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

Genome Biology

Volumn 10, Issue 10, 2009, Pages

  Schüffler, Peter ^a   Mikeska, Thomas ^b   Waha, Andreas ^c   Lengauer, Thomas ^a   Bock, Christoph ^a  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^b PETER MACCALLUM CANCER CENTRE   (Australia)

^c UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; DNA METHYLTRANSFERASE; MGMT PROTEIN, HUMAN; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; TUMOR SUPPRESSOR PROTEIN;

ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA DETERMINATION; DNA METHYLATION; DNA SEQUENCE; WEB BROWSER; BIOASSAY; GENETICS; HUMAN; METABOLISM; METHODOLOGY; REPRODUCIBILITY;

BIOLOGICAL ASSAY; BIOLOGICAL MARKERS; DNA METHYLATION; DNA MODIFICATION METHYLASES; DNA REPAIR ENZYMES; HUMANS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SOFTWARE; SOFTWARE DESIGN; TUMOR SUPPRESSOR PROTEINS;

EID: 75349090090     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-10-r105     Document Type: Article

References (37)

1. Laird PW. Cancer epigenetics. Hum Mol Genet 2005, 14(Spec No 1):R65-76. 10.1093/hmg/ddi113, 15809275.
2. Esteller M. Epigenetics in cancer. N Engl J Med 2008, 358:1148-1159. 10.1056/NEJMra072067, 18337604.
3. Bock C, Walter J, Paulsen M, Lengauer T. CpG island mapping by epigenome prediction. PLoS Comput Biol 2007, 3:e110. 10.1371/journal.pcbi.0030110, 1892605,1892605, 17559301.
4. Baylin SB, Ohm JE. Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction?. Nat Rev Cancer 2006, 6:107-116. 10.1038/nrc1799, 16491070.
5. Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer 2003, 3:253-266. 10.1038/nrc1045, 12671664.
6. Teodoridis JM, Strathdee G, Brown R. Epigenetic silencing mediated by CpG island methylation: potential as a therapeutic target and as a biomarker. Drug Resist Updat 2004, 7:267-278. 10.1016/j.drup.2004.06.005, 15533764.
7. Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet 2006, 7:21-33. 10.1038/nrg1748, 16369569.
8. Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, Danenberg PV, Laird PW. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 2000, 28:E32. 10.1093/nar/28.8.e32, 102836, 10734209.
9. Uhlmann K, Brinckmann A, Toliat MR, Ritter H, Nurnberg P. Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis. Electrophoresis 2002, 23:4072-4079. 10.1002/elps.200290023, 12481262.
10. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R. Sensitive and quantitative universal pyrosequencing methylation analysis of CpG sites. Biotechniques 2003, 35:146-150.
11. Tost J, Dunker J, Gut IG. Analysis and quantification of multiple methylation variable positions in CpG islands by pyrosequencing. Biotechniques 2003, 35:152-156.
12. Xiong Z, Laird PW. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 1997, 25:2532-2534. 10.1093/nar/25.12.2532, 146738, 9171110.
13. El-Maarri O, Herbiniaux U, Walter J, Oldenburg J. A rapid, quantitative, non-radioactive bisulfite-SNuPE-IP RP HPLC assay for methylation analysis at specific CpG sites. Nucleic Acids Res 2002, 30:e25. 10.1093/nar/30.6.e25, 101369, 11884644.
14. Gonzalgo ML, Jones PA. Quantitative methylation analysis using methylation-sensitive single-nucleotide primer extension (Ms-SNuPE). Methods 2002, 27:128-133. 10.1016/S1046-2023(02)00064-6, 12095270.
15. Mikeska T, Bock C, El-Maarri O, Hübner A, Ehrentraut D, Schramm J, Felsberg J, Kahl P, Büttner R, Pietsch T, Waha A. Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis. J Mol Diagn 2007, 9:368-381. 10.2353/jmoldx.2007.060167, 1899414, 17591937.
16. Bock C. Epigenetic biomarker development. Epigenomics 2009, 1:99-110.
17. Bock C, Lengauer T. Computational epigenetics. Bioinformatics 2008, 24:1-10. 10.1093/bioinformatics/btm546, 18024971.
18. Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res 2007, 17:960-964. 10.1101/gr.5578007, 1891355, 17568012.
19. Bock C, Halachev K, Büch J, Lengauer T. EpiGRAPH: User-friendly software for statistical analysis and prediction of (epi-) genomic data. Genome Biol 2009, 10:R14. 10.1186/gb-2009-10-2-r14, 2688269, 19208250.
20. Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 2005, 21:4067-4068. 10.1093/bioinformatics/bti652, 16141249.
21. Kumaki Y, Oda M, Okano M. QUMA: quantification tool for methylation analysis. Nucleic Acids Res 2008, (36 Web Server):W170-175. 10.1093/nar/gkn294, 2447804, 18487274.
22. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G, Cantor CR, Field JK, Boom D. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci USA 2005, 102:15785-15790. 10.1073/pnas.0507816102, 1276092, 16243968.
23. PMML Version 3.2. , http://www.dmg.org/pmml-v3-2.html
24. Gerson SL. MGMT: its role in cancer aetiology and cancer therapeutics. Nat Rev Cancer 2004, 4:296-307. 10.1038/nrc1319, 15057289.
25. Jacinto FV, Esteller M. MGMT hypermethylation: a prognostic foe, a predictive friend. DNA Repair (Amst) 2007, 6:1155-1160. 10.1016/j.dnarep.2007.03.013, 17482895.
26. Iafrate AJ, Louis DN. "MGMT for pt mgmt": is methylguanine-DNA methyltransferase testing ready for patient management?. J Mol Diagn 2008, 10:308-310. 10.2353/jmoldx.2008.080043, 2438198, 18556768.
27. Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 2008, 36:D773-779. 10.1093/nar/gkm966, 2238835, 18086701.
28. Methyl Primer Express. , http://docs.appliedbiosystems.com/pebiodocs/04370961.pdf
29. Bisulfite sequencing of small DNA/cell samples (PROT35). , http://www.epigenome-noe.net/researchtools/protocol.php?protid=35
30. Hegi ME, Diserens AC, Gorlia T, Hamou MF, de Tribolet N, Weller M, Kros JM, Hainfellner JA, Mason W, Mariani L, Bromberg JE, Hau P, Mirimanoff RO, Cairncross JG, Janzer RC, Stupp R. MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med 2005, 352:997-1003. 10.1056/NEJMoa043331, 15758010.
31. Esteller M, Garcia-Foncillas J, Andion E, Goodman SN, Hidalgo OF, Vanaclocha V, Baylin SB, Herman JG. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 2000, 343:1350-1354. 10.1056/NEJM200011093431901, 11070098.
32. Hegi ME, Diserens AC, Godard S, Dietrich PY, Regli L, Ostermann S, Otten P, Van Melle G, de Tribolet N, Stupp R. Clinical trial substantiates the predictive value of O-6-methylguanine-DNA methyltransferase promoter methylation in glioblastoma patients treated with temozolomide. Clin Cancer Res 2004, 10:1871-1874. 10.1158/1078-0432.CCR-03-0384, 15041700.
33. Hajkova P, el-Maarri O, Engemann S, Oswald J, Olek A, Walter J. DNA-methylation analysis by the bisulfite-assisted genomic sequencing method. Methods Mol Biol 2002, 200:143-154.
34. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453. 10.1016/0022-2836(70)90057-4, 5420325.
35. Pelizzola M, Koga Y, Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM. MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Res 2008, 18:1652-1659. 10.1101/gr.080721.108, 2556264, 18765822.
36. Bock C, Walter J, Paulsen M, Lengauer T. Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res 2008, 36:e55. 10.1093/nar/gkn122, 2425484, 18413340.
37. Frank E, Hall M, Trigg L, Holmes G, Witten IH. Data mining in bioinformatics using Weka. Bioinformatics 2004, 20:2479-2481. 10.1093/bioinformatics/bth261, 15073010.