MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays

doi:10.1186/gb-2009-10-10-r105

Genome Biology

Volume 10
Issue 10

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Schüffler P
Mikeska T
Waha A
Lengauer T
Bock C

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Waha A
Lengauer T
Bock C
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MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays

Peter Schüffler¹ , Thomas Mikeska² , Andreas Waha³ , Thomas Lengauer¹ and Christoph Bock¹

¹Max-Planck-Institut für Informatik, Campus E1.4, 66123 Saarbrücken, Germany

²Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, A'Beckett Street, Melbourne, Victoria 8006, Australia

³Department of Neuropathology, University of Bonn Medical Centre, Sigmund-Freud-Straße, 53105 Bonn, Germany

author email corresponding author email

Genome Biology 2009, 10:R105doi:10.1186/gb-2009-10-10-r105


Published:	5 October 2009

Subject areas: Bioinformatics, Cancer, Medicine

Abstract

DNA methylation is a key mechanism of epigenetic regulation that is frequently altered in diseases such as cancer. To confirm the biological or clinical relevance of such changes, gene-specific DNA methylation changes need to be validated in multiple samples. We have developed the MethMarker http://methmarker.mpi-inf.mpg.de/ webcite software to help design robust and cost-efficient DNA methylation assays for six widely used methods. Furthermore, MethMarker implements a bioinformatic workflow for transforming disease-specific differentially methylated genomic regions into robust clinical biomarkers.