Quantitation of DNA methylation by melt curve analysis

BMC Cancer

Volumn 9, Issue , 2009, Pages

  Smith, Eric ^a   Jones, Michael E ^b   Drew, Paul A ^c  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b FLINDERS UNIVERSITY   (Australia)

^c FLINDERS UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; BISULFITE MODIFIED DNA; CELL DNA; DNA; DOUBLE STRANDED DNA; GENOMIC DNA; METHYLATED DNA PROTEIN CYSTEINE METHYLTRANSFERASE; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG; 5 AZA 2' DEOXYCYTIDINE; ANTINEOPLASTIC ANTIMETABOLITE; AZACITIDINE; CYCLIN DEPENDENT KINASE INHIBITOR 2A; DNA METHYLTRANSFERASE; DRUG DERIVATIVE; MGMT PROTEIN, HUMAN; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; TIMP3 PROTEIN, HUMAN; TISSUE INHIBITOR OF METALLOPROTEINASE 3; TUMOR SUPPRESSOR PROTEIN;

AMPLICON; ANALYTIC METHOD; ANALYTICAL PARAMETERS; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MODIFICATION; FLUORESCENCE ANALYSIS; GENE EXPRESSION; GENE LOSS; HIGH TEMPERATURE; HUMAN; HUMAN CELL; MATHEMATICAL COMPUTING; MELT CURVE; MELTING TEMPERATURE; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; REAL TIME THERMOCYCLER; REPRODUCIBILITY; TISSUE FIXATION; ALGORITHM; CHEMISTRY; COLORECTAL TUMOR; DNA DENATURATION; DRUG EFFECT; ESOPHAGUS TUMOR; GENETICS; HEAT; IMMUNOHISTOCHEMISTRY; METABOLISM; PATHOLOGY; PROMOTER REGION; TUMOR CELL LINE;

ALGORITHMS; ANTIMETABOLITES, ANTINEOPLASTIC; AZACITIDINE; CELL LINE, TUMOR; COLORECTAL NEOPLASMS; CYCLIN-DEPENDENT KINASE INHIBITOR P16; DNA METHYLATION; DNA MODIFICATION METHYLASES; DNA REPAIR ENZYMES; DNA, NEOPLASM; ESOPHAGEAL NEOPLASMS; HOT TEMPERATURE; HUMANS; IMMUNOHISTOCHEMISTRY; NUCLEIC ACID DENATURATION; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; TISSUE INHIBITOR OF METALLOPROTEINASE-3; TUMOR SUPPRESSOR PROTEINS;

EID: 65549117575     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/1471-2407-9-123     Document Type: Article

References (20)

1. Fraga MF Esteller M DNA methylation: A profile of methods and applications Biotechniques 2002, 33:632-634, 636-649 12238773
2. Wong IH Qualitative and quantitative polymerase chain reaction-based methods for DNA methylation analyses Methods Mol Biol 2006, 336:33-43. 16916251
3. Frommer M McDonald LE Millar DS Collis CM Watt F Grigg GW Molloy PL Paul CL A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands Proc Natl Acad Sci USA 1992, 89:1827-1831. 48546 1542678 10.1073/pnas.89.5.1827
4. Tost J Dunker J Gut IG Analysis and quantification of multiple methylation variable positions in CpG islands by Pyrosequencing Biotechniques 2003, 35:152-156. 12866415
5. Ehrich M Nelson MR Stanssens P Zabeau M Liloglou T Xinarianos G Cantor CR Field JK Boom van den 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. 1276092 16243968 10.1073/ pnas.0507816102
6. Herman JG Graff JR Myohanen 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. 38513 8790415 10.1073/pnas.93.18.9821
7. Ririe KM Rasmussen RP Wittwer CT Product differentiation by analysis of DNA melting curves during the polymerase chain reaction Anal Biochem 1997, 245:154-160. 10.1006/abio.1996.9916 9056205
8. Wittwer CT Reed GH Gundry CN Vandersteen JG Pryor RJ High-resolution genotyping by amplicon melting analysis using LCGreen Clin Chem 2003, 49:853-860. 10.1373/49.6.853 12765979
9. Worm J Aggerholm A Guldberg P In-tube DNA methylation profiling by fluorescence melting curve analysis Clin Chem 2001, 47:1183-1189. 11427447
10. Wojdacz TK Dobrovic A Methylation-sensitive high resolution melting (MS-HRM): A new approach for sensitive and high-throughput assessment of methylation Nucleic Acids Res 2007, 35:e41. 1874596 17289753 10.1093/nar/ gkm013
11. Frigola J Song J Stirzaker C Hinshelwood RA Peinado MA Clark SJ Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band Nat Genet 2006, 38:540-549. 10.1038/ng1781 16642018
12. Lorente A Mueller W Urdangarin E Lazcoz P von Deimling A Castresana JS Detection of methylation in promoter sequences by melting curve analysis-based semiquantitative real time PCR BMC Cancer 2008, 8:61. 2266933 18298842 10.1186/1471-2407-8-61
13. Smith E Drew PA Tian ZQ De Young NJ Liu JF Mayne GC Ruszkiewicz AR Watson DI Jamieson GG Metallothionien 3 expression is frequently down-regulated in oesophageal squamous cell carcinoma by DNA methylation Mol Cancer 2005, 4:42. 1343579 16351731 10.1186/1476-4598-4-42
14. Smith E De Young NJ Tian ZQ Caruso M Ruszkiewicz AR Liu JF Jamieson GG Drew PA Methylation of TIMP3 in esophageal squamous cell carcinoma World J Gastroenterol 2008, 14:203-210. 10.3748/wjg.14.203 18186556
15. Smith E De Young NJ Pavey SJ Hayward NK Nancarrow DJ Whiteman DC Smithers BM Ruszkiewicz AR Clouston AD Gotley DC et al Similarity of aberrant DNA methylation in Barrett's esophgus and esophageal adenocarcinoma Mol Cancer 2008, 7:75. 2567345 18831746 10.1186/ 1476-4598-7-75
16. Siegel S Castellan NJ Nonparametric statistics for the behavioral sciences Singapore: McGraw-Hill Inc. Second 1988
17. Nagasaka T Goel A Notohara K Takahata T Sasamoto H Uchida T Nishida N Tanaka N Boland CR Matsubara N Methylation pattern of the O6-methylguanine-DNA methyltransferase gene in colon during progressive colorectal tumorigenesis Int J Cancer 2008, 122:2429-2436. 10.1002/ ijc.23398 18240147
18. Akey DT Akey JM Zhang K Jin L Assaying DNA methylation based on high-throughput melting curve approaches Genomics 2002, 80:376-384. 10.1006/geno.2002.6851 12376091
19. Guldberg P Worm J Gronbaek K Profiling DNA methylation by melting analysis Methods 2002, 27:121-127. 10.1016/S1046-2023(02)00063-4 12095269
20. 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. 2425484 18413340 10.1093/nar/gkn122