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Updated: Apr 15, 2026
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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
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Formalin-fixed, paraffin-embedded (FFPE) tissue epigenomics using Infinium HumanMethylation450 BeadChip assays
Tim C de Ruijter1, Joep P J de Hoon1, Jeroen Slaats1
11] Division of Medical Oncology, Maastricht University Medical Center, Maastricht, The Netherlands [2] GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.
Summary
A DNA restoration protocol enables genome-wide DNA methylation analysis using formalin-fixed, paraffin-embedded (FFPE) tissues. This method provides accurate and reproducible results comparable to fresh-frozen samples, expanding epigenomics research on archived tissues.
Area of Science:
- Epigenetics and Genomics
- Molecular Pathology
- Cancer Research
Background:
- Current genome-wide DNA methylation detection methods require high-quality DNA from fresh-frozen (FF) samples.
- Archived clinical samples are predominantly formalin-fixed, paraffin-embedded (FFPE), yielding poor-quality DNA unsuitable for standard analysis.
Purpose of the Study:
- To evaluate a DNA restoration protocol for the Infinium HumanMethylation450 BeadChip assay (HM-450K) using FFPE DNA.
- To assess the accuracy, reproducibility, and robustness of DNA methylation analysis on FFPE-derived DNA after restoration.
Main Methods:
- DNA samples from normal colon and breast cancer tissues were analyzed using HM-450K.
- FFPE DNA was processed with (FFPEr) and without a DNA restoration protocol.
- Differentially methylated genes were validated using nested methylation-specific PCR (MSP).
Main Results:
- High correlation (ρ=0.9590) was observed between matched FF and FFPEr samples, significantly higher than FF/FFPE (ρ=0.8051).
- Probe detection rates in FFPEr samples (98.37%) were comparable to FF samples (99.98%), unlike FFPE samples (82.31%).
- Assay robustness was maintained with sample archival up to 10 years and with 100 ng DNA input; 4/5 differentially methylated genes were validated by MSP.
Conclusions:
- The FFPE DNA restoration protocol enables robust, accurate, and reproducible HM-450K DNA methylation analysis on FFPE-derived DNA.
- Results are comparable to those obtained from FF tissues, facilitating epigenomics research on valuable archived samples.
- This approach provides an epigenomics platform for molecular pathological epidemiology on limited, archived tissue specimens.
