DNA fingerprinting techniques for the analysis of genetic and epigenetic alterations in colorectal cancer

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 693, Issue 1-2, 2010, Pages 61-76

  Samuelsson, Johanna K ^a   Alonso, Sergio ^a   Yamamoto, Fumiichiro ^a   Perucho, Manuel ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

Colorectal cancer; DNA fingerprinting; Epigenetics; Genetics

Indexed keywords

FOLLISTATIN; POLYCOMB GROUP PROTEIN; TRANSCRIPTION FACTOR PAX6;

AMPLICON; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANEUPLOIDY; CARCINOGENESIS; CHROMOSOMAL INSTABILITY; CHROMOSOME NUMBER; COLORECTAL CANCER; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; CPG ISLAND; DNA FINGERPRINTING; DNA METHYLATION; EPIGENETICS; GENE DOSAGE; GENE MUTATION; GENE SILENCING; GENETIC ANALYSIS; HETEROZYGOSITY LOSS; HUMAN; MICROSATELLITE INSTABILITY; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN DOMAIN; RANDOM AMPLIFIED POLYMORPHIC DNA; REVIEW; TRANSCRIPTION REGULATION;

CHROMOSOME ABERRATIONS; COLORECTAL NEOPLASMS; DNA COPY NUMBER VARIATIONS; DNA FINGERPRINTING; EPIGENESIS, GENETIC; HUMANS; MUTATION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH;

EID: 78049423669     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2010.08.010     Document Type: Review

References (151)

1. Goldfarb M., Shimizu K., Perucho M., Wigler M. Isolation and preliminary characterization of a human transforming gene from T24 bladder carcinoma cells. Nature 1982, 296:404-409.
2. Pulciani S., Santos E., Lauver A.V., Long L.K., Robbins K.C., Barbacid M. Oncogenes in human tumor cell lines: molecular cloning of a transforming gene from human bladder carcinoma cells. Proc. Natl. Acad. Sci. U.S.A. 1982, 79:2845-2849.
3. Shih C., Weinberg R.A. Isolation of a transforming sequence from a human bladder carcinoma cell line. Cell 1982, 29:161-169.
4. Dryja T.P., Friend S., Weinberg R.A. Genetic sequences that predispose to retinoblastoma and osteosarcoma. Symp. Fundam. Cancer Res. 1986, 39:115-119.
5. Alberts B. Molecular Biology of the Cell 2002, Garland Science, New York.
6. Lewin B. Genes IX 2008, Jones and Bartlett Publishers, Sudbury, MA.
7. Tomlinson I.P., Novelli M.R., Bodmer W.F. The mutation rate and cancer. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:14800-14803.
8. Li R., Sonik A., Stindl R., Rasnick D., Duesberg P. Aneuploidy vs. gene mutation hypothesis of cancer: recent study claims mutation but is found to support aneuploidy. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:3236-3241.
9. Pellman D. Cell biology: aneuploidy and cancer. Nature 2007, 446:38-39.
10. Aaltonen L.A., Peltomaki P., Leach F.S., Sistonen P., Pylkkanen L., Mecklin J.P., Jarvinen H., Powell S.M., Jen J., Hamilton S.R., et al. Clues to the pathogenesis of familial colorectal cancer. Science 1993, 260:812-816.
11. Ionov Y., Peinado M.A., Malkhosyan S., Shibata D., Perucho M. Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic carcinogenesis. Nature 1993, 363:558-561.
12. Thibodeau S.N., Bren G., Schaid D. Microsatellite instability in cancer of the proximal colon. Science 1993, 260:816-819.
13. Sjoblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K., Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E. The consensus coding sequences of human breast and colorectal cancers. Science 2006, 314:268-274.
14. Forrest W.F., Cavet G. Comment on " The consensus coding sequences of human breast and colorectal cancers" Science 2007, 317:1500. (author reply 1500).
15. Getz G., Hofling H., Mesirov J.P., Golub T.R., Meyerson M., Tibshirani R., Lander E.S. Comment on " The consensus coding sequences of human breast and colorectal cancers" Science 2007, 317:1500.
16. Rubin A.F., Green P. Comment on " The consensus coding sequences of human breast and colorectal cancers" Science 2007, 317:1500.
17. Wood L.D., Parsons D.W., Jones S., Lin J., Sjoblom T., Leary R.J., Shen D., Boca S.M., Barber T., Ptak J., Silliman N., Szabo S., Dezso Z., Ustyanksky V., Nikolskaya T., Nikolsky Y., Karchin R., Wilson P.A., Kaminker J.S., Zhang Z., Croshaw R., Willis J., Dawson D., Shipitsin M., Willson J.K., Sukumar S., Polyak K., Park B.H., Pethiyagoda C.L., Pant P.V., Ballinger D.G., Sparks A.B., Hartigan J., Smith D.R., Suh E., Papadopoulos N., Buckhaults P., Markowitz S.D., Parmigiani G., Kinzler K.W., Velculescu V.E., Vogelstein B. The genomic landscapes of human breast and colorectal cancers. Science 2007, 318:1108-1113.
18. Saxonov S., Berg P., Brutlag D.L. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:1412-1417.
19. Diala E.S., Hoffman R.M. Hypomethylation of HeLa cell DNA and the absence of 5-methylcytosine in SV40 and adenovirus (type 2) DNA: analysis by HPLC. Biochem. Biophys. Res. Commun. 1982, 107:19-26.
20. Feinberg A.P., Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 1983, 301:89-92.
21. Feinberg A.P., Vogelstein B. Hypomethylation of ras oncogenes in primary human cancers. Biochem. Biophys. Res. Commun. 1983, 111:47-54.
22. Greger V., Passarge E., Hopping W., Messmer E., Horsthemke B. Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma. Hum. Genet. 1989, 83:155-158.
23. Esteller M. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum. Mol. Genet. 2007, 16(Spec No. 1):R50-59.
24. Lyko F., Brown R. DNA methyltransferase inhibitors and the development of epigenetic cancer therapies. J. Natl. Cancer Inst. 2005, 97:1498-1506.
25. Southern E.M. DNA microarrays. History and overview. Methods Mol. Biol. 2001, 170:1-15.
26. Bennett S., Solexa Ltd Pharmacogenomics 2004, 5:433-438.
27. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
28. Shendure J., Porreca G.J., Reppas N.B., Lin X., McCutcheon J.P., Rosenbaum A.M., Wang M.D., Zhang K., Mitra R.D., Church G.M. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005, 309:1728-1732.
29. Mardis E.R. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 2008, 9:387-402.
30. Irizarry R.A., Ladd-Acosta C., Carvalho B., Wu H., Brandenburg S.A., Jeddeloh J.A., Wen B., Feinberg A.P. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 2008, 18:780-790.
31. Irizarry R.A., Ladd-Acosta C., Wen B., Wu Z., Montano C., Onyango P., Cui H., Gabo K., Rongione M., Webster M., Ji H., Potash J.B., Sabunciyan S., Feinberg A.P. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 2009, 41:178-186.
32. Mullis K., Faloona F., Scharf S., Saiki R., Horn G., Erlich H. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 1986, 51(Pt 1):263-273.
33. Welsh J., McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990, 18:7213-7218.
34. Williams J.G., Kubelik A.R., Livak K.J., Rafalski J.A., Tingey S.V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990, 18:6531-6535.
35. Navarro J.M., Jorcano J.L. The use of arbitrarily primed polymerase chain reaction in cancer research. Electrophoresis 1999, 20:283-290.
36. Arribas R., Capella G., Tortola S., Masramon L., Grizzle W.E., Perucho M., Peinado M.A. Assessment of genomic damage in colorectal cancer by DNA fingerprinting: prognostic applications. J. Clin. Oncol. 1997, 15:3230-3240.
37. Risques R.A., Moreno V., Ribas M., Marcuello E., Capella G., Peinado M.A. Genetic pathways and genome-wide determinants of clinical outcome in colorectal cancer. Cancer Res. 2003, 63:7206-7214.
38. Vogt T., Stolz W., Landthaler M., Ruschoff J., Schlegel J. Nonradioactive arbitrarily primed polymerase chain reaction: a novel technique for detecting genetic defects in skin tumors. J. Invest. Dermatol. 1996, 106:194-197.
39. Yasuda J., Kashiwabara H., Kawakami K., Uematsu K., Sugano K., Perucho M., Sekiya T. Detection of microsatellite instability in cancers by arbitrarily primed-PCR fingerprinting using a fluorescently labeled primer (FAP-PCR). Biol. Chem. 1996, 377:563-570.
40. Dil A., Misra A., Sulaiman I.M., Sinha S., Sarkar C., Mahapatra A.K., Hasnain S.E. Genetic alterations in brain tumors identified by RAPD analysis. Gene 1998, 206:45-48.
41. Ong T.M., Song B., Qian H.W., Wu Z.L., Whong W.Z. Detection of genomic instability in lung cancer tissues by random amplified polymorphic DNA analysis. Carcinogenesis 1998, 19:233-235.
42. Wang J., Wang Q., Ye F. Genetic instability in cancer tissues analyzed by random amplified polymorphic DNA PCR. Chin. Med. J. (Engl.) 2002, 115:430-432.
43. Atienzar F.A., Jha A.N. The random amplified polymorphic DNA (RAPD) assay and related techniques applied to genotoxicity and carcinogenesis studies: a critical review. Mutat. Res. 2006, 613:76-102.
44. Peinado M.A., Malkhosyan S., Velazquez A., Perucho M. Isolation and characterization of allelic losses and gains in colorectal tumors by arbitrarily primed polymerase chain reaction. Proc. Natl. Acad. Sci. U.S.A. 1992, 89:10065-10069.
45. Kohno T., Morishita K., Takano H., Shapiro D.N., Yokota J. Homozygous deletion at chromosome 2q33 in human small-cell lung carcinoma identified by arbitrarily primed PCR genomic fingerprinting. Oncogene 1994, 9:103-108.
46. Malkhosyan S., Yasuda J., Soto J.L., Sekiya T., Yokota J., Perucho M. Molecular karyotype (amplotype) of metastatic colorectal cancer by unbiased arbitrarily primed PCR DNA fingerprinting. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:10170-10175.
47. Piao Z., Lee K.S., Kim H., Perucho M., Malkhosyan S. Identification of novel deletion regions on chromosome arms 2q and 6p in breast carcinomas by amplotype analysis. Genes Chromosomes Cancer 2001, 30:113-122.
48. Achille A., Biasi M.O., Zamboni G., Bogina G., Magalini A.R., Pederzoli P., Perucho M., Scarpa A. Chromosome 7q allelic losses in pancreatic carcinoma. Cancer Res. 1996, 56:3808-3813.
49. Suzuki K., Ohnami S., Tanabe C., Sasaki H., Yasuda J., Katai H., Yoshimura K., Terada M., Perucho M., Yoshida T. The genomic damage estimated by arbitrarily primed PCR DNA fingerprinting is useful for the prognosis of gastric cancer. Gastroenterology 2003, 125:1330-1340.
50. Suzuki K., Suzuki I., Leodolter A., Alonso S., Horiuchi S., Yamashita K., Perucho M. Global DNA demethylation in gastrointestinal cancer is age dependent and precedes genomic damage. Cancer Cell 2006, 9:199-207.
51. Kinzler K.W., Vogelstein B. Lessons from hereditary colorectal cancer. Cell 1996, 87:159-170.
52. Perucho M. Cancer of the microsatellite mutator phenotype. Biol. Chem. 1996, 377:675-684.
53. Leach F.S., Nicolaides N.C., Papadopoulos N., Liu B., Jen J., Parsons R., Peltomaki P., Sistonen P., Aaltonen L.A., Nystrom-Lahti M., et al. Mutations of a mutS homolog in hereditary nonpolyposis colorectal cancer. Cell 1993, 75:1215-1225.
54. Papadopoulos N., Nicolaides N.C., Wei Y.F., Ruben S.M., Carter K.C., Rosen C.A., Haseltine W.A., Fleischmann R.D., Fraser C.M., Adams M.D., et al. Mutation of a mutL homolog in hereditary colon cancer. Science 1994, 263:1625-1629.
55. Kolodner R.D., Marsischky G.T. Eukaryotic DNA mismatch repair. Curr. Opin. Genet. Dev. 1999, 9:89-96.
56. Yamashita K., Dai T., Dai Y., Yamamoto F., Perucho M. Genetics supersedes epigenetics in colon cancer phenotype. Cancer Cell 2003, 4:121-131.
57. Perucho M., Peinado M.A., Ionov Y., Casares S., Malkhosyan S., Stanbridge E. Defects in replication fidelity of simple repeated sequences reveal a new mutator mechanism for oncogenesis. Cold Spring Harb. Symp. Quant. Biol. 1994, 59:339-348.
58. Cahill D.P., Kinzler K.W., Vogelstein B., Lengauer C. Genetic instability and darwinian selection in tumours. Trends Cell Biol. 1999, 9:M57-60.
59. Markowitz S., Wang J., Myeroff L., Parsons R., Sun L., Lutterbaugh J., Fan R.S., Zborowska E., Kinzler K.W., Vogelstein B., et al. Inactivation of the type II TGF-beta receptor in colon cancer cells with microsatellite instability. Science 1995, 268:1336-1338.
60. Rampino N., Yamamoto H., Ionov Y., Li Y., Sawai H., Reed J.C., Perucho M. Somatic frameshift mutations in the BAX gene in colon cancers of the microsatellite mutator phenotype. Science 1997, 275:967-969.
61. Yamamoto H., Sawai H., Perucho M. Frameshift somatic mutations in gastrointestinal cancer of the microsatellite mutator phenotype. Cancer Res. 1997, 57:4420-4426.
62. Lindblom A. Different mechanisms in the tumorigenesis of proximal and distal colon cancers. Curr. Opin. Oncol. 2001, 13:63-69.
63. Kim H., Jen J., Vogelstein B., Hamilton S.R. Clinical and pathological characteristics of sporadic colorectal carcinomas with DNA replication errors in microsatellite sequences. Am. J. Pathol. 1994, 145:148-156.
64. Konishi M., Kikuchi-Yanoshita R., Tanaka K., Muraoka M., Onda A., Okumura Y., Kishi N., Iwama T., Mori T., Koike M., Ushio K., Chiba M., Nomizu S., Konishi F., Utsunomiya J., Miyaki M. Molecular nature of colon tumors in hereditary nonpolyposis colon cancer, familial polyposis, and sporadic colon cancer. Gastroenterology 1996, 111:307-317.
65. Breivik J, Lothe R.A., Meling G.I., Rognum T.O., Borresen-Dale A.L., Gaudernack G. Different genetic pathways to proximal and distal colorectal cancer influenced by sex-related factors. Int. J. Cancer 1997, 74:664-669.
66. Olschwang S., Hamelin R., Laurent-Puig P., Thuille B., De Rycke Y., Li Y.J., Muzeau F., Girodet J., Salmon R.J., Thomas G. Alternative genetic pathways in colorectal carcinogenesis. Proc. Natl. Acad. Sci. U.S.A. 1997, 94:12122-12127.
67. Woerner S.M., Benner A., Sutter C., Schiller M., Yuan Y.P., Keller G., Bork P., Doeberitz M.K., Gebert J.F. Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes. Oncogene 2003, 22:2226-2235.
68. Royrvik E.C., Ahlquist T., Rognes T., Lothe R.A. Slip slidin' away: a duodecennial review of targeted genes in mismatch repair deficient colorectal cancer. Crit. Rev. Oncog. 2007, 13:229-257.
69. Perucho M. Microsatellite instability: the mutator that mutates the other mutator. Nat. Med. 1996, 2:630-631.
70. Suzuki K., Dai T., Suzuki I., Dai Y., Yamashita K., Perucho M. Low mutation incidence in polymorphic noncoding short mononucleotide repeats in gastrointestinal cancer of the microsatellite mutator phenotype pathway. Cancer Res. 2002, 62:1961-1965.
71. Yasuda J., Navarro J.M., Malkhosyan S., Velazquez A., Arribas R., Sekiya T., Perucho M. Chromosomal assignment of human DNA fingerprint sequences by simultaneous hybridization to arbitrarily primed PCR products from human/rodent monochromosome cell hybrids. Genomics 1996, 34:1-8.
72. Malkhosyan S.R., Baranovskaya S. Comparative hybridization of AP-PCR arrays, new method for analysis of single copy chromosomal losses and gains in cancer cell genome innovative molecular analysis technologies. 2nd Principal Investigators Meeting 2001, Riitz-Carlton, Washington, DC.
73. Barrett M.T., Scheffer A., Ben-Dor A., Sampas N., Lipson D., Kincaid R., Tsang P., Curry B., Baird K., Meltzer P.S., Yakhini Z., Bruhn L., Laderman S. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:17765-17770.
74. Vogelstein B., Fearon E.R., Kern S.E., Hamilton S.R., Preisinger A.C., Nakamura Y., White R. Allelotype of colorectal carcinomas. Science 1989, 244:207-211.
75. Trautmann K., Terdiman J.P., French A.J., Roydasgupta R., Sein N., Kakar S., Fridlyand J., Snijders A.M., Albertson D.G., Thibodeau S.N., Waldman F.M. Chromosomal instability in microsatellite-unstable and stable colon cancer. Clin. Cancer Res. 2006, 12:6379-6385.
76. du Manoir S., Speicher M.R., Joos S., Schrock E., Popp S., Dohner H., Kovacs G., Robert-Nicoud M., Lichter P., Cremer T. Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization. Hum. Genet. 1993, 90:590-610.
77. Kallioniemi O.P., Kallioniemi A., Sudar D., Rutovitz D., Gray J.W., Waldman F., Pinkel D. Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin. Cancer Biol. 1993, 4:41-46.
78. Kallioniemi O.P., Kallioniemi A., Piper J., Isola J., Waldman F.M., Gray J.W., Pinkel D. Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors. Genes Chromosomes Cancer 1994, 10:231-243.
79. Lisitsyn N., Wigler M. Cloning the differences between two complex genomes. Science 1993, 259:946-951.
80. Lisitsyn N.A., Lisitsina N.M., Dalbagni G., Barker P., Sanchez C.A., Gnarra J., Linehan W.M., Reid B.J., Wigler M.H. Comparative genomic analysis of tumors: detection of DNA losses and amplification. Proc. Natl. Acad. Sci. U.S.A. 1995, 92:151-155.
81. Lucito R., West J., Reiner A., Alexander J., Esposito D., Mishra B., Powers S., Norton L., Wigler M. Detecting gene copy number fluctuations in tumor cells by microarray analysis of genomic representations. Genome Res. 2000, 10:1726-1736.
82. Pollack J.R., Perou C.M., Alizadeh A.A., Eisen M.B., Pergamenschikov A., Williams C.F., Jeffrey S.S., Botstein D., Brown P.O. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 1999, 23:41-46.
83. Pinkel D., Segraves R., Sudar D., Clark S., Poole I., Kowbel D., Collins C., Kuo W.L., Chen C., Zhai Y., Dairkee S.H., Ljung B.M., Gray J.W., Albertson D.G. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 1998, 20:207-211.
84. Snijders A.M., Nowak N., Segraves R., Blackwood S., Brown N., Conroy J., Hamilton G., Hindle A.K., Huey B., Kimura K., Law S., Myambo K., Palmer J., Ylstra B., Yue J.P., Gray J.W., Jain A.N., Pinkel D., Albertson D.G. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet. 2001, 29:263-264.
85. Pinkel D., Albertson D.G. Comparative genomic hybridization. Annu. Rev. Genomics Hum. Genet. 2005, 6:331-354.
86. Ishkanian A.S., Malloff C.A., Watson S.K., DeLeeuw R.J., Chi B., Coe B.P., Snijders A., Albertson D.G., Pinkel D., Marra M.A., Ling V., MacAulay C., Lam W.L. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet. 2004, 36:299-303.
87. Kallioniemi A. CGH microarrays and cancer. Curr. Opin. Biotechnol. 2008, 19:36-40.
88. Thompson C.L., Plummer S.J., Acheson L.S., Tucker T.C., Casey G., Li L. Association of common genetic variants in SMAD7 and risk of colon cancer. Carcinogenesis 2009, 30:982-986.
89. Frommer M., McDonald L.E., Millar D.S., Collis C.M., Watt F., Grigg G.W., Molloy P.L., Paul C.L. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. U.S.A. 1992, 89:1827-1831.
90. 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. U.S.A. 1996, 93:9821-9826.
91. Eads C.A., Danenberg K.D., Kawakami K., Saltz L.B., Blake C., Shibata D., Danenberg P.V., Laird P.W. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 2000, 28:E32.
92. Eads C.A., Laird P.W. Combined bisulfite restriction analysis (COBRA). Methods Mol. Biol. 2002, 200:71-85.
93. Bibikova M., Lin Z., Zhou L., Chudin E., Garcia E.W., Wu B., Doucet D., Thomas N.J., Wang Y., Vollmer E., Goldmann T., Seifart C., Jiang W., Barker D.L., Chee M.S., Floros J., Fan J.B. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 2006, 16:383-393.
94. Fraga M.F., Esteller M. DNA methylation: a profile of methods and applications. Biotechniques 2002, 33:636-649. 632-634.
95. Zuo T., Tycko B., Liu T.M., Lin H.J., Huang T.H. Methods in DNA methylation profiling. Epigenomics 2009, 1:331-345.
96. Hatada I., Hayashizaki Y., Hirotsune S., Komatsubara H., Mukai T. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc. Natl. Acad. Sci. U.S.A. 1991, 88:9523-9527.
97. Hayashizaki Y., Hirotsune S., Okazaki Y., Hatada I., Shibata H., Kawai J., Hirose K., Watanabe S., Fushiki S., Wada S., et al. Restriction landmark genomic scanning method and its various applications. Electrophoresis 1993, 14:251-258.
98. Rush L.J., Plass C. Restriction landmark genomic scanning for DNA methylation in cancer: past, present, and future applications. Anal. Biochem. 2002, 307:191-201.
99. Matsuyama T, Kimura M.T., Koike K., Abe T., Nakano T., Asami T., Ebisuzaki T., Held W.A., Yoshida S., Nagase H. Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS). Nucleic Acids Res. 2003, 31:4490-4496.
100. Rouillard J.M., Erson A.E., Kuick R., Asakawa J., Wimmer K., Muleris M., Petty E.M., Hanash S. Virtual genome scan: a tool for restriction landmark-based scanning of the human genome. Genome Res. 2001, 11:1453-1459.
101. Zardo G., Tiirikainen M.I., Hong C., Misra A., Feuerstein B.G., Volik S., Collins C.C., Lamborn K.R., Bollen A., Pinkel D., Albertson D.G., Costello J.F. Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat. Genet. 2002, 32:453-458.
102. Ho S.M., Tang W.Y. Techniques used in studies of epigenome dysregulation due to aberrant DNA methylation: an emphasis on fetal-based adult diseases. Reprod. Toxicol. 2007, 23:267-282.
103. Kim Y.S., Yoo H.S., Lee K.T., Goh S.H., Jung J.S., Oh S.W., Baba M., Yasuda T., Matsubara K., Nagai H. Detection of genetic alterations in the human gastric cancer cell lines by two-dimensional analysis of genomic DNA. Int. J. Oncol. 2000, 17:297-308.
104. Dai Z., Lakshmanan R.R., Zhu W.G., Smiraglia D.J., Rush L.J., Fruhwald M.C., Brena R.M., Li B., Wright F.A., Ross P., Otterson G.A., Plass C. Global methylation profiling of lung cancer identifies novel methylated genes. Neoplasia 2001, 3:314-323.
105. Dai Z., Zhu W.G., Morrison C.D., Brena R.M., Smiraglia D.J., Raval A., Wu Y.Z., Rush L.J., Ross P., Molina J.R., Otterson G.A., Plass C. A comprehensive search for DNA amplification in lung cancer identifies inhibitors of apoptosis cIAP1 and cIAP2 as candidate oncogenes. Hum. Mol. Genet. 2003, 12:791-801.
106. Motiwala T., Ghoshal K., Das A., Majumder S., Weichenhan D., Wu Y.Z., Holman K., James S.J., Jacob S.T., Plass C. Suppression of the protein tyrosine phosphatase receptor type O gene (PTPRO) by methylation in hepatocellular carcinomas. Oncogene 2003, 22:6319-6331.
107. Wu R., Lin L., Beer D.G., Ellenson L.H., Lamb B.J., Rouillard J.M., Kuick R., Hanash S., Schwartz D.R., Fearon E.R., Cho K.R. Amplification and overexpression of the L-MYC proto-oncogene in ovarian carcinomas. Am. J. Pathol. 2003, 162:1603-1610.
108. Park J., Brena R.M., Gruidl M., Zhou J., Huang T., Plass C., Tockman M.S. CpG island hypermethylation profiling of lung cancer using restriction landmark genomic scanning (RLGS) analysis. Cancer Biomark 2005, 1:193-200.
109. Asaga S., Ueda M., Jinno H., Kikuchi K., Itano O., Ikeda T., Kitajima M. Identification of a new breast cancer-related gene by restriction landmark genomic scanning. Anticancer Res. 2006, 26:35-42.
110. Smith J.F., Mahmood S., Song F., Morrow A., Smiraglia D., Zhang X., Rajput A., Higgins M.J., Krumm A., Petrelli N.J., Costello J.F., Nagase H., Plass C., Held W.A. Identification of DNA methylation in 3' genomic regions that are associated with upregulation of gene expression in colorectal cancer. Epigenetics 2007, 2:161-172.
111. Gonzalgo M.L., Liang G., Spruck C.H., Zingg J.M., Rideout W.M., Jones P.A. Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR. Cancer Res. 1997, 57:594-599.
112. Huang T.H., Laux D.E., Hamlin B.C., Tran P., Tran H., Lubahn D.B. Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique. Cancer Res. 1997, 57:1030-1034.
113. Kohno T., Kawanishi M., Inazawa J., Yokota J. Identification of CpG islands hypermethylated in human lung cancer by the arbitrarily primed-PCR method. Hum. Genet. 1998, 102:258-264.
114. Liang G., Robertson K.D., Talmadge C., Sumegi J., Jones P.A. The gene for a novel transmembrane protein containing epidermal growth factor and follistatin domains is frequently hypermethylated in human tumor cells. Cancer Res. 2000, 60:4907-4912.
115. Salem C.E., Markl I.D., Bender C.M., Gonzales F.A., Jones P.A., Liang G. PAX6 methylation and ectopic expression in human tumor cells. Int. J. Cancer 2000, 87:179-185.
116. Markl I.D., Cheng J., Liang G., Shibata D., Laird P.W., Jones P.A. Global and gene-specific epigenetic patterns in human bladder cancer genomes are relatively stable in vivo and in vitro over time. Cancer Res. 2001, 61:5875-5884.
117. Lo K.W., Tsang Y.S., Kwong J., To K.F., Teo P.M., Huang D.P. Promoter hypermethylation of the EDNRB gene in nasopharyngeal carcinoma. Int. J. Cancer 2002, 98:651-655.
118. Bahar A., Simpson D.J., Cutty S.J., Bicknell J.E., Hoban P.R., Holley S., Mourtada-Maarabouni M., Williams G.T., Clayton R.N., Farrell W.E. Isolation and characterization of a novel pituitary tumor apoptosis gene. Mol. Endocrinol. 2004, 18:1827-1839.
119. Wu M., Ho S.M. PMP24, a gene identified by MSRF, undergoes DNA hypermethylation-associated gene silencing during cancer progression in an LNCaP model. Oncogene 2004, 23:250-259.
120. Costa F.F, Paixao V.A., Cavalher F.P., Ribeiro K.B., Cunha I.W., Rinck J.A., O'Hare M., Mackay A., Soares F.A., Brentani R.R., Camargo A.A. SATR-1 hypomethylation is a common and early event in breast cancer. Cancer Genet. Cytogenet. 2006, 165:135-143.
121. Estecio M.R., Youssef E.M., Rahal P., Fukuyama E.E., Gois-Filho J.F., Maniglia J.V., Goloni-Bertollo E.M., Issa J.P., Tajara E.H. LHX6 is a sensitive methylation marker in head and neck carcinomas. Oncogene 2006, 25:5018-5026.
122. Lv Z., Zhang M., Bi J., Xu F., Hu S., Wen J. Promoter hypermethylation of a novel gene, ZHX2, in hepatocellular carcinoma. Am. J. Clin. Pathol. 2006, 125:740-746.
123. Tryndyak V, Kovalchuk O., Pogribny I.P. Identification of differentially methylated sites within unmethylated DNA domains in normal and cancer cells. Anal. Biochem. 2006, 356:202-207.
124. Kuznetsova E.B., Kekeeva T.V., Larin S.S., Zemlyakova V.V., Khomyakova A.V., Babenko O.V., Nemtsova M.V., Zaletayev D.V., Strelnikov V.V. Methylation of the BIN1 gene promoter CpG island associated with breast and prostate cancer. J. Carcinog. 2007, 6:9.
125. Zhao B.J., Tan S.N., Cui Y., Sun D.G., Ma X. Aberrant promoter methylation of the TPEF gene in esophageal squamous cell carcinoma. Dis. Esophagus 2008, 21:582-588.
126. Liu W.B., Liu J.Y., Ao L., Zhou Z.Y., Zhou Y.H., Cui Z.H., Yang H., Cao J. Dynamic changes in DNA methylation during multistep rat lung carcinogenesis induced by 3-methylcholanthrene and diethylnitrosamine. Toxicol. Lett. 2009, 189:5-13.
127. Zhao B.J., Sun D.G., Zhang M., Tan S.N., Ma X. Identification of aberrant promoter methylation of EDNRB gene in esophageal squamous cell carcinoma. Dis. Esophagus 2009, 22:55-61.
128. Frigola J., Ribas M., Risques R.A., Peinado M.A. Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS). Nucleic Acids Res. 2002, 30:e28.
129. Toyota M., Ho C., Ahuja N., Jair K.W., Li Q., Ohe-Toyota M., Baylin S.B., Issa J.P. Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res. 1999, 59:2307-2312.
130. Paz M.F., Wei S., Cigudosa J.C., Rodriguez-Perales S., Peinado M.A., Huang T.H., Esteller M. Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases. Hum. Mol. Genet. 2003, 12:2209-2219.
131. Sadikovic B., Haines T.R., Butcher D.T., Rodenhiser D.I. Chemically induced DNA hypomethylation in breast carcinoma cells detected by the amplification of intermethylated sites. Breast Cancer Res. 2004, 6:R329-337.
132. Frigola J., Sole X., Paz M.F., Moreno V., Esteller M., Capella G., Peinado M.A. Differential DNA hypermethylation and hypomethylation signatures in colorectal cancer. Hum. Mol. Genet. 2005, 14:319-326.
133. Frigola J., Song J., Stirzaker C., Hinshelwood R.A., Peinado M.A., Clark S.J. Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat. Genet. 2006, 38:540-549.
134. Fraga M.F., Ballestar E., Paz M.F., Ropero S., Setien F., Ballestar M.L., Heine-Suner D., Cigudosa J.C., Urioste M., Benitez J., Boix-Chornet M., Sanchez-Aguilera A., Ling C., Carlsson E., Poulsen P., Vaag A., Stephan Z., Spector T.D., Wu Y.Z., Plass C., Esteller M. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:10604-10609.
135. Yamamoto F., Yamamoto M., Soto J.L., Kojima E., Wang E.N., Perucho M., Sekiya T., Yamanaka H. Notl-Msell methylation-sensitive amplied fragment length polymorhism for DNA methylation analysis of human cancers. Electrophoresis 2001, 22:1946-1956.
136. Vos P., Hogers R., Bleeker M., Reijans M., van de Lee T., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M., et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995, 23:4407-4414.
137. Kageyama S., Shinmura K., Yamamoto H., Goto M., Suzuki K., Tanioka F., Tsuneyoshi T., Sugimura H. Fluorescence-labeled methylation-sensitive amplified fragment length polymorphism (FL-MS-AFLP) analysis for quantitative determination of DNA methylation and demethylation status. Jpn. J. Clin. Oncol. 2008, 38:317-322.
138. Yamamoto F., Yamamoto M. A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses. Mol. Genet. Genomics 2004, 271:678-686.
139. Albertson D.G., Ylstra B., Segraves R., Collins C., Dairkee S.H., Kowbel D., Kuo W.L., Gray J.W., Pinkel D. Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat. Genet. 2000, 25:144-146.
140. Kutsenko A.S., Gizatullin R.Z., Al-Amin A.N., Wang F., Kvasha S.M., Podowski R.M., Matushkin Y.G., Gyanchandani A., Muravenko O.V., Levitsky V.G., Kolchanov N.A., Protopopov A.I., Kashuba V.I., Kisselev L.L., Wasserman W., Wahlestedt C., Zabarovsky E.R. NotI flanking sequences: a tool for gene discovery and verification of the human genome. Nucleic Acids Res. 2002, 30:3163-3170.
141. Ahuja N., Mohan A.L., Li Q., Stolker J.M., Herman J.G., Hamilton S.R., Baylin S.B., Issa J.P. Association between CpG island methylation and microsatellite instability in colorectal cancer. Cancer Res. 1997, 57:3370-3374.
142. Weisenberger D.J., Siegmund K.D., Campan M., Young J., Long T.I., Faasse M.A., Kang G.H., Widschwendter M., Weener D., Buchanan D., Koh H., Simms L., Barker M., Leggett B., Levine J., Kim M., French A.J., Thibodeau S.N., Jass J., Haile R., Laird P.W. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat. Genet. 2006, 38:787-793.
143. Issa J.P., Shen L., Toyota M. CIMP, at last. Gastroenterology 2005, 129:1121-1124.
144. Issa J.P Colon cancer: it's CIN or CIMP. Clin. Cancer Res. 2008, 14:5939-5940.
145. Perucho M., Suzuki K. Reply to Commentary. New insights into a controversial topic: the methylation-cancer connection. Gastroenterology 2007, 132:2070-2071.
146. Vire E., Brenner C., Deplus R., Blanchon L., Fraga M., Didelot C., Morey L., Van Eynde A., Bernard D., Vanderwinden J.M., Bollen M., Esteller M., Di Croce L., de Launoit Y., Fuks F. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2006, 439:871-874.
147. Schlesinger Y., Straussman R., Keshet I., Farkash S., Hecht M., Zimmerman J., Eden E., Yakhini Z., Ben-Shushan E., Reubinoff B.E., Bergman Y., Simon I., Cedar H. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet. 2007, 39:232-236.
148. Widschwendter M., Fiegl H., Egle D., Mueller-Holzner E., Spizzo G., Marth C., Weisenberger D.J., Campan M., Young J., Jacobs I., Laird P.W. Epigenetic stem cell signature in cancer. Nat. Genet. 2007, 39:157-158.
149. Kane M.F., Loda M., Gaida G.M., Lipman J., Mishra R., Goldman H., Jessup J.M., Kolodner R. Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res. 1997, 57:808-811.
150. Veigl M.L., Kasturi L., Olechnowicz J., Ma A.H., Lutterbaugh J.D., Periyasamy S., Li G.M., Drummond J., Modrich P.L., Sedwick W.D., Markowitz S.D. Biallelic inactivation of hMLH1 by epigenetic gene silencing, a novel mechanism causing human MSI cancers. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:8698-8702.
151. Bracken A.P, Dietrich N., Pasini D., Hansen K.H., Helin K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 2006, 20:1123-1136.