Paraffin Embedded Tissue Blocks


Paraffin-embedded tissue blocks usually refer to formalin fixed paraffin embedded (FFPE) tissue specimens that have been used in various therapeutic applications and research for many decades. It is a method used to preserve and prepare biospecimens to be used in experimental research, examination, diagnosis, and therapeutic development. The tissue sample is first preserved through fixation using formalin or formaldehyde to ensure that the vital structures and proteins within the tissue stay as close as possible to the condition when it is still part of the host. After fixation, it is embedded in a paraffin wax block to make it easier for sectioning and mounting on microscopic slides for examination purposes.


The tissues are first collected from both diseased and normal hosts. In cancer biospecimens, oncologist often compares the primary tumor with samples that are obtained from distant metastatic sites. The tissues obtained usually measure only a few centimeters depending on nature and source and tissue. Immediately after excision, the biospecimen is immersed in 10% neutral buffered formalin for 18 to 24 hours to harden the tissue. It is then dehydrated and cleared using increasing concentrates of ethanol. It is then embedded into immunohistochemistry grade paraffin that is specifically used for embedding formalin-fixed tissues. One of the most crucial factors is the time of fixation as tissues that are fixed too soon may be unusable for molecular biology studies. The duration of fixation has the be long enough to ensure preservation.

Once acquired, the samples are handled carefully to maintain quality. Failure of proper handling can lead to an exhibition of unusual characteristics that can affect research results or deductions. The preparation method usually depends on the research team's requirements. It can range from specifications regarding tissue purpose, size, or cut of the tissue. One good example would be the cut of muscle along the muscle fiber "grain" or across them. Throughout the sample preparation, a certified medical pathologist will be involved to ensure that the procedure is completed accurately and also for quality assessment.

Once the samples are completed, they are stored in tissue banks. Useful records such as demographic information and when the tissue was collected or preserved should also be kept as it can be useful for the research team. Other critical information that should be stored includes signed consent forms and legal documents affiliated with the biospecimen as it can impact the usability of the biospecimen in research and clinical trials. 


Paraffin-embedded tissue blocks have many applications in research. These tissue blocks are often used in immunohistochemistry where the tissue sections are mounted on a slide. These sections are then bathed using a solution that contains antibodies that bind to proteins and structures. Staining can also be performed to help visualization of the antibodies which shows the location of structures that are present in the sample. This information can be critical to aid diagnoses of diseases such as Alzheimer's disease or cancer. The information gained form immunohistochemistry is also vital to many cancer projects that are being performed in laboratories today. Some of the therapeutic areas where the tissue samples are commonly used are:

  1. Immunology – responses of the immune system are analyzed in both the diseased and healthy state. The study of tissue samples from a patient with the autoimmune disease helps determine the cause and development of therapy for those affected.

  2. Hematology – paraffin-embedded tissue blocks are vital in the study of various blood and related disorders. Hematology is a crucial field that has helped with the discovery of many cures to diseases related to the blood and its components. Some studies that are related to this field include bone marrow studies which can include genetics, toxicology, and tissue regeneration.

  3. Oncology – paraffin-embedded tissue blocks are important in oncology as the preserved tumor tissues have characteristic morphologies that are not present in other tissue. Research teams often use these samples to look for proteins that can aid in the diagnosis and assessment of the disease. Formalin-fixed paraffin embedded (FFPE) tumor tissues generally should have 60% tumor content.

  4. Comparative – there are also paraffin-embedded tissue blocks that are healthy tissue collected from healthy donors. These tissues are used for comparative purposes and are also important for research and development.


In paraffin embedded tissue blocks, the fixation process usually requires the use of formalin or formaldehyde that denatures the proteins that are in the tissue sample. This can cause the proteins to be invisible to antibodies that are specifically developed to detect them. To compensate, antigen retrieval techniques have been developed to specifically recover proteins, DNA, and RNA from these tissue blocks. This helps open up a vast archive of preserved and annotated material for biochemistry and molecular biology studies. 


The quality of paraffin-embedded tissue blocks is crucial for work using these samples as a source of proteins, DNA, and RNA. This is due to the fact that even the best-preserved tissue will contain partially degraded inactive proteins, DNA, and RNA.


  1. What is FFPE tissue and what are its uses. BioChain. Accessed 5/16/2019.

  2. Paraffin processing of tissue. Protocols Online. Accessed 5/16/2019.