Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies

Cancer Epidemiology Biomarkers and Prevention

Volumn 23, Issue 12, 2014, Pages 2622-2631

  Siegel, Erin M ^a   Berglund, Anders E ^a   Riggs, Bridget M ^a   Eschrich, Steven A ^a   Putney, Ryan M ^a   Ajidahun, Abidemi O ^a   Coppola, Domenico ^a   Shibata, David ^a  

^a H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; DNA; FORMALDEHYDE; LIGASE; PARAFFIN;

CANCER TISSUE; COLON ADENOCARCINOMA; CONTROLLED STUDY; CPG ISLAND; DNA DETERMINATION; DNA EXTRACTION; DNA METHYLATION; DNA REPAIR; EPIGENETICS; FEMALE; GENE LOCUS; GENETIC ASSOCIATION; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; MALE; REVIEW; TISSUE FIXATION; GENETICS; NEOPLASM; PROCEDURES;

DNA REPAIR; EPIGENOMICS; FORMALDEHYDE; HUMANS; NEOPLASMS; PARAFFIN EMBEDDING; TISSUE FIXATION;

EID: 84919391826     PISSN: 10559965     EISSN: 15387755     Source Type: Journal    
DOI: 10.1158/1055-9965.EPI-14-0464     Document Type: Review

References (31)

1. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, et al. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods 2013; 10: 949-55.
2. Rakyan VK, Down TA, Balding D.J., Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet 2011; 12: 529-41.
3. Feinberg AP. Genome-scale approaches to the epigenetics of common human disease. Virchows Arch 2010; 456: 13-21.
4. Feinberg AP. Phenotypic plasticity and the epigenetics of human disease. Nature 2007; 447: 433-40.
5. Besingi W, Johansson A. Smoke-related DNA methylation changes in the etiology of human disease. Hum Mol Genet 2014; 23: 2290-7.
6. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13: 484-92.
7. Timp W, Feinberg AP Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer 2013; 13: 497-510.
8. Brait M, Sidransky D. Cancer epigenetics: above and beyond. Toxicol Mech Methods 2011; 21: 275-88.
9. Taby R, Issa JP Cancer epigenetics. CA Cancer J Clin 2010; 60: 376-92.
10. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006; 314: 268-74.
11. Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, et al. Genome-wide DNA methylation profiling using Infinium(R) assay. Epigenomics 2009; 1: 177-200.
12. Dedeurwaerder S, Defrance M, Calonne E., Denis H, Sotiriou C, Fuks F. Evaluation of the Infinium Methylation 450K technology. Epigenomics 2011; 3: 771-84.
13. Mohn F, Weber M, Schubeler D., Roloff TC. Methylated DNA immu-noprecipitation (MeDIP). Methods Mol Biol 2009; 507: 55-64.
14. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 2011; 6: 468-81.
15. Bosso M, Al-Mulla F. Whole genome amplification of DNA extracted from FFPE tissues. Methods Mol Biol 2011; 724: 161-80.
16. Gilbert MT, Haselkorn T, Bunce M., Sanchez JJ, Lucas SB, Jewell LD, et al The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when? PLoS ONE 2007; 2:e537.
17. Thirwell C, Eymard M, Feber A., Teschendorff A, Pearce K, Lechner M., et al. Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium Human-Methylation27 BeadChip. Methods 2010; 52: 248-54.
18. Jasmine F, Rahaman R, Roy S., Raza M, Paul R, Rakibuz-Zaman M, et al. Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue. BMC Res Notes 2012; 5:117.
19. Illumina. Infinium HD FFPE Restore Protocol, Catalog # WG-901-2004. 2011 [cited 2012 06/20/2012]; Available from: http://supportres.illumina.com/documents/myillumina/5c3d90a3-793c-4a8b-932b-0434590f98ef/infinium-ffpe-sample-restore-book-let-15014614-c.pdf
20. Grunau C, Clark SJ, Rosenthal A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 2001; 29:E65-5.
21. Ajani JA, Winter KA, Gunderson L.L., Pedersen J., Benson AB III, Thomas CR Jr, et al. Fluorouracil, mitomycin, and radiotherapy vsfluorouracil, cisplatin, and radiotherapy for carcinoma of the anal canal: a randomized controlled trial. JAMA 2008; 299: 1914-21.
22. Siegel EM, Eschrich SA, Winter K.A., Riggs B., Berglund A, Ajidahun A, et al Epigenomic characterization of locally advanced anal cancer: an RTOG 98-11 specimen study. Dis Colon Rectum 2014; 57: 941-57.
23. Hansen K, Aryee M. Minfi: Analyze Illumina 450k Methylation Arrays. Rpackage version 12; 2012.
24. Maksimovic J, Gordon L, Oshlack A. SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 Bead-Chips. Genome Biol 2012; 13:R44.
25. Pidsley R, Wong CC, Volta M, Lunnon K., Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics 2013; 14:293.
26. Gentleman RC, Carey VJ, Bates D.M., Bolstad B., Dettling M, Dudoit S, et al Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5:R80.
27. Schalkwyk LC, Pidsley R, Wong C.C., Wfcbn T., Defrance M, Teschendorff AE, et al wateRmelon: Illumina 450 methylation array normalization and metrics. R package. 1.4.0. ed; 2013.
28. Wilhelm-Benartzi C.S., Koestler DC, Karagas M.R., Flanagan JM, Christensen BC, Kelsey KT, et al Review of processing and analysis methods for DNA methylation array data. Br J Cancer 2013; 109: 1394-402.
29. Wu MC, Joubert BR, Kuan P.F., Haberg SE, Nystad W, Peddada SD, et al A systematic assessment of normalization approaches for the Infinium 450K methylation platform. Epigenetics 2014; 9: 318-29.
30. Lechner M, Fenton T, West J., Wilson G, Feber A, Henderson S., et al. Identification and functional validation of HPV-mediated hypermethy-lation in head and neck squamous cell carcinoma. Genome Med 2013; 5:15.
31. Dumenil TD, Wockner LF, Bettington M, McKeone D.M., Klein K., Bowdler LM, et al. Genome-wide DNA methylation analysis of formalin-fixed paraffin embedded colorectal cancer tissue. Genes Chromosomes Cancer 2014; 53: 537-48.