousseeuw, P.J. Finding Groups in Data: an Introduction to Cluster Analysis (Wiley Interscience, New York, 1990).

    Book  Google Scholar 

  8. 8

    McLachlan, G. & Peel, D. Finite Mixture Models (John Wiley & Sons, New York, 2000).

  9. 9

    Kambara, T. et al. BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum. Gut 53, 1137–1144 (2004).

    CAS  Article  Google Scholar 

  10. 10

    Toyota, M., Ohe-Toyota, M., Ahuja, N. & Issa, J.P. Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype. Proc. Natl. Acad. Sci. USA 97, 710–715 (2000).

    CAS  Article  Google Scholar 

  11. 11

    Bakin, A.V. & Curran, T. Role of DNA 5-methylcytosine transferase in cell transformation by fos. Science 283, 387–390 (1999).

    CAS  Article  Google Scholar 

  12. 12

    Ordway, J.M., Williams, K. & Curran, T. Transcription repression in oncogenic transformation: common targets of epigenetic repression in cells transformed by Fos, Ras or Dnmt1. Oncogene 23, 3737–3748 (2004).

    CAS  Article  Google Scholar 

  13. 13

    Miller, S.A., Dykes, D.D. & Polesky, H.F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16, 1215 (1988).

    CAS  Article  Google Scholar 

  14. 14

    Whitehall, V.L. et al. Morphological and molecular heterogeneity within nonmicrosatellite instability-high colorectal cancer. Cancer Res. 62, 6011–6014 (2002).

    CAS  Google Scholar 

  15. 15

    Wellbrock, C., Karasarides, M. & Marais, R. The RAF proteins take centre stage. Nat. Rev. Mol. Cell Biol. 5, 875–885 (2004).

    CAS  Article  Google Scholar 

  16. 16

    Young, J. et al. Evidence for BRAF mutation and variable levels of microsatellite instability in a syndrome of familial colorectal cancer. Clin. Gastroenterol. Hepatol. 3, 254–263 (2005).

    CAS  Article  Google Scholar 

  17. 17

    Young, J. et al. Features of colorectal cancers with high-level microsatellite instability occurring in familial and sporadic settings: parallel pathways of tumorigenesis. Am. J. Pathol. 159, 2107–2116 (2001).

    CAS  Article  Google Scholar 

  18. 18

    Weisenberger, D.J. et al. Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res. 33, 6823–6836 (2005).

    CAS  Article  Google Scholar 

  19. 19

    Eads, C.A. et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 28, E32 (2000).

    CAS  Article  Google Scholar 

  20. 20

    Eads, C.A. et al. Epigenetic patterns in the progression of esophageal adenocarcinoma. Cancer Res. 61, 3410–3418 (2001).

    CAS  Google Scholar 

  21. 21

    Widschwendter, M. et al. Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen. Cancer Res. 64, 3807–3813 (2004).

    CAS  Article  Google Scholar 

  22. 22

    Breiman, L., Friedman, J.H., Olshen, R.A. & Stone, C.J. Classification and Regression Trees 1st edn. (Wadsworth, Belmont, California, 1984).

  23. 23

    Hastie, T. et al. 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol. 1, RESEARCH0003.1–RESEARCH0003.21 (2000).

    Article  Google Scholar 

  24. 24

    Herman, J.G., Graff, J.R., Myohanen, S., Nelkin, B.D. & Baylin, S.B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93, 9821–9826 (1996).

    CAS  Article  Google Scholar 

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The work described in this manuscript was supported by US National Institutes of Health grant R01 CA075090 awarded to P.W.L.

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Corresponding author

Correspondence to Peter W Laird.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Figure 1

Methylation-specific PCR of the New CIMP Panel on CIMP+ and CIMP− colon tumor DNA samples. (PDF 318 kb)

Supplementary Table 1

MethyLight reaction details. (PDF 265 kb)

Supplementary Table 2

New CIMP Classification Panel. (PDF 46 kb)

Supplementary Table 3

Cross-panel classification error rates among various CIMP classification panels, expressed as percentages. (PDF 35 kb)

Supplementary Table 4

Methylation frequency by KRAS and BRAF status. (PDF 44 kb)

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Weisenberger, D., Siegmund, K., Campan, M. et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 38, 787–793 (2006).

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