Effective Extraction of DNA, RNA and Proteins from FFPE blocks

Biorepositories form the foundation of much contemporary research in translational medicine. Without the availability of these, many research programs would not have the necessary materials to conduct study into the development and progression of a host of important diseases. Still, questions of sample quality and fragmentation plague the FFPE landscape and one might wonder if there are better protocols that can be developed to circumvent the cost of frozen human tissue samples and that avoid the problems associated with FFPE blocks.


Many pre-analytical factors exist that affect the uniformity of FFPE tissue samples, specifically in regards to extracting high quality DNA and RNA from these widely available sources. FFPE blocks have been advocated as an alternative to frozen human tissue specimens as they are a more cost effective approach and can be stored at room temperature. The clinical data and annotations associated with FFPE blocks serve to make them appear an even more attractive alternative but problems associated with fragmentation and the quality of the DNA, RNA and proteins extracted bring up some important considerations. Many pre-analytical factors affect the quality of the nucleotides extracted and recent studies have identified all 19 of the relevant factors exert an influence on sample quality. These considerations include decalcification, specimen size, fixation temperature and fixative buffer. All of these variables and many others affect molecular analysis and exert an influence on the quality of the samples and thus the quality of downstream results. While FFPE blocks have substantial value as sources for diseased human tissue, particularly when it comes to comparisons of pathology and clinical outcome, a number of important pre-analytical variables have yet to be exhaustively studied.

The current age of molecular approaches and translational medicine brings advances that could not have been conceived of years ago. However questions remain as to whether we are using these new tools as well as we could. A recent review of translational medicine advanced that many attempts to develop biomarkers have not become important tools in the clinic indicating a disconnect between results from the field and the subsequent development of tools that depend on these advances and that can deliver a higher quality of patient care. The lack of quality specimens and a means for determining them, few standard operating requirements and the unavailability of requirements for the validation of assays all affect the translation of results from research into effective clinical tools. While pathology laboratories have largely integrated collection and documentation of pre-analytical variables, researchers should continue to question the reliability of quality of materials output from available methods on FFPE blocks especially when the effects of handling, fixation and storage are largely unknown.