The Importance of FFPE in Modern Research

Introduction To FFPE

What does FFPE Stand For?

FFPE stands for Formalin-Fixed Paraffin Embedded

What is FFPE Tissue?

FFPE is a common method for storing tissue samples. FFPE tissues can be stored for decades and as such are very important to disease research.

What is FFPE Protocol?

Formalin-fixed paraffin-embedded (FFPE) specimens have played a crucial role in research for decades. FFPE is a method used for the preparation and preservation of specimens used in research and therapeutic development. A tissue specimen is first obtained from both normal and diseased donors. Both the normal and diseased tissue can be obtained from the same donor as the similarities can help simply the process. FFPE specimens can be obtained from humans or even sometimes animals. Preservation of proteins and vital structures of the tissue is first accomplished by fixing specimens in a 10% neutral-buffered formalin as this process hardens the tissue. The specimen is then dehydrated and cleared using increasing concentrates of ethanol. It is then embedded in a paraffin block which enables it to be sliced in the required size. It is then mounted on a microscopic slide for examination purposes.

Care and Storage

During preparation, a certified medical pathologist is required to ensure that the procedure is performed accurately and to assess the quality of the sample once it is complete. Once the FFPE block is acquired, it has to be handled and stored properly to maintain the quality of the specimen. FFPE blocks are usually stored in tissue banks such as research centers or hospitals. Records regarding the collection, preservation, and demographic information should be kept as it can be useful to researchers in the future. Signed consent forms and legal documents for the specimen should also be available as it can impact clinical trials and research. FFPE blocks are very durable and can be stored at room temperature for many years.

Oncology Research

Cancer research revolves around the identification and understanding of cellular and molecular components of diseased cells. It also involves discovering the reasons why these cells become different from normal cells. This means that high-quality specimens are vital in cancer research. Since it can sometimes be hard to find enough fresh specimens, more researchers have turned to FFPE tissues in their studies. Some of the following studies help others to understand the importance and value of FFPE specimens in oncology research programs:


a)       Stratifying breast cancer patients using gene expression analyses

Cancer is a disease that has distinct biology, progression, and clinical behavior. Using FFPE specimens for gene expression analysis, researchers are trying to stratify patients for the risk of recurrence and matching appropriate treatment regimes for specific molecular tumor subtypes. Researchers were able to group breast cancer patients into different subtypes based on their gene expression patterns. Each profile helps to predict the clinical behavior of the tumor.


b)      Using FFPE specimens for genomic profiling of tumor cell populations

One research program aims to develop high-definition computational tools to study the nature of cancer genomes. A wide variety of human tissue tumors such as bladder, brain, breast, ovarian, and pancreas were used. The scientists were able to hypothesize that gene mutations and amplifications are key in the progression of cancer.


c)       Evaluation of key biomarker in gastric cancer using FFPE tissues

Since researchers have arrived at the conclusion that the biomarker miR-106a is increased in gastric cancer, they have yet to understand its significance in the progression and development of cancer. FFPE specimens and fresh specimens were used for comparison purposes. The team concluded that FFPE samples are important as early changes of miR-106a that were detected in FFPE specimens may be helpful since it serves as a potential biomarker in gastric cancer diagnosis.


Other Applications

FFPE tissues are widely used in immunohistochemistry where the information obtained can be important for physicians looking for signs of disease or in research. Some of the applications of FFPE tissues include:


a)       Hematology

FFPE tissues are vital in the study of blood-related disorders. Hematology is an important field as it has helped pave the way for the development of cures and therapy that are caused by anomalies in the blood. The study of hematology is also applicable in tissue regeneration, toxicology, and genetics.


b)      Immunology

The study in the field of immunology is based on the immune system in both normal and diseased state. By examining specimens from a patient with autoimmune disease helps researchers to determine how and why the disease started. It also helps in the development of therapy for the condition.


c)       Research and development  

There are many donors who have donated their bodies for science. Normal samples are obtained from these donors as healthy tissue is also important for comparative purposes in researches. Healthy tissue is also important for research and development.



FFPE tissues are extremely valuable in modern research as it can be used to study disease progression and development. Results from samples also help to determine prognosis and in the development of therapy. Today, there are many ongoing research studies where there is a central role for FFPE tissue specimens.



1)      Doitron L. The importance of FFPE tissue in oncology research. Folio Conversant. Accessed 8/29/2018.

2)      FFPE Methodology: Preparation and Storage. BioChain. Accessed 8/29/2018.