title: Expanding epigenomics to archived FFPE tissues: an evaluation of DNA repair methodologies.
abstract: BACKGROUND
  Epigenome-wide association studies are emerging in the field of cancer epidemiology with the rapid development of large-scale methylation array platforms. Until recently, these methods were only valid for DNA from flash frozen (FF) tissues. Novel techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissues have emerged; however, a direct comparison of FFPE DNA repair methods before analysis on genome-wide methylation array to matched FF tissues has not been conducted.
  
  
  METHODS
  We conducted a systematic performance comparison of two DNA repair methods (REPLI-g Ligase vs. Infinium HD Restore Kit) on FFPE-DNA compared with matched FF tissues on the Infinium 450K array. A threshold of discordant methylation between FF-FFPE pairs was set at Δβ > 0.3. The correlations of β-values from FF-FFPE pairs were compared across methods and experimental conditions.
  
  
  RESULTS
  The Illumina Restore kit outperformed the REPLI-g ligation method with respect to reproducibility of replicates (R(2) > 0.970), highly correlated β-values between FF-FFPE (R(2) > 0.888), and fewest discordant loci between FF-FFPE (≤0.61%). The performance of the Restore kit was validated in an independent set of 121 FFPE tissues.
  
  
  CONCLUSIONS
  The Restore kit outperformed RELPI-g ligation in restoring FFPE-derived DNA before analysis on the Infinium 450K methylation array. Our findings provide critical guidance that may significantly enhance the breadth of diseases that can be studied by methylomic profiling.
  
  
  CONCLUSIONS
  Epigenomic studies using FFPE tissues should now be considered among cancers that have not been fully characterized from an epigenomic standpoint. These findings promote novel epigenome-wide studies focused on cancer etiology, identification of novel biomarkers, and developing targeted therapies. See all the articles in this CEBP Focus section, "Biomarkers, Biospecimens, and New Technologies in Molecular Epidemiology."
authors.affiliation: Department of Cancer Epidemiology, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. Erin.Siegel@moffitt.org david.shibata@moffitt.org.
authors.forename: Erin M
authors.initials: EM
authors.lastname: Siegel
authors.affiliation: Department of Biostatistics and Bioinformatics, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
authors.forename: Anders E
authors.initials: AE
authors.lastname: Berglund
authors.affiliation: Department of Cancer Epidemiology, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
authors.forename: Bridget M
authors.initials: BM
authors.lastname: Riggs
authors.affiliation: Department of Biostatistics and Bioinformatics, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Eschrich
authors.affiliation: Department of Biostatistics and Bioinformatics, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
authors.forename: Ryan M
authors.initials: RM
authors.lastname: Putney
authors.affiliation: Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
authors.forename: Abidemi O
authors.initials: AO
authors.lastname: Ajidahun
authors.affiliation: Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
authors.forename: Domenico
authors.initials: D
authors.lastname: Coppola
authors.affiliation: Department of Cancer Epidemiology, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. Erin.Siegel@moffitt.org david.shibata@moffitt.org.
authors.forename: David
authors.initials: D
authors.lastname: Shibata
mesh_terms: D004260:DNA Repair / Q000235:genetics*; D057890:Epigenomics / Q000379:methods*; D005557:Formaldehyde; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D016612:Paraffin Embedding; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D005557:Formaldehyde