Across the globe, tissue banks and biorepositories store huge numbers of Formalin-Fixed, Paraffin-Embedded (FFPE) samples; some reports claim that there are millions of FFPE samples worldwide. These preserved tissues are often very well annotated, containing highly useful clinical and demographic data. Scientists desperately need good quality FFPE samples to help advance molecular studies and develop targeted therapies.
Louis Staudt, MD, PhD, of the Center for Cancer Research at the National Cancer Institute, commented recently about The Cancer Genome Atlas (TCGA) project. He opined that if tissue samples representing 10,000 patients per tumor type were sequenced, then rare variants that contribute to cancer could be discovered. But to do that, he noted, researchers need to use FFPE tissue so that sequencing could be completed in a reasonable timeframe.
FFPE samples historically have had limitations for researchers seeking to extract useable DNA, RNA, and protein material. This is because formalin cross-links nucleic acids, making FFPE samples difficult to use for genetic research. And, since there is no industry standard at present for FFPE collection and fixation, there can be wide variability in sample quality due to differences in biospecimen handling, fixation and embedding.
Advances in extracting useful genetic material from FFPE tissues have been made. But, finding high-quality FFPE samples with top-notch regulatory and clinical documentation can still be challenging. Here are a few tips for those seeking to purchase reliable FFPE samples.
1. Licensed pathologist oversight
Biospecimen integrity is affected by lots of factors during surgery, including anesthesia administration, vessel ligation, and removal from the body. Degradation begins almost immediately and can limit the specimen’s value for genetic research unless proper oversight occurs. It’s important for a licensed pathologist to be available so that tissue collection occurs expeditiously and key times relevant to specimen collection are recorded. The pathologist also evaluates samples to ensure they are acceptable research specimens.
2. Quality control
Once collected, fixed and embedded, the FFPE sample block should undergo a thorough quality control evaluation by the receiving tissue bank. The FFPE blocks should be reviewed grossly and microscopically to verify that samples will meet requested project criteria. This helps ensure that organizations get actionable information from that biospecimen.
3. Annotation data
The level of data provided is important so that researchers have the right sample with the correct clinical profile. Look for FFPE samples that include a pathology report and demographic details, as well as staging and treatment status where available.
4. Genetic profiling information
The availability of genetic profile data, such as the ten most common oncogenes, makes the FFPE sample more valuable for studies that focus on drug targets of interest. When genetic profiles are provided with each sample, it means less work for technical staff and quicker results.
5. Fixation protocols
Formalin composition, whether or not neutral-buffered formalin was used, tissue sample thickness, and fixation duration can all impact the quality of formalin fixation. Because fixation processes can vary and there is no one set fixation standard, it’s important that specimen purchasers have access to that information if desired.
6. Laboratory capabilities
Tissue banks do not offer the same level of scientific expertise and range of lab capabilities. Find out about the end-to-end sample workflow and processing protocols. Ask to speak to key personnel involved in biospecimen procurement.
Finding a trusted partner to supply your FFPE tissues is one of the most important steps in accelerating important molecular research. What unique patient profile are you seeking?