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Bioinformatics Advance Access originally published online on June 26, 2009
Bioinformatics 2009 25(17):2164-2170; doi:10.1093/bioinformatics/btp382
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Reid F. Thompson 1, Masako Suzuki 1, Kevin W. Lau 1 and John M. Greally 1,2,*

1 Departments of Genetics and 2 Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA

* To whom correspondence should be addressed.


  Abstract

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{at}aecom.yu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: John Quackenbush

Received on April 6, 2009; revised on May 21, 2009; accepted on June 16, 2009

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