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Research Paper

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

, , , , , , & show all
Pages 772-780 | Published online: 01 Jul 2012

References

  • Jones PA, Baylin SB. The epigenomics of cancer. Cell 2007; 128:683 - 92; http://dx.doi.org/10.1016/j.cell.2007.01.029; PMID: 17320506
  • 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 - 4; http://dx.doi.org/10.1056/NEJM200011093431901; PMID: 11070098
  • 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; http://dx.doi.org/10.1056/NEJMoa043331; PMID: 15758010
  • 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 - 8; http://dx.doi.org/10.1200/JCO.2008.18.2485; PMID: 19470943
  • 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 U S A 1996; 93:9821 - 6; http://dx.doi.org/10.1073/pnas.93.18.9821; PMID: 8790415
  • 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 - 8; PMID: 11085511
  • 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:E32; http://dx.doi.org/10.1093/nar/28.8.e32; PMID: 10734209
  • 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 - 27; http://dx.doi.org/10.1373/clinchem.2007.094011; PMID: 17962364
  • 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 - 83; http://dx.doi.org/10.1373/clinchem.2008.121962; PMID: 19520761
  • Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994; 22:2990 - 7; http://dx.doi.org/10.1093/nar/22.15.2990; PMID: 8065911
  • Tost J, Dunker J, Gut IG. Analysis and quantification of multiple methylation variable positions in CpG islands by Pyrosequencing. Biotechniques 2003; 35:152 - 6; PMID: 12866415
  • Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G, et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci U S A 2005; 102:15785 - 90; http://dx.doi.org/10.1073/pnas.0507816102; PMID: 16243968
  • 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 - 74; http://dx.doi.org/10.1038/ng1521; PMID: 15723065
  • 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 - 93; PMID: 18575765
  • 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; http://dx.doi.org/10.1186/1471-2407-9-173; PMID: 19500415
  • Asirvatham AJ, Schmidt MA, Chaudhary J. Non-redundant inhibitor of differentiation (Id) gene expression and function in human prostate epithelial cells. Prostate 2006; 66:921 - 35; http://dx.doi.org/10.1002/pros.20366; PMID: 16541417
  • 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; http://dx.doi.org/10.1186/1471-2407-8-154; PMID: 18513385
  • 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 - 53; http://dx.doi.org/10.1038/sj.onc.1206799; PMID: 14534543
  • 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 - 71; http://dx.doi.org/10.1182/blood-2010-05-284638; PMID: 21098398
  • 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 - 53; http://dx.doi.org/10.1111/j.1365-2141.2008.07242.x; PMID: 18537968
  • Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987; 196:261 - 82; http://dx.doi.org/10.1016/0022-2836(87)90689-9; PMID: 3656447
  • 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; http://dx.doi.org/10.1016/j.leukres.2009.09.031; PMID: 19853913
  • Altman DG, Royston P. The cost of dichotomising continuous variables. BMJ 2006; 332:1080; http://dx.doi.org/10.1136/bmj.332.7549.1080; PMID: 16675816
  • Galm O, Herman JG. Methylation-specific polymerase chain reaction. Methods Mol Med 2005; 113:279 - 91; PMID: 15968111
  • 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; http://dx.doi.org/10.1186/1471-2105-11-230; PMID: 20459626
  • Cohen J. A coefficient of agreement for nominal scales.. Educational and Psychological Measurement 1960; 20:37 - 46
  • R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2012.

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