Quantitative analysis of DNA methylation after whole bisulfitome amplification of a minute amount of DNA from body fluids

Epigenetics

Volumn 4, Issue 4, 2009, Pages 221-230

  Vaissière, Thomas ^a   Cuenin, Cyrille ^a   Paliwal, Anupam ^a   Vineis, Paolo ^b   Hainaut, Pierre ^a   Herceg, Zdenko ^a   Hoek, G ^c   Krzyzanowski, M ^c   Airoldi, L ^c   Dunning, A ^c   Garte, S ^c   Hainaut, P ^c   Malaveille, C ^c   Overvad, K ^c   Clavel Chapelon, F ^c   Linseisen, J ^c   Boeing, H ^c   Trichopoulou, A ^c   Trichopoulos, D ^c   Kaladidi, A ^c   Palli, D ^c   Krogh, V ^c   Tumino, R ^c   Panico, S ^c   Bueno De Mesquita, H B ^c   Peeters, P H ^c   Kumle, M ^c   Gonzalez, C A ^c   Martinez, C ^c   Dorronsoro, M ^c   Barricarte, A ^c   Navarro, C ^c   Quiros, J R ^c   Berglund, G ^c   Janzon, L ^c   Jarvholm, B ^c   Day, N E ^c   Key, T J ^c   Saracci, R ^c   Kaaks, R ^c   Riboli, E ^c   more..

^a INTERNATIONAL AGENCY FOR RESEARCH ON CANCER   (France)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c NONE

Author keywords

Biomarkers; Cancer; DNA methylation; Epigenetics; Plasma DNA; Quantitative detection

Indexed keywords

5,10 METHYLENETETRAHYDROFOLATE REDUCTASE (FADH2); BISULFITE; CYCLIN DEPENDENT KINASE INHIBITOR 2A; PROTEIN MLH1; RAS ASSOCIATION DOMAIN FAMILY PROTEIN 1A;

ACCURACY; ANALYTIC METHOD; ARTICLE; BODY FLUID; CONTROLLED STUDY; CPG ISLAND; DNA DETERMINATION; DNA METHYLATION; DNA SEQUENCE; DNA TEMPLATE; EPIGENETICS; GENE AMPLIFICATION; HUMAN; LONG INTERSPERSED REPEAT; PYROSEQUENCING; QUANTITATIVE ANALYSIS; QUANTITATIVE METHYLATION ANALYSIS OF MINUTE DNA AMOUNT AFTER WHOLE BISULFITOME AMPLIFICATION; VALIDATION PROCESS;

EID: 69949108607     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.8833     Document Type: Article

References (24)

1. Chen XQ, Stroun M, Magnenat JL, Nicod LP, Kurt AM, Lyautey J, et al. Microsatellite alterations in plasma DNA of small cell lung cancer patients. Nat Med 1996; 2:1033-5.
2. Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, et al. Circulating mutant DNA to assess tumor dynamics. Nat Med 2008; 14:985-90.
3. Herceg Z. Epigenetics and cancer: towards an evaluation of the impact of environmental and dietary factors. Mutagenesis 2007; 22:91-103.
4. Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer 2003; 3:253-66.
5. Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007; 8:286-98.
6. Sanchez-Cespedes M, Esteller M, Wu L, Nawroz-Danish H, Yoo GH, Koch WM, et al. Gene promoter hypermethylation in tumors and serum of head and neck cancer patients. Cancer Res 2000; 60:892-5.
7. Rosas SL, Koch W, da Costa Carvalho MG, Wu L, Califano J, Westra W, et al. Promoter hypermethylation patterns of p16, O6-methylguanine-DNA-methyltransferase, and death-associated protein kinase in tumors and saliva of head and neck cancer patients. Cancer Res 2001; 61:939-42.
8. Cairns P, Esteller M, Herman JG, Schoenberg M, Jeronimo C, Sanchez-Cespedes M, et al. Molecular detection of prostate cancer in urine by GSTP1 hypermethylation. Clin Cancer Res 2001; 7:2727-30.
9. Belinsky SA, Palmisano WA, Gilliland FD, Crooks LA, Divine KK, Winters SA, et al. Aberrant promoter methylation in bronchial epithelium and sputum from current and former smokers. Cancer Res 2002; 62:2370-7.
10. Bearzatto A, Conte D, Frattini M, Zaffaroni N, Andriani F, Balestra D, et al. p16(INK4A) Hypermethylation detected by fluorescent methylation-specific PCR in plasmas from non-small cell lung cancer. Clin Cancer Res 2002; 8:3782-7.
11. ARF methylation as a potential biomarker for human bladder cancer. Biochem Biophys Res Commun 2006; 339:790-6.
12. Belinsky SA, Klinge DM, Dekker JD, Smith MW, Bocklage TJ, Gilliland FD, et al. Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clin Cancer Res 2005; 11:6505-11.
13. Shaw RJ, Akufo-Tetteh EK, Risk JM, Field JK, Liloglou T. Methylation enrichment pyrosequencing: combining the specificity of MSP with validation by pyrosequencing. Nucleic Acids Res 2006; 34:78.
14. Tost J, Dunker J, Gut IG. Analysis and quantification of multiple methylation variable positions in CpG islands by Pyrosequencing. Biotechniques 2003; 35:152-6.
15. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R. Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques 2003; 35:146-50.
16. Yang AS, Estecio MR, Doshi K, Kondo Y, Tajara EH, Issa JP. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 2004; 32:38.
17. Mill J, Yazdanpanah S, Guckel E, Ziegler S, Kaminsky Z, Petronis A. Whole genome amplification of sodium bisulfite-treated DNA allows the accurate estimate of methylated cytosine density in limited DNA resources. Biotechniques 2006; 41:603-7.
18. Peluso M, Hainaut P, Airoldi L, Autrup H, Dunning A, Garte S, et al. Methodology of laboratory measurements in prospective studies on gene-environment interactions: the experience of GenAir. Mutat Res 2005; 574:92-104.
19. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 2006; 38:1378-85.
20. 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; 28:32.
21. Riboli E, Kaaks R. The EPIC Project: rationale and study design. European Prospective Investigation into Cancer and Nutrition. Int J Epidemiol 1997; 26:6-14.
22. Slimani N, Kaaks R, Ferrari P, Casagrande C, Clavel-Chapelon F, Lotze G, et al. European Prospective Investigation into Cancer and Nutrition (EPIC) calibration study: rationale, design and population characteristics. Public Health Nutr 2002; 5:1125-45.
23. Gormally E, Vineis P, Matullo G, Veglia F, Caboux E, Le Roux E, et al. TP53 and KRAS2 mutations in plasma DNA of healthy subjects and subsequent cancer occurrence: a prospective study. Cancer Res 2006; 66:6871-6.
24. Vaissiere T, Hung RJ, Zaridze D, Moukeria A, Cuenin C, Fasolo V, et al. Quantitative analysis of DNA methylation profiles in lung cancer identifies aberrant DNA methylation of specific genes and its association with gender and cancer risk factors. Cancer Res 2009; 69:243-52.