FFPE Tissue: Everything You Need to Know

FFPE tissue is often used in immunohistochemistry (IHC). This process involves mounting tissue sections on slides and bathing them in a solution containing antibodies that bind to specific proteins or structures in the samples. This type of study can reveal a wide variety of information. In most cancer research projects, this information can be crucial.


The most common method for performing tissue biopsies is the FFPE technique. So what is FFPE tissue? It ensures high-quality RNA, which is required for downstream RNA analysis. The FFPE procedure separates the tissue from its paraffin matrix to isolate the RNA biomolecules. These samples are then rehydrated. The goal of sample preparation is to maximize the yield of RNA and minimize the degradation of the nucleic acids.

RNA and DNA are present in the tissue, but FFPE techniques have limitations. Tissues fixed too quickly may not be helpful for molecular biology studies. Moreover, samples must be fixed long enough to preserve the RNA. An in situ hybridization method can serve as a rough estimate of RNA content. In some cases, the RNA can also be recovered after the tissue has been fixed.

RNA from FFPE tissues can be used to perform microarray analysis. However, the quality of FFPE tissues can vary due to different harvesting and storage conditions. Furthermore, the formalin fixation and autolysis time can affect the RNA yield. Also, the number of nucleotide modifications in individual specimens can differ, which may interfere with downstream applications. Furthermore, the sensitivity of FFPE RNA is less than that of RNA isolated from frozen tissue.

RNA in FFPE tissue is a valuable tool for detecting alterations in gene expression. The FFPE technique also allows researchers to extract RNA from tumor tissue. However, the process of obtaining usable RNA from frozen tissues has proved to be challenging. The preservation of proteins and the architecture of the tissues also make it difficult to isolate RNA from FFPE tissue. Nevertheless, considerable efforts have been made to improve the efficiency of FFPE tissue RNA extraction.

RNA is a critical component of FFPE tissues. The FFPE procedure has many advantages but also results in degraded RNA that limits gene detection. Furthermore, the process introduces artifacts during sequencing. Despite these drawbacks, FFPE tissue represents a valuable resource for RNA expression profiling.


A recent study evaluated DNA extracted from FFPE tissue to assess genomic variations. The analysis focused on 42 FFPE tissues, which were deparaffinized and cut into 5-mm sections. The tissue sections were then marked with H&E stain to identify regions rich in tumor DNA. The study also evaluated the concordance of FFPE DNA with DNA from FF samples.

The yield of DNA obtained from FFPE tissue was lower than that of FF samples, although the difference was not statistically significant. The quantification of double-stranded DNA from FFPE tissue was significantly lower than that of FF samples, although denaturation may have lowered the concentration.

DNA from FFPE tissue can be extracted using a kit that is specifically designed for this purpose. The kit contains a specific lysis buffer and a silica-based column that captures DNA and contaminants. As the DNA binds to the silica column, impurities are removed, and the isolated DNA is ready for downstream applications like PCR or qPCR.

DNA extracted from FFPE tissue samples is remarkably stable. This means that it can be used for microscopic analysis after sectioning. However, it is crucial to use FFPE tissue samples immediately after sectioning to avoid the degradation of target molecules. If you need to make a chemical extraction from FFPE tissue, it’s best to get a thick section that’s a few micrometers thick.

DNA extracted from FFPE tissue is often the only sample type for definitive diagnosis. In many cases, the tumor cells have become infected with a virus, such as a reticuloendotheliosis virus. To identify these tumor cells, researchers used optimized immunohistochemistry techniques. They also used quantitative polymerase chain reaction to detect DNA fragmented by fixation.