A systematic comparison of quantitative high-resolution DNA methylation analysis and methylation-specific PCR

Epigenetics

Volumn 7, Issue 7, 2012, Pages 772-780

  Claus, Rainer ^a   Wilop, Stefan ^b   Hielscher, Thomas ^a   Sonnet, Miriam ^a   Dahl, Edgar ^c   Galm, Oliver ^b   Jost, Edgar ^b   Plass, Christoph ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b RWTH AACHEN UNIVERSITY   (Germany)

^c UNIVERSITY HOSPITAL RWTH AACHEN   (Germany)

Author keywords

AML; Biomarker; ID4; MassARRAY; MSP; Pyrosequencing; Quantitative DNA methylation analysis; SFRP

Indexed keywords

DNA;

ACUTE GRANULOCYTIC LEUKEMIA; ADULT; ARTICLE; DNA METHYLATION; FEMALE; GENE; GENE LOCUS; GENE SEQUENCE; GENE SILENCING; HUMAN; ID4 GENE; MAJOR CLINICAL STUDY; MALE; MASS SPECTROMETRY; METHYLATION SPECIFIC POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SFRP GENE;

EID: 84863794936     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.20299     Document Type: Article

References (27)

1. Jones PA, Baylin SB. The epigenomics of cancer. Cell 2007; 128:683-692. PMID:17320506; http://dx.doi.org/10.1016/j.cell.2007.01.029.
2. Esteller M, Garcia-Foncillas J, Andion E, Goodman SN, Hidalgo OF, Vanaclocha V, et al. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 2000; 343:1350-1354. PMID:11070098; http://dx.doi.org/10.1056/NEJM200011093431901.
3. Hegi ME, Diserens AC, Gorlia T, Hamou MF, de Tribolet N, Weller M, et al. MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med 2005; 352:997-1003. PMID:15758010; http://dx.doi.org/10.1056/NEJMoa043331.
4. Richiardi L, Fiano V, Vizzini L, De Marco L, Delsedime L, Akre O, et al. Promoter methylation in APC, RUNX3 and GSTP1 and mortality in prostate cancer patients. J Clin Oncol 2009; 27:3161-3168. PMID:19470943; http://dx.doi.org/10.1200/JCO.2008.18.2485.
5. Herman JG, Graff JR, Myöhänen S, Nelkin BD, Baylin SB. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 1996; 93:9821-9826. PMID:8790415; http://dx.doi.org/10.1073/pnas.93.18.9821.
6. Palmisano WA, Divine KK, Saccomanno G, Gilliland FD, Baylin SB, Herman JG, et al. Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Res 2000; 60:5954-5958. PMID:11085511.
7. Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 2000; 28:32. PMID:10734209; http://dx.doi.org/10.1093/nar/28.8.e32.
8. Bonanno C, Shehi E, Adlerstein D, Makrigiorgos GM. MS-FLAG, a novel real-time signal generation method for methylation-specific PCR. Clin Chem 2007; 53:2119-2127. PMID:17962364; http://dx.doi.org/10.1373/clinchem.2007.094011.
9. Kristensen LS, Hansen LL. PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics and response to treatment. Clin Chem 2009; 55:1471-1483; PMID:19520761; http://dx.doi.org/10.1373/clinchem.2008.121962.
10. Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994; 22:2990-2997; PMID:8065911; http://dx.doi.org/10.1093/nar/22.15.2990.
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; PMID:12866415.
12. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G, et al. Quantitative highthroughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci USA 2005; 102:15785-15790; PMID:16243968; http://dx.doi.org/10.1073/pnas.0507816102.
13. Yu L, Liu C, Vandeusen J, Becknell B, Dai Z, Wu YZ, et al. Global assessment of promoter methylation in a mouse model of cancer identifies ID4 as a putative tumor-suppressor gene in human leukemia. Nat Genet 2005; 37:265-274; PMID:15723065; http://dx.doi.org/10.1038/ng1521.
14. Gómez Del Pulgar T, Valdés-Mora F, Bandrés E, Pérez-Palacios R, Espina C, Cejas P, et al. Cdc42 is highly expressed in colorectal adenocarcinoma and downregulates ID4 through an epigenetic mechanism. Int J Oncol 2008; 33:185-193; PMID:18575765.
15. Carey JP, Asirvatham AJ, Galm O, Ghogomu TA, Chaudhary J. Inhibitor of differentiation 4 (Id4) is a potential tumor suppressor in prostate cancer. BMC Cancer 2009; 9:173; PMID:19500415; http://dx.doi.org/10.1186/1471-2407-9-173.
16. Asirvatham AJ, Schmidt MA, Chaudhary J. Nonredundant inhibitor of differentiation (Id) gene expression and function in human prostate epithelial cells. Prostate 2006; 66:921-935; PMID:16541417; http://dx.doi.org/10.1002/pros.20366.
17. Noetzel E, Veeck J, Niederacher D, Galm O, Horn F, Hartmann A, et al. Promoter methylation-associated loss of ID4 expression is a marker of tumour recurrence in human breast cancer. BMC Cancer 2008; 8:154; PMID:18513385; http://dx.doi.org/10.1186/1471-2407-8-154.
18. Chan AS, Tsui WY, Chen X, Chu KM, Chan TL, Chan AS, et al. Downregulation of ID4 by promoter hypermethylation in gastric adenocarcinoma. Oncogene 2003; 22:6946-6953. PMID:14534543; http://dx.doi.org/10.1038/sj.onc.1206799.
19. Chen SS, Claus R, Lucas DM, Yu L, Qian J, Ruppert AS, et al. Silencing of the inhibitor of DNA binding protein 4 (ID4) contributes to the pathogenesis of mouse and human CLL. Blood 2011; 117:862-871; PMID:21098398; http://dx.doi.org/10.1182/blood-2010-05-284638.
20. Jost E, Schmid J, Wilop S, Schubert C, Suzuki H, Herman JG, et al. Epigenetic inactivation of secreted Frizzled-related proteins in acute myeloid leukaemia. Br J Haematol 2008; 142:745-753; PMID:18537968; http://dx.doi.org/10.1111/j.1365-2141.2008.07242.x.
21. Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987; 196:261-282; PMID:3656447; http://dx.doi.org/10.1016/0022-2836(87)90689-9.
22. Wang H, Wang XQ, Xu XP, Lin GW. ID4 methylation predicts high risk of leukemic transformation in patients with myelodysplastic syndrome. Leuk Res 2010; 34:598-604; PMID:19853913; http://dx.doi.org/10.1016/j.leukres.2009.09.031.
23. Altman DG, Royston P. The cost of dichotomizing continuous variables. BMJ 2006; 332:1080; PMID:16675816; http://dx.doi.org/10.1136/bmj.332.7549.1080.
24. Galm O, Herman JG. Methylation-specific polymerase chain reaction. Methods Mol Med 2005; 113:279-291; PMID:15968111.
25. Rohde C, Zhang Y, Reinhardt R, Jeltsch A. BISMA- fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. BMC Bioinformatics 2010; 11:230; PMID:20459626; http://dx.doi.org/10.1186/1471-2105-11-230.
26. Cohen J. A coefficient of agreement for nominal scales. Educational and Psychological Measurement 1960; 20:37-46.
27. R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2012.