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Updated: Feb 12, 2026

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
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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
PubMed

Insights

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.
Keywords:
DNA methylationDegraded DNAEpigeneticsFFPEFormalin-fixed, paraffin-embeddedMethylationMicroarrayRestoration

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