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

abstract

• 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.

authors

• Suzuki, Masako

published proceedings

• Bioinformatics

altmetric score

• 7

author list (cited authors)

• Thompson, R. F., Suzuki, M., Lau, K. W., & Greally, J. M.

citation count

• 69

publication date

• September 2009

publisher

• Oxford University Press (OUP)  Publisher

keywords

• Animals
• Cell Line
• Computational Biology
• DNA Methylation
• Dinucleoside Phosphates
• Male
• Mass Spectrometry
• Mice
• Polymorphism, Single Nucleotide
• Rats
• Rats, Sprague-Dawley
• Reproducibility Of Results
• Sulfites

Digital Object Identifier (DOI)

• 10.1093/bioinformatics/btp382

start page

• 2164

end page

• 2170

volume

• 25

issue

• 17

URL

• http://dx.doi.org/10.1093/bioinformatics/btp382