How Storage Time of FFPE Blocks Affects Quality

Tissue procurement of human tissue specimens from biorepositories of high quality samples facilitates the progress of both basic and clinical research into a host of important diseases. More recently, many studies of various ailments depend on Formalin-fixed paraffin-embedded (FFPE) blocks to study DNA, RNA and proteins. FFPE blocks facilitate the study of a wide range of biomarkers. Recent research indicates that the storage time of such blocks has no significant effect on the quantity and quality of extracted nucleic acids and proteins. We discuss a study that demonstrated that for time periods of 11–12 years, 5–7 years, and 1–2 years there was no significant difference between the extracted macromolecules for current year blocks. This study systematically examined the quality and quantity of nucleic acids and total protein in FFPE blocks of various malignant tumors that had been stored over periods of many years and compared the results to current blocks and concluded that no significant difference in extracted materials obtained.


Advances in molecular biological techniques have resulted in the ability to extract fragmented DNA, RNA and proteins from FFPE blocks. This is an important development as archived FFPE blocks now represent a source of materials that can facilitate the study of biomarkers for targeted therapies and prognosis. Fragmented macromolecules have been successfully used in downstream analyses where short fragments are all that is required. Fragmented DNA has been amplified via PCR, biomarker analysis has been facilitated via micro RNAs and fragmented proteins have been useful in mass spectrometry. Considering the large amount of archived material available in the form of FFPE blocks, questions have been raised as to whether the amount and quality of extracted macromolecules depend on storage time. Recent results indicate that across all previously mentioned time scales extracted DNA, RNA and proteins show no significant difference with frozen controls.

In the study researchers extracted RNA and DNA from a single sample of FFPE tissue curls. Protein was extracted from the additional tissue curls. Frozen tissues were used as controls. Frozen tissue was not matched across storage periods to the FFPE tissues. This reflected the clinical setting in which there are usually large samples of FFPE tissue but frozen material is collected as necessary. This is the first study to extract protein from the same tissue as DNA and RNA for comparison and it is the second study to report extraction of DNA and RNA from the a single set of FFPE curls.

The study of biomarkers taken from human tissue samples play a vital role in the study of disease. Tissue procurement from quality biorepositories facilitates such research. Human tissue samples in the form of FFPE blocks are some of the the raw materials necessary for developing novel therapies and refining prognoses. There are large archives of FFPE tissue blocks that can be made available for molecular biological applications. Using these sources reduces the cost of research for certain applications because specimens do not need to be frozen. For research that can use fragmented macromolecules in downstream analysis FFPE tissue blocks provide a reasonable alternative to frozen tissue samples.