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Updated: Feb 12, 2026
08:30
Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
Published on: August 21, 2016
52.1K
Infinium DNA Methylation Microarrays on Formalin-Fixed, Paraffin-Embedded Samples
Sebastian Moran1, Manel Esteller2,3,4
1Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.
Methods in Molecular Biology (Clifton, N.J.)
|April 2, 2018
Summary
Formalin-fixed, paraffin-embedded (FFPE) samples can now yield high-quality DNA for methylation profiling. A novel FFPE restoration procedure enables the use of Infinium Methylation beadchips, opening new research opportunities.
Area of Science:
- Epigenetics
- Molecular Biology
- Genomics
Background:
- Formalin-fixed, paraffin-embedded (FFPE) samples are a valuable resource but typically yield fragmented DNA.
- Fragmented DNA from FFPE samples is incompatible with standard Infinium Methylation beadchip platforms.
- This limitation hinders large-scale epigenetic studies using FFPE tissues.
Purpose of the Study:
- To detail a comprehensive FFPE restoration procedure.
- To enable high-throughput DNA methylation profiling from FFPE samples.
- To expand the utility of Infinium Methylation beadchips for FFPE-derived DNA.
Main Methods:
- A step-by-step FFPE DNA restoration protocol is described.
- The protocol focuses on recovering DNA quality suitable for downstream analysis.
- The optimized DNA is then processed using Infinium Methylation beadchips.
Main Results:
- Successful generation of high-quality methylation profiles from FFPE samples.
- Demonstration of FFPE sample compatibility with Infinium Methylation beadchips after restoration.
- Validation of the FFPE restoration procedure for epigenetic studies.
Conclusions:
- The FFPE restoration procedure effectively overcomes DNA fragmentation issues.
- This method significantly broadens the application of Infinium Methylation beadchips.
- New avenues for epigenetic research using archival FFPE samples are now accessible.
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