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Daniel J. Weisenberger

Mihaela Campan

Tiffany I. Long

Peter W. Laird

Determination of the CpG Island Methylator Phenotype \(CIMP) in colorectal cancer using MethyLight

MethyLight is a sensitive, quantitative, TaqMan-based, real-time PCR assay for measuring DNA methylation profiles. The MethyLight-based data is presented as a percentage relative to an M.SssI-treated methylated DNA reference sample \(PMR). We have extended the applicability of MethyLight technology to assay for the presence of the CpG island methylator phenotype \(CIMP) in human colorectal cancer. We provide here a detailed, step-by-step protocol of the MethyLight assay for detection of CIMP with high sensitivity and specificity in colorectal cancer using a five marker panel composed of CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1. Our criteria state that a sample with &#x2265;3 of five markers posititve for methylation \(PMR&gt;10) is CIMP positive \(CIMP+), while a sample with &#x2264;2 of the five markers positive for methylation is considered CIMP negative \(CIMP-).

Eads, C.A., Danenberg, K.D., Kawakami, K. Saltz, L.B. Danenberg, P.V., Laird, P.W. CpG Island Hypermethylation in Human Colorectal Tumors is Not Associated with DNA Methyltransferase Overexpression. _Cancer Res_ **59**, 2302-2306 \(1999).





Eads, C.A., Danenberg, K.D., Kawakami, K., Saltz, L.B., Blake C., Shibata, D., Danenberg, P.V, and Laird, P.W. MethyLight: a high-throughput assay to measure DNA methylation. _Nucleic Acids Res_ **28**, e32 \(2000).





Eads, C.A., Lord, R.V., Wickramasinghe, K., Long, T.I., Kurumboor, S.K., Bernstein, L., Peters, J.H., DeMeester, T.R., Skinner, K.A., and Laird, P.W. Epigenetic Patterns in the Progression of Esophageal Adenocarcinoma. _Cancer Res_ **61**,3410-3418 \(2001).





Siegmund, K.D. and Laird, P.W. Analysis of Complex Methylation Data. _Methods_ **27**,170-178 \(2002).





Weisenberger, D.J., Campan, M., Long, T.I., Kim, M.K., Woods, C., Fiala, E., Ehrlich, M. and Laird, P.W. Analysis of repetitive elements DNA methylation by MethyLight. _Nucleic Acids Res_ **33**,6823-6836 \(2005).

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Determination of the CpG Island Methylator Phenotype (CIMP) in colorectal cancer using MethyLight

Genetics

Method Article

Daniel J. Weisenberger, Mihaela Campan, Tiffany I. Long, Peter W. Laird

Daniel J. Weisenberger

University of Southern California

Mihaela Campan

University of Southern California

Tiffany I. Long

University of Southern California

Peter W. Laird

University of Southern California

DOI:

10.1038/nprot.2006.152

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

by Weisenberger, D.J. et al.

Nature Genetics (06 June, 2006)

Method Article

Daniel J. Weisenberger, Mihaela Campan, Tiffany I. Long, Peter W. Laird

Daniel J. Weisenberger

University of Southern California

Mihaela Campan

University of Southern California

Tiffany I. Long

University of Southern California

Peter W. Laird

University of Southern California

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DOI:

10.1038/nprot.2006.152

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

by Weisenberger, D.J. et al.

Nature Genetics (06 June, 2006)

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