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Nucleic Acids Research Advance Access originally published online on May 14, 2008
Nucleic Acids Research 2008 36(11):e64; doi:10.1093/nar/gkn210
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Nucleic Acids Research, 2008, Vol. 36, No. 11 e64
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms

Tatiana I. Leakey1, Jerzy Zielinski1,2,5, Rachel N. Siegfried1, Eric R. Siegel3, Chun-Yang Fan4,5 and Craig A. Cooney1,5,*

1Department of Biochemistry and Molecular Biology, 2Department of Geriatrics, 3Department of Biostatistics, 4Department of Pathology, The University of Arkansas for Medical Sciences and 5Central Arkansas Veterans Health Care Systems, Little Rock AR, USA

*To whom correspondence should be addressed. Tel: +501 960 0900; Fax: +501 686 8169; Email: CooneyCraigA{at}uams.edu

Received March 21, 2008. Revised April 7, 2008. Accepted April 8, 2008.

DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.


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