FFPE Tissue and it's Use in Biobanks


The process of fixation of tissue using formalin and embedding it in paraffin helps to preserve the morphology and cellular details of the biospecimens. Formalin-fixed paraffin-embedded (FFPE) tissues have now become the standard preservation procedure for tissue samples obtained for diagnostic surgical pathology. One of the main advantages of this method is the long-term storage at ambient temperature which helps it to be cost-effective compared to the requirements of frozen tissue storage at ultra-low temperatures due to labor costs, space, and maintenance. Vast numbers of FFPE blocks are routinely stored by pathology departments compared to frozen tissues due to its cost efficiency. It is a valuable untapped resource for translational clinical research.


FFPE tissues are often used in experimental research, development of therapy, and diagnosis. 

The tissue is first obtained from the donor. It can be diseased or normal. In oncology, primary tumor samples and tissues from distant metastatic sites are often compared. In some cases, four samples are obtained:

  • Normal tissue for FFPE

  • Diseased tissue for FFPE

  • Normal tissue for freezing 

  • Diseased tissue for freezing

A block of tissue is first excised from the donor. Ideally, the excised sample measures only a few centimeters. It is then prepared by fixing the specimen in a solution of 10% neutral buffered formalin to help preserve the vital structures and proteins in the tissue. This process takes 18 to 24 hours. It aims to harden the tissue to ensure it survives the subsequent process. The tissue is then dehydrated and cleared using increasing concentrates of ethanol. It is then embedded in paraffin to make it easier for sectioning purposes. It is then mounted on a microscopic slide for examination. The fixation time is vital as tissues that are fixed too soon becomes useless for molecular biology studies. Samples that are acquired must be handled with care to ensure the quality of the specimen. This is important as low-quality samples can cause anomalies in research data leading to misleading deductions. 

The researcher requesting for the FFPE sample can also ask for samples that fit their specifications in terms of size, the way the tissue is cut, and purpose. In the preparation of the sample, a certified medical pathologist will be involved to ensure that the sample is prepared properly via accurate procedures. The pathologist will also assess the sample quality. Completed samples are stored in biobanks located in various research centers or hospitals. The biobank should also keep records or data associated with the sample such as when the tissue was collected, preserved, and donor information (age, gender, ethnicity, etcetera). 

FFPE Tissue Applications

FFPE tissues are often used in immunohistochemistry (IHC) where the tissue sections are mounted, bathed in an antibody solution that binds to proteins or other structures, and stained to help visualize the proteins and structures located in the tissue. This information can be crucial for physicians who are looking for signs of disease such as Alzheimer’s disease and cancer. The information gained from IHC is also important for various cancer research projects that are currently being performed. Some uses of FFPE tissue include:

  • Immunology – FFPE tissue is used to help analysis of the immune system response in both the healthy and diseased state. The analysis of tissue samples from an individual suffering from an autoimmune disease can help researchers to determine the cause and develop a therapy for the condition.

  • Hematology – FFPE tissue in hematology is vital to help researchers learn more regarding the blood and its related conditions. It also helps with the discovery of various cures for anomalies in the blood components. Besides blood-related conditions, it also aids in bone marrow studies regarding tissue regeneration, genetics, and toxicology.

  • Oncology – FFPE tissues in oncology are important as tissue samples from donors with cancer may exhibit characteristic morphologies. Researchers often look for specific proteins in FFPE tissue as the presence of these proteins helps with diagnosis. It also helps to assess if a treatment would be beneficial for the patient. FFPE tumor tissues should have at least 60 percent of tumor content.

  • Comparative – FFPE tissues in comparative studies compare diseased and healthy tissue. 

One of the main disadvantages of the FFPE method is the possible denaturation of proteins due to the formaldehyde fixation process. This can cause the proteins to be invisible to the antibodies used to detect them. To compensate for this issue, antigen retrieval techniques can be used. Newer techniques have also been developed to help recover proteins, DNA, and RNA from FFPE tissue samples. This leads to a trove of material that can be used in biochemistry studies and molecular biology. This improvement has led to more work that has started to use FFPE specimens as a source of proteins, DNA, and RNA from documented and archived materials. However, the FFPE tissue quality is crucial as even well-preserved tissue may contain partially denatured DNA, RNA, and inactive proteins. This limits the selection of healthy archived materials.


  1. What is FFPE tissue and what are its uses. BioChain. Accessed 6/14/2019. https://www.biochain.com/general/what-is-ffpe-tissue/

  2. Kokkat TJ, Patel MS, McGarvey D, LiVolsi VA, Baloch ZW. Archived formalin-fixed paraffin-embedded (FFPE) blocks: a valuable underexploited resource for extraction of DNA, RNA, and protein. Biopreservation and Biobanking. 2013; 11(2): 101-106.