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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
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Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium
Sebastián Moran1, Miguel Vizoso1, Anna Martinez-Cardús1
1Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); Barcelona, Catalonia, Spain.
Epigenetics
|April 16, 2014
Summary
Restoring degraded DNA from formalin-fixed paraffin-embedded (FFPE) samples enables their use with Infinium Methylation arrays. This DNA repair and ligation method validates FFPE data against fresh-frozen samples.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- Formalin-fixed paraffin-embedded (FFPE) samples often contain highly degraded DNA.
- Degraded DNA quality restricts the application of sensitive molecular techniques like Infinium Methylation microarrays.
Purpose of the Study:
- To develop and validate a DNA restoration procedure for FFPE samples.
- To enable the use of FFPE samples for Infinium HumanMethylation450 BeadChip analysis.
Main Methods:
- An FFPE DNA restoration protocol involving DNA repair and ligation was applied.
- Paired fresh-frozen (FF) and FFPE samples were analyzed.
- FFPE sample results were validated against matched FF samples.
Main Results:
- The FFPE restoration procedure successfully improved DNA quality.
- Methylation data from restored FFPE samples were comparable to matched FF samples.
- The Infinium HumanMethylation450 BeadChip assay could be reliably performed on restored FFPE DNA.
Conclusions:
- DNA restoration is effective for analyzing FFPE samples using methylation arrays.
- This method expands the utility of archived FFPE tissues for epigenetic studies.
- FFPE samples can be a valuable resource for high-throughput methylation analysis with appropriate processing.
