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

Abstract

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.

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Acknowledgements

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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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). https://doi.org/10.1038/ng1834

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