Clinical Chemistry
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Clinical Chemistry 55: 1471-1483, 2009. First published June 11, 2009; 10.1373/clinchem.2008.121962
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(Clinical Chemistry. 2009;55:1471-1483.)
© 2009 American Association for Clinical Chemistry, Inc.

Review

PCR-Based Methods for Detecting Single-Locus DNA Methylation Biomarkers in Cancer Diagnostics, Prognostics, and Response to Treatment

Lasse Sommer Kristensen1,a and Lise Lotte Hansen1

1 Institute of Human Genetics, University of Aarhus, Aarhus, Denmark.

aAddress correspondence to this author at: Institute of Human Genetics, University of Aarhus, Wilhelm Meyers Allé, Bygn. 1242, Universitetsparken, Aarhus C, 8000, Denmark. Fax +45-86-12-31-73; e-mail lasse{at}humgen.au.dk.

Background: DNA methylation is a highly characterized epigenetic modification of the human genome that is implicated in cancer. The altered DNA methylation patterns found in cancer cells include not only global hypomethylation but also discrete hypermethylation of specific genes. In particular, numerous tumor suppressor genes undergo epigenetic silencing because of hypermethylated promoter regions. Some of these genes are considered promising DNA methylation biomarkers for early cancer diagnostics, and some have been shown to be valuable for predicting prognosis or the response to therapy.

Content: PCR-based methods that use sodium bisulfite–treated DNA as a template are generally accepted as the most analytically sensitive and specific techniques for analyzing DNA methylation at single loci. A number of new methods, such as methylation-specific fluorescent amplicon generation (MS-FLAG), methylation-sensitive high-resolution melting (MS-HRM), and sensitive melting analysis after real-time methylation-specific PCR (SMART-MSP), now complement the traditional PCR-based methods and promise to be valuable diagnostic tools. In particular, the HRM technique shows great potential as a diagnostic tool because of its closed-tube format and cost-effectiveness.

Summary: Numerous traditional and new PCR-based methods have been developed for detecting DNA methylation at single loci. All have characteristic advantages and disadvantages, particularly with regard to use in clinical settings.






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Copyright © 2009 by the American Association for Clinical Chemistry.