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

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

Research output: Contribution to journalReview article

9 Citations (Scopus)

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 Db > 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 (R2 > 0.970), highly correlated β-values between FF-FFPE (R2 > 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.

Impact: 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.

Original languageEnglish (US)
Pages (from-to)2622-2631
Number of pages10
JournalCancer Epidemiology Biomarkers and Prevention
Volume23
Issue number12
DOIs
StatePublished - Dec 1 2014

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Epigenomics
DNA Repair
Paraffin
Formaldehyde
Methylation
DNA
Ligation
Neoplasms
Ligases
Epidemiology
Biomarkers
Genome

All Science Journal Classification (ASJC) codes

  • Epidemiology
  • Oncology

Cite this

Expanding epigenomics to archived FFPE tissues : An evaluation of DNA repair methodologies. / Siegel, Erin M.; Berglund, Anders E.; Riggs, Bridget M.; Eschrich, Steven A.; Putney, Ryan M.; Ajidahun, Abidemi O.; Coppola, Domenico; Shibata, David.

In: Cancer Epidemiology Biomarkers and Prevention, Vol. 23, No. 12, 01.12.2014, p. 2622-2631.

Research output: Contribution to journalReview article

Siegel, EM, Berglund, AE, Riggs, BM, Eschrich, SA, Putney, RM, Ajidahun, AO, Coppola, D & Shibata, D 2014, 'Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies', Cancer Epidemiology Biomarkers and Prevention, vol. 23, no. 12, pp. 2622-2631. https://doi.org/10.1158/1055-9965.EPI-14-0464
Siegel, Erin M. ; Berglund, Anders E. ; Riggs, Bridget M. ; Eschrich, Steven A. ; Putney, Ryan M. ; Ajidahun, Abidemi O. ; Coppola, Domenico ; Shibata, David. / Expanding epigenomics to archived FFPE tissues : An evaluation of DNA repair methodologies. In: Cancer Epidemiology Biomarkers and Prevention. 2014 ; Vol. 23, No. 12. pp. 2622-2631.
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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 Db > 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 (R2 > 0.970), highly correlated β-values between FF-FFPE (R2 > 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.Impact: 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.",
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T1 - Expanding epigenomics to archived FFPE tissues

T2 - An evaluation of DNA repair methodologies

AU - Siegel, Erin M.

AU - Berglund, Anders E.

AU - Riggs, Bridget M.

AU - Eschrich, Steven A.

AU - Putney, Ryan M.

AU - Ajidahun, Abidemi O.

AU - Coppola, Domenico

AU - Shibata, David

PY - 2014/12/1

Y1 - 2014/12/1

N2 - 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 Db > 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 (R2 > 0.970), highly correlated β-values between FF-FFPE (R2 > 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.Impact: 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.

AB - 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 Db > 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 (R2 > 0.970), highly correlated β-values between FF-FFPE (R2 > 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.Impact: 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.

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