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

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 calculat

SUBMITTER: Thompson RF 

PROVIDER: S-EPMC2800352 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature