Data from Expanding Epigenomics to Archived FFPE Tissues: An Evaluation of DNA Repair Methodologies

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<div>Abstract<p><b>Background:</b> 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.</p><p><b>Methods:</b> 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.</p><p><b>Results:</b> The Illumina Restore kit outperformed the REPLI-g ligation method with respect to reproducibility of replicates (<i>R</i><sup>2</sup> > 0.970), highly correlated β-values between FF-FFPE (<i>R</i><sup>2</sup> > 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.</p><p><b>Conclusions:</b> 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.</p><p><b>Impact:</b> 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.</p><p>See all the articles in this <a href="http://cebp.aacrjournals.org/content/23/12.toc#CEBPFocus" target="_blank"><i>CEBP Focus</i></a> section, “Biomarkers, Biospecimens, and New Technologies in Molecular Epidemiology.”</p><p><i>Cancer Epidemiol Biomarkers Prev; 23(12); 2622–31. ©2014 AACR</i>.</p></div>