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What is FFPE Tissue?

Updated on October 25, 2017
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Freelance Writer and blogger "This is no art, we all can taste life as it is, once we stop judging and start accepting."

FFPE stands for formalin-fixed, paraffin-embedded tissue. Tissue samples are stored as fresh-frozen tissue in bio-banks or as formalin-fixed paraffin-embedded tissue FFPE sections in clinical archives.

If a biopsy specimen is sent to a hospital for examination, it will be preserved in formalin (formaldehyde), and then embedded in a paraffin wax block.

In recent times, techniques have been developed to recover DNA, RNA, and proteins from FFPE tissue sections. This opens up a vast section of preserved, annotated material that can be used for molecular biology and biochemistry studies.

Harvesting of FFPE tissue sections

In FFPE, two enrichment techniques are often utilized:

  • laser capture micro-dissection (LCM),
  • microtome sectioning

LCM enables highly focused tissue harvesting. It can be used to isolate specific, well-preserved cell types in heterogeneous tissues.

Microtome sectioning is a process where thin sections are cut from FFPE tissue sections. Microtome-cut sections often include tissue that is heterogeneous in cell preservation and composition. This may lead to the homogenization of molecular features which are best investigated separately.

Preparation and preservation of FFPE tissue sections

Tissue sections are preserved for IHC by processes like fixation, embedding and freezing.

Fixation of the tissue section is necessary to maintain cell and tissue morphology during the IHC experiment and during storage. This also prevents the autolysis and necrosis of excised tissues. It also preserves antigenicity and enhances the refractive index of tissue constituents.

The tissue sample is then embedded in paraffin. Embedding is significant in conserving skin morphology and providing support throughout segmenting. The tissue is typically cut into thin sections (5-10 µm) or smaller pieces (for whole mount studies) to facilitate further study.

Uses of FFPE tissue sections

  • These FFPE tissues are used in a technique called Immunohistochemistry (IHC).

This technique involves mounting FFPE tissue sections on a slide, and then bathing in a solution containing antibodies that will bind to specific proteins. Stains are then used to visualize the antibodies, which will show what proteins, and where they are.

This information is important to a doctor looking for signs of cancer, Alzheimer’s disease or any other disease.

  • FFPE tissues sections are important to the study of Oncology.

Formalin-fixed and paraffin-embedded (FFPE) tissues sections are often used for histopathology in the diagnosis of diseases like cancer.

Preserved tumor tissues exhibit very characteristic morphologies, which can be used clinically for diagnostic purposes.

Researchers use FFPE tissue sections to look for specific proteins. The presence of these proteins can be used for diagnosis or assess whether a therapeutic antibody is useful for treatment.

  • FFPE tissue sections are used in Immunology.

Studying the FFPE tissue sections of a person with an autoimmune disease makes it possible to determine the cause. This allows researchers develop medication for the defect.

Pros and Cons of using FFPE to preserve tissue samples -


  • Formalin-fixed paraffin-embedded (FFPE) tissue can be stored long term at room temperature unlike frozen tissue which can only be stored for up to one year at -80 °C.
  • FFPE tissue sections are thin hence increasing microscopic resolution. This increases the ability to capture tissue morphology in detail.
  • Unlike frozen tissue, FFPE tissue section cannot form ice crystals. Thus the subcellular detail is not affected and does not impact IHC staining.


  • Formalin is volatile and toxic.
  • Most fixation and paraffin-embedding procedures are tedious and time-consuming.
  • While proteins are preserved, they are also denatured. They are no longer biologically active and may not bind to the same antibodies as the non-denatured versions of the same proteins. This limits their use for certain types of IHC studies.
  • Another issue is that the nucleic acids (DNA and RNA) in FFPE tissue sections are not preserved very well. Therefore, FFPE tissue sections may not always be suitable for molecular genetic analysis.
  • Lastly, most of the FFPE protocols are not standardized. The non-standardized preparation methods can disproportionately affect the results gained from them, especially in the case of molecular genetic analysis.

© 2017 Sonal


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