A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry.
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.
Thompson
Reid F
RF
Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
Suzuki
Masako
M
Lau
Kevin W
KW
Greally
John M
JM
D000818:Animals; D002460:Cell Line; D019295:Computational Biology; D019175:DNA Methylation / Q000235:genetics*; D015226:Dinucleoside Phosphates / Q000235:genetics*; D008297:Male; D013058:Mass Spectrometry / Q000379:methods*; D051379:Mice; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D051381:Rats; D017207:Rats, Sprague-Dawley; D015203:Reproducibility of Results; D013447:Sulfites
D015226:Dinucleoside Phosphates; D013447:Sulfites; C015772:CpG dinucleotide; C042345:hydrogen sulfite