Journal Article

A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry

Reid F. Thompson, Masako Suzuki, Kevin W. Lau and John M. Greally

in Bioinformatics

Volume 25, issue 17, pages 2164-2170
Published in print September 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp382
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry

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Motivation: DNA cytosine methylation is an important epigenetic regulator, critical for mammalian development and the control of gene expression. Numerous techniques using either restriction enzyme or affinity-based approaches have been developed to interrogate cytosine methylation status genome-wide, however these assays must be validated by a more quantitative approach, such as MALDI-TOF mass spectrometry of bisulphite-converted DNA (commercialized as Sequenom's EpiTYPER assay using the MassArray system). Here, we present an R package (‘MassArray’) that assists in assay design and uses the standard Sequenom output file as the input to a pipeline of analyses not available as part of the commercial software. The tools in this package include bisulphite conversion efficiency calculation, sequence polymorphism flagging and visualization tools that combine multiple experimental replicates and create tracks for genome browser viewing.

Contact: jgreally@aecom.yu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  4940 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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