Polymerase chain reaction-based methods of DNA methylation analysis

Analytical Biochemistry

Volumn 317, Issue 2, 2003, Pages 259-265

  Liu, Ze Jun ^a   Maekawa, Masato ^b  

^a THIRD MILITARY MEDICAL UNIVERSITY   (China)

^b HAMAMATSU UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATION; DIAGNOSIS; DISEASES; DNA; GENES; METHYLATION;

CANCER DIAGNOSIS; CANCER RECURRENCE; DETECTION METHODS; DNA METHYLATION ANALYSIS; EPIGENETIC MODIFICATION; HYPERMETHYLATION; SCIENTIFIC LITERATURE; TUMOR SUPPRESSOR GENES;

POLYMERASE CHAIN REACTION;

BISULFITE; DNA; DNA MARKER; ENZYME;

ANALYTIC METHOD; ARTICLE; BISULFITE SEQUENCING; CANCER DIAGNOSIS; CANCER GENETICS; CANCER RESEARCH; CANCER SCREENING; COMBINED BISULFITE RESTRICTION ANALYSIS; CPG ISLAND; DNA DETERMINATION; DNA METHYLATION; ENZYME ACTIVITY; FLUORESCENCE ANALYSIS; FLUORESCENCE MELTING CURVE ANALYSIS; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; METHODOLOGY; METHYLATION; METHYLATION SENSITIVE SINGLE NUCLEOTIDE PRIMER EXTENSION; METHYLATION SPECIFIC POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; RESTRICTION MAPPING; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SOUTHERN BLOTTING; TECHNIQUE;

EID: 0038732266     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0003-2697(03)00169-6     Document Type: Article

References (40)

1. Jones P.A., Tatki D. The role of DNA methylation in mammalian epigenetics. Science. 293:2001;1068-1070.
2. Herman J.G., Latif F., Weng W., Lerman M.I., Zbar B., Liu S.et al. Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinomas. Proc. Natl. Acad. Sci. USA. 91:1994;9700-9704.
3. ′ CpG island methylation is associated with transcriptional silencing of the tumor suppressor p16/CDKN2/MTS1 in human cancers Nat. Med. 1:1995;686-692.
4. Herman J.G., Umar A., Polyak K., Graff J.R., Ahuja N., Issa J.P.et al. Incidence of functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. Proc. Natl. Acad. Sci. USA. 95:1998;6870-6875.
5. Lee W.H., Morton P.A., Epstein J.I., Brooks J.D., Campbell P.A., Bova G.S.et al. Cytidine methylation of regulatory sequences near the pi-class glutathione S-transferase gene accompanies human prostatic carcinogenesis. Proc. Natl. Acad. Sci. USA. 91:1994;11733-11737.
6. Esteller M., Corn P.G., Urena J.M., Gabrielson E., Baylin S.B., Herman J.G. Inactivation of glutathione S-transferase P1 gene by promoter hypermethylation in human neoplasia. Cancer Res. 58:1998;4515-4518.
7. 6 -methylguanine-DNA-methyltransferase by promoter hypermethylation is a common event in multiple human neoplasia Cancer Res. 59:1999;793-797.
8. Katzenellenbogen R.A., Baylin S.B., Herman J.G. Hypermethylation of the DAP-Kinase CpG island is a common alteration in B-cell malignancies. Blood. 93:1999;4347-4353.
9. Esteller M., Sanchez-Cespedes M., Rosell R., Sigransky D., Baylin S.B., Herman J.G. Detection of aberrant promoter hypermethylation of tumor suppressor genes in serum DNA from non-small cell lung cancer patients. Cancer Res. 59:1999;67-70.
10. ′ CpG islands increases with malignant progression in human breast cancer Cancer Res. 60:2000;4346-4348.
11. Baylin S.B., Herman J.G., Graff J.R., Vertino P.M., Issa J.P. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv. Cancer Res. 72:1998;141-196.
12. Palmisana W.A., Divine K.K., Saccomanno G., Gilliland G.D., Baylin S.B., Herman J.G.et al. Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Res. 60:2000;5954-5958.
13. Esteller M., Corn P.G., Baylin S.B., Herman J.G. A gene hypermethylation profile of human cancer. Cancer Res. 61:2001;3225-3229.
14. McClelland M. The effect of sequence specific DNA methylation restriction endonuclease cleavage. Nucleic Acids Res. 9:1981;5859-5866.
15. Issa J.P., Ottaviano Y.L., Celano P., Hamilton S.R., Davidson N.E., Baylin S.B. Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon. Nat. Genet. 7:1994;536-540.
16. Singer-Sam J., Grant M., LeVon J.M., Okuyama K., Chapman V., Monk M., Riggs A.D. Use of a Hpall-polymerase chain reaction assay to study DNA methylation in the pgk-1 GpG island of mouse embryos at the time of X-chromosome inactivation. Mol. Cell. Biol. 10:1990;4987-4989.
17. Sadri R., Hornsby P.J. Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification. Nucleic Acids Res. 24:1996;5058-5059.
18. Xiong Z., Laird P.W. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res. 25:1997;2532-2534.
19. Maekawa M., Sugano K., Kashiwabara H., Ushiama M., Fujita S., Yoshimori M.et al. DNA methylation analysis using bisulfite treatment and PCR-Single-Strand conformation polymorphism in colorectal cancer showing microsatellite instability. Biochem. Biophys. Res. Commun. 262:1999;671-676.
20. Maekawa M., Sugano K., Ushiama M., Fukayama N., Nomoto K., Kashiwabara H.et al. Heterogeneity of DNA methylation status analyzed by Bisulfite-PCR-SSCP and correlation with clinico-pathological characteristics in colorectal cancer. Clin. Chem. Lab. Med. 39:2001;121-128.
21. Worm J., Aggerholm A., Guldberg P. In-tube DNA methylation profiling by fluorescence melting curve analysis. Clin. Chem. 47:2001;1183-1189.
22. Frommer M., McDonald L.E., Millar D.S., Collies C.M., Watt F., Grigg G.W.et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA. 89:1992;1827-1831.
23. Myohanen S., wahlfors J., Janne J. Automated fluorescent genomic sequencing as applied to the methylation analysis of the human ornithine decarboxylase gene. DNA Sequence. 5:1994;1-8.
24. Gonzalgo M.L., Jones P.A. Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE). Nucleic Acids Res. 25:1997;2529-2531.
25. Herman J.G., Graff J.R., Myohanen S., Nelkin B.D., Baylin S.B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA. 93:1996;9821-9826.
26. Wong I.H., Lo Y.M., Johnson P.J. Epigenetic tumor markers in plasma and serum: biology and applications to molecular diagnosis and disease monitoring. Ann. N. Y. Acad. Sci. 945:2001;36-50.
27. Eads C.A., Kanenberg K.D., Kawakami K., Saltz L.B., Blake C., Shibata D.et al. Methylight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 28:2000;e32.
28. Lo Y.M., Wong I.H., Zhang J., Tein M.S., Ng M.H., Hjelm N.M. Quantitative analysis of aberrant p16 methylation using real-time quantitative methylation-specific polymerase chain reaction. Cancer Res. 59:1999;3899-3903.
29. Yang X., Yan L., Davidson N.E. DNA methylation in breast cancer. Endocr. Relat. Cancer. 8:2001;115-127.
30. Esteller M., Herman J.G. Cancer as an epigenetic disease: DNA methylation and chromatic alterations in human tumors. J. Pathol. 196:2002;1-7.
31. Evron E., Dooley W.C., Umbricht C.B., Rosenthal D., Sacchi N., Gabrielson E.et al. Detection of breast cancer cells in ductal lavage fluid by methylation-specific PCR. Lancet. 357:2001;1335-1336.
32. Sanchez-Cespedes M., Esteller M., Wu L., Nawroz-Danish H., Yoo G.H., Koch W.M.et al. Gene promoter hypermethylation in tumors and serum of head and neck cancer patients. Cancer Res. 60:2000;892-895.
33. Adorjan P., Distler J., Lipscher E., Model F., Muller J., Pelet C.et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 30:2002;e21.
34. Oakeley E.J. DNA methylation: a review of current methodologies. Pharmacol. Ther. 84:1999;389-400.
35. Havlis J., Trbusek M. 5-Methylcytosine as a marker for the monitoring of DNA methylation. J. Chromatogr. B. 781(1-2):2002;373-392.
36. Deng D., Deng G., Smith M.F., Zhou J., Xin H., Powell S.M., Lu Y. Simultaneous detection of CpG methylation and single nucleotide polymorphism by denaturing high performance liquid chromatography. Nucleic Acids Res. 30:2002;e13.
37. Gitan R.S., Shi H., Chen C.M., Yan P.S., Huang T.H.M. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res. 12:2002;158-164.
38. Toyooka K.O., Toyooka S., Maitra A., Feng Q., Kiviat N.C., Smith A.et al. Establishment and validation of real-time polymerase chain reaction method for CDH1 promoter methylation. Am. J. Pathol. 161:2002;629-634.
39. Galm O., Rountree M.R., Bachman K.E., Jair K.W., Baylin S.B., Herman J.G. Enzymatic regional methylation assay: a novel method to quantify regional CpG methylation density. Genome Res. 12:2002;153-157.
40. Brock G.J.R., Huang T.H.M., Chen C.M., Johnson K.J. A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP). Nucleic Acids Res. 29:2001;e123.