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

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

Research output: Contribution to journalArticle

62 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2164-2170
Number of pages7
JournalBioinformatics
Volume25
Issue number17
DOIs
StatePublished - Sep 14 2009
Externally publishedYes

Fingerprint

Methylation
Cytosine
Mass Spectrometry
Quantitative Analysis
Mass spectrometry
Assays
Genome
Pipelines
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
DNA Methylation
Polymorphism
Genes
Chemical analysis
Epigenomics
Regulator
Gene Expression
Affine transformation
Enzymes
Software
Visualization

ASJC Scopus subject areas

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. / Thompson, Reid; Suzuki, Masako; Lau, Kevin W.; Greally, John M.

In: Bioinformatics, Vol. 25, No. 17, 14.09.2009, p. 2164-2170.

Research output: Contribution to journalArticle

Thompson, Reid ; Suzuki, Masako ; Lau, Kevin W. ; Greally, John M. / A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. In: Bioinformatics. 2009 ; Vol. 25, No. 17. pp. 2164-2170.
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