Assessment of three epigenotypes in colorectal cancer by combined bisulfite restriction analysis

Molecular Carcinogenesis

Volumn 51, Issue 12, 2012, Pages 1003-1008

  Karpinski, Pawel ^a   Szmida, Elzbieta ^a   Misiak, Blazej ^a   Ramsey, David ^b   Leszczynski, Przemyslaw ^a   Bebenek, Marek ^c   Sedziak, Tomasz ^c   Grzebieniak, Zygmunt ^a   Jonkisz, Anna ^a   Lebioda, Arleta ^a   Sasiadek, Maria M ^a  

^a WROCLAW MEDICAL UNIVERSITY   (Poland)

^b UNIVERSITY OF LIMERICK   (Ireland)

^c Wroclaw   (Poland)

Author keywords

COBRA; Colorectal cancer; Epigenotypes; Methylation; Methylator

Indexed keywords

B RAF KINASE; K RAS PROTEIN; PROTEIN MLH1;

ADULT; AGED; ARTICLE; BRAF GENE; COLON; COLORECTAL CANCER; COMBINED BISULFITE RESTRICTION ANALYSIS; CONTROLLED STUDY; DNA METHYLATION; EPIGENETICS; FEMALE; GENE; GENE MUTATION; GENOTYPE; HEREDITY; HIGH METHYLATION EPIGENOTYPE; HUMAN; HUMAN TISSUE; INTERMEDIATE METHYLATION EPIGENOTYPE; KRAS GENE; LOW METHYLATION EPIGENOTYPE; MAJOR CLINICAL STUDY; MALE; MICROSATELLITE INSTABILITY; MLH1 GENE; PRIORITY JOURNAL; RESTRICTION MAPPING;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; AGED; BASE SEQUENCE; CLUSTER ANALYSIS; COLORECTAL NEOPLASMS; DNA METHYLATION; DNA PRIMERS; EPIGENESIS, GENETIC; FEMALE; GENES, RAS; GENOTYPE; HUMANS; MALE; MIDDLE AGED; NUCLEAR PROTEINS; POLYMERASE CHAIN REACTION; PROTO-ONCOGENE PROTEINS B-RAF; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84867745258     PISSN: 08991987     EISSN: 10982744     Source Type: Journal    
DOI: 10.1002/mc.20871     Document Type: Article

References (20)

1. Schuebel KE, Chen W, Cope L, et al. Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet 2007;3:1709-1723.
2. Weisenberger DJ, Siegmund KD, Campan M, et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 2006;38:787-793.
3. Nosho K, Irahara N, Shima K, et al. Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample. PLoS One 2008;3:e3698.
4. Yagi K, Akagi K, Hayashi H, et al. Three DNA methylation epigenotypes in human colorectal cancer. Clin Cancer Res 2010;16:21-33.
5. Ogino S, Kawasaki T, Kirkner GJ, Loda M, Fuchs CS. CpG island methylator phenotype-low (CIMP-low) in colorectal cancer: Possible associations with male sex and KRAS mutations. J Mol Diagn 2006;8:582-588.
6. Shen L, Toyota M, Kondo Y, et al. Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc Natl Acad Sci USA 2007;104:18654-18659.
7. Ogino S, Goel A. Molecular classification and correlates in colorectal cancer. J Mol Diagn 2008;10:13-27.
8. Hinoue T, Weisenberger DJ, Lange CP, et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 2011; DOI: 10.1101/gr.117523.110.
9. Ogino S, Hazra A, Tranah GJ, et al. MGMT germline polymorphism is associated with somatic MGMT promoter methylation and gene silencing in colorectal cancer. Carcinogenesis 2007;28:1985-1990.
10. 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.
11. Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M. DNA methylation: Bisulphite modification and analysis. Nat Protoc 2006;1:2353-2364.
12. Moskalev EA, Zavgorodnij MG, Majorova SP, et al. Correction of PCR-bias in quantitative DNA methylation studies by means of cubic polynomial regression. Nucleic Acids Res 2011;39:e77.
13. Docherty SJ, Davis OS, Haworth CM, Plomin R, Mill J. Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation. Epigenetics Chromatin 2009;2:3.
14. Samowitz WS, Albertsen H, Herrick J, et al. Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer. Gastroenterology 2005;129:837-845.
15. Sapio MR, Posca D, Troncone G, et al. Detection of BRAF mutation in thyroid papillary carcinomas by mutant allele-specific PCR amplification (MASA). Eur J Endocrinol 2006;154:341-348.
16. Miranda E, Destro A, Malesci A, et al. Genetic and epigenetic changes in primary metastatic and nonmetastatic colorectal cancer. Br J Cancer 2006;95:1101-1107.
17. Buhard O, Cattaneo F, Wong YF, et al. Multipopulation analysis of polymorphisms in five mononucleotide repeats used to determine the microsatellite instability status of human tumors. J Clin Oncol 2006;24:241-251.
18. Xiong Z, Laird PW. COBRA: A sensitive and quantitative DNA methylation assay. Nucleic Acids Res 1997;25:2532-2534.
19. Vincze T, Posfai J, Roberts RJ. NEBcutter: A program to cleave DNA with restriction enzymes. Nucleic Acids Res 2003;31:3688-3691.
20. Chan AO, Issa JP, Morris JS, Hamilton SR, Rashid A. Concordant CpG island methylation in hyperplastic polyposis. Am J Pathol 2002;160:529-536.