FFPE vs Tissue Microarray's


Formalin-fixed paraffin-embedded (FFPE) samples are crucial for use in the tissue microarray (TMA) technique. FFPE samples are important for the study of morphology, cell biology, biochemistry, and disease in all living organisms. FFPE is a method that preserves tissue samples using formalin to paralyze cell metabolism. After fixation, paraffin helps to seal the tissue as it decreases the rates of oxidation. Various tissue samples are stored using the FFPE method as it is cost-effective due to low storage cost. FFPE biospecimens have played a vital role in drug discovery, biotech research, and retrospective gene studies over the last few decades. Samples that are preserved using this method enables it to be stored for decades making it an invaluable source in the discovery of new drugs, therapy, correlation of clinical outcome, and molecular findings. Since these specimens are embedded in paraffin wax, it can be sectioned easily to be mounted on a microscope for examination purposes. 

Uses, Advantages, and Disadvantages of FFPE

FFPE tissues are commonly used in immunohistochemistry where the tissue is mounted on a slide and bathed in a solution containing antibodies, so it binds to proteins and other structures. Staining helps visualize the antibodies to show where the proteins are on the specimen. This is vital in studies involving diseases such as Alzheimer’s disease and cancer. FFPE tissues are therefore crucial in immunology, oncology, and hematology. In the hospital, when a biopsy is obtained, a portion of the sample will be archived for second opinions. Donated samples or tissues from humans or animals can be preserved using the FFPE method and stored in archives for other studies. These archives are known as biobanks or biorepositories that may be found in universities, hospitals, or organizations that serve the research community. 

As previously mentioned, FFPE samples are cost-efficient due to its storage at room temperature. It is also a crucial source of research material as the specimen remains viable despite not requiring any specialized equipment. The disadvantages of this method would be the use of formalin for fixation, non-standardized procedures to prepare the specimen, and time-consuming process to fix and embed the tissue sample. This method can cause the proteins in the specimen to become denatured thus limiting the use of FFPE samples to only specific studies. A good example would be that FFPE samples cannot be used for molecular analysis as the results from it is not on par with results from frozen tissue samples. 

Tissue Microarray (TMA)

TMA is a technique that is invented to overcome issues where marker validation is costly, labor-intensive, and time-consuming. This method allows parallel molecular profiling of tissue samples at protein, DNA, and RNA level. It also allows the analysis of samples using RNA in situ hybridization, fluorescence in situ hybridization, and immunohistochemistry at a shorter time and lower costs. TMAs can be constructed using paraffin blocks and extracted cylindrical core biopsies from donor blocks. The core is then embedded into a recipient block or microarray with specific array coordinates. Obtained donor blocks are retrieved then sectioned to produce standard slides which are stained with hematoxylin and eosin. When ready, the slides are examined and arrayed. The core can be retrieved using a TMA instrument and inserted into an empty recipient block. The sampling process can be repeated numerous times using different cores until there are multiple cores in one recipient block. A microtome can be used to cut the sections to produce slides that are used in molecular and immunohistochemical analyses. 

Uses, Advantages, and Disadvantages of TMAs

TMAs are useful as it can be used to amplify a scarce resource. While a standard histological section which is about 3 to 5 millimeters thick yields about 100 assays, the TMA technique produced material enough for 500,000 assays. The TMA technique also allows simultaneous analysis of multiple specimens due to high throughput data acquisition. Since the TMA technique enables all tissue samples to be treated uniformly, there is less variability. With TMA, it enables the analysis of the entire cohort while standardizing variables such as reagent concentration, incubation times, temperature, washing procedure, and antigen retrieval. It is also a method that is both time and cost-efficient as it only requires small amounts of reagents for analysis. Another important advantage of the TMA technique would be the conservation of the original block of the tissue sample. 

One of the main disadvantages of the TMA technique that is commonly highlighted would be that the cores used in TMA may not represent the entire tumor. This is especially concerning for heterogeneous tumors such as prostate adenocarcinoma and Hodgkin lymphoma. However, this concern has been proven by many studies to be trivial. The studies show high concordance between TMA spots and whole sections of different tumors. Another minor critique regarding this technique is the absence of one or more core sections. This issue is easily addressed through the statistical power of analysis as a single data point out of hundreds to thousands of cases is easily eliminated. 


  1. The pros and cons of FFPE vs frozen tissue samples. Accessed 9/10/2019. https://www.geneticistinc.com/blog/the-pros-and-cons-of-ffpe-vs-frozen-tissue-samples

  2. FFPE vs frozen tissue samples. Accessed 9/10/2019. https://www.geneticistinc.com/blog/ffpe-vs-frozen-tissue-samples

  3. Tissue microarray. Accessed 9/10/2019. https://www.geneticistinc.com/blog/category/Tissue+Microarrays

  4. FFPE and tissue microarray samples. Accessed 9/10/2019. https://www.geneticistinc.com/blog/ffpe-and-tissue-microarray-samples

  5. What is FFPE and what are its uses. BioChain. Accessed 9/10/2019. https://www.biochain.com/general/what-is-ffpe-tissue/