Literature DB >> 19804638

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

Peter Schüffler1, Thomas Mikeska, Andreas Waha, Thomas Lengauer, Christoph Bock.   

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/ 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.

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Year:  2009        PMID： 19804638      PMCID： PMC2784320          DOI： 10.1186/gb-2009-10-10-r105

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  34 in total

1.  BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.

Authors:  Christoph Bock; Sabine Reither; Thomas Mikeska; Martina Paulsen; Jörn Walter; Thomas Lengauer
Journal:  Bioinformatics       Date:  2005-09-01       Impact factor: 6.937

Review 2.  Computational epigenetics.

Authors:  Christoph Bock; Thomas Lengauer
Journal:  Bioinformatics       Date:  2007-11-17       Impact factor: 6.937

Review 3.  Epigenetics in cancer.

Authors:  Manel Esteller
Journal:  N Engl J Med       Date:  2008-03-13       Impact factor: 91.245

4.  A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

Authors:  Daniel Blankenberg; James Taylor; Ian Schenck; Jianbin He; Yi Zhang; Matthew Ghent; Narayanan Veeraraghavan; Istvan Albert; Webb Miller; Kateryna D Makova; Ross C Hardison; Anton Nekrutenko
Journal:  Genome Res       Date:  2007-06       Impact factor: 9.043

5.  Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry.

Authors:  Mathias Ehrich; Matthew R Nelson; Patrick Stanssens; Marc Zabeau; Triantafillos Liloglou; George Xinarianos; Charles R Cantor; John K Field; Dirk van den Boom
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-21       Impact factor: 11.205

Review 6.  MGMT hypermethylation: a prognostic foe, a predictive friend.

Authors:  Filipe V Jacinto; Manel Esteller
Journal:  DNA Repair (Amst)       Date:  2007-05-07

Review 7.  Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction?

Authors:  Stephen B Baylin; Joyce E Ohm
Journal:  Nat Rev Cancer       Date:  2006-02       Impact factor: 60.716

8.  Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis.

Authors:  Thomas Mikeska; Christoph Bock; Osman El-Maarri; Anika Hübner; Denise Ehrentraut; Johannes Schramm; Jörg Felsberg; Philip Kahl; Reinhard Büttner; Torsten Pietsch; Andreas Waha
Journal:  J Mol Diagn       Date:  2007-07       Impact factor: 5.568

9.  CpG island mapping by epigenome prediction.

Authors:  Christoph Bock; Jörn Walter; Martina Paulsen; Thomas Lengauer
Journal:  PLoS Comput Biol       Date:  2007-05-02       Impact factor: 4.475

10.  The UCSC Genome Browser Database: 2008 update.

Authors:  D Karolchik; R M Kuhn; R Baertsch; G P Barber; H Clawson; M Diekhans; B Giardine; R A Harte; A S Hinrichs; F Hsu; K M Kober; W Miller; J S Pedersen; A Pohl; B J Raney; B Rhead; K R Rosenbloom; K E Smith; M Stanke; A Thakkapallayil; H Trumbower; T Wang; A S Zweig; D Haussler; W J Kent
Journal:  Nucleic Acids Res       Date:  2007-12-17       Impact factor: 16.971
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  6 in total

Review 1.  Analysing and interpreting DNA methylation data.

Authors:  Christoph Bock
Journal:  Nat Rev Genet       Date:  2012-10       Impact factor: 53.242

2.  Bi-PROF: bisulfite profiling of target regions using 454 GS FLX Titanium technology.

Authors:  Jasmin Gries; Dirk Schumacher; Julia Arand; Pavlo Lutsik; Maria Rivera Markelova; Iduna Fichtner; Jörn Walter; Christine Sers; Sascha Tierling
Journal:  Epigenetics       Date:  2013-06-10       Impact factor: 4.528

3.  BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.

Authors:  Pavlo Lutsik; Lars Feuerbach; Julia Arand; Thomas Lengauer; Jörn Walter; Christoph Bock
Journal:  Nucleic Acids Res       Date:  2011-05-11       Impact factor: 16.971

4.  Heterogeneous DNA Methylation Patterns in the GSTP1 Promoter Lead to Discordant Results between Assay Technologies and Impede Its Implementation as Epigenetic Biomarkers in Breast Cancer.

Authors:  Grethe I Grenaker Alnaes; Jo Anders Ronneberg; Vessela N Kristensen; Jörg Tost
Journal:  Genes (Basel)       Date:  2015-09-17       Impact factor: 4.096

5.  MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics.

Authors:  Ram Vinay Pandey; Walter Pulverer; Rainer Kallmeyer; Gabriel Beikircher; Stephan Pabinger; Albert Kriegner; Andreas Weinhäusel
Journal:  Clin Epigenetics       Date:  2016-09-21       Impact factor: 6.551

6.  BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.

Authors:  Daniel Becker; Pavlo Lutsik; Peter Ebert; Christoph Bock; Thomas Lengauer; Jörn Walter
Journal:  Nucleic Acids Res       Date:  2014-05-29       Impact factor: 16.971
  6 in total

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