Design, measurement and processing of region-specific DNA methylation assays: the mass spectrometry-based method EpiTYPER

EpiTYPER® is a mass spectrometry-based bisulfite sequencing method that enables region-specific DNA methylation analysis in a quantitative and high-throughput fashion. The technology targets genomic regions of 100-600 base pairs and results in the quantitative measurement of DNA methylation levels l...

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Bibliographic Details
Published inFrontiers in genetics Vol. 6; p. 287
Main Authors Suchiman, H. Eka D., Slieker, Roderick C., Kremer, Dennis, Slagboom, P. Eline, Heijmans, Bastiaan T., Tobi, Elmar W.
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media S.A 17.09.2015
Subjects
Data handling
DNA Methylation
Genetics
MALDI-TOF MS
Mass Spectrometry
protocol
Quality control
DNA methylation
mass spectrometry
region-specific
EpiTYPER
bisulfite
quantitative
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Summary:EpiTYPER® is a mass spectrometry-based bisulfite sequencing method that enables region-specific DNA methylation analysis in a quantitative and high-throughput fashion. The technology targets genomic regions of 100-600 base pairs and results in the quantitative measurement of DNA methylation levels largely at single-nucleotide resolution. It is particularly suitable for larger scale efforts to study candidate regions or to validate regions from genome-wide DNA methylation studies. Here, we describe in detail how to design and perform EpiTYPER measurements and preprocess the data, providing details for high quality measurements not provided in the standard EpiTYPER protocol.
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Reviewed by: Simonetta Friso, University of Verona School of Medicine, Italy; Jorg Tost, Commissariat à l'Energie Atomique, Institut de Génomique, France
Edited by: Krassimir Yankulov, University of Guelph, Canada
This article was submitted to Epigenomics and Epigenetics, a section of the journal Frontiers in Genetics
These authors have contributed equally to this work.
ISSN:1664-8021
1664-8021
DOI:10.3389/fgene.2015.00287