5 Questions to Ask Your FFPE Provider (and What Their Answers Should Be)
FFPE tissue samples are critical for research, but are you getting what you think? A few simple questions can help validate your supplier and give confidence in your samples.
May 26, 2022
Never Miss an Update
Sign up and receive Discovery updates, blogs, and market news directly to your inbox.Subscribe Now
A few simple questions can help you get the measure of an FFPE provider before you order any samples. Just a little bit of due diligence can save you a lot of work on the back end.
How can you ensure the quality of your samples?
The only way for a provider to be sure of the quality of samples is for them to have insight into and ideally control over the processing and preservation process. In an ideal world, the collection sites would all be using protocols written by the supplier, and conforming to the standards set by a professional body such as the College of American Pathologists (CAP) in order to ensure each sample is prepared
according to the highest standards, and that samples from any two collection centers are comparable. In addition, the provider should have their own rigorous quality review process in place for all incoming samples. A pathologist should review the sample and confirm the original diagnosis, plus reviewing all of the accompanying documentation for accuracy and completeness.
At Discovery all of our US-based collection centers are CAP certified, and our European collection centers also use CAP-approved protocols, even though CAP is not required in Europe. Additionally, all prospectively collected samples are fully consented. Upon receipt of a sample, Discovery pathologists conduct a thorough review of the sample, reconfirming the original diagnosis and adding increased detail, such as tumor % and necrosis % within a sample. Discovery also takes Aperio scans of each sample upon receipt, so that customers can have their own pathologist review images prior to purchasing. Through these measures, Discovery ensures consistent high quality across all our samples, something that is hard to achieve without such a high level of consistency in processing.
At Discovery all of our US-based collection centers are CAP certified, and our European collection centers also use CAP-approved protocols, even though CAP is not required in Europe
Can you ensure I’m receiving unique patient cases?
This is a short, but very important point. One surgical resection will generate multiple FFPE blocks, as the tissue must be cut down to about the thickness of a coin in order for the processing reagents to properly permeate. Each tissue slice will be processed into FFPE. It is quite possible for these samples to be sent to different tissue sample banks and providers. This means that the same patient case can show up on the inventory of different suppliers, and creates a problem for researchers, who, in sourcing FFPE samples for a study may believe that they are getting 20 unique disease state samples from 2 different providers but may, in fact, be receiving an unknown number of duplicates since the samples their providers have are not unique, and both suppliers may be unknowingly supplying some samples from the same cases.
At Discovery all our FFPE cases are unique. Our contracts with collection centers require that we receive 100% of the blocks from any case. In this way, we can guarantee that our samples are unique specimens and that 10, 20, or 100 individual samples supplied by us are exactly that, with no fear of duplication.
All our FFPE cases are unique. Our contracts with collection centers require that we receive 100% of the blocks from any case.
How many times have your FFPE blocks been reviewed by a pathologist?
To ensure you are receiving samples with the selection criteria you require it is important that your samples have been independently reviewed by two or more pathologists. The first (original hospital review) contains only the information necessary for patient care, typically just the diagnosis and extent of disease. This initial review does not contain information such as the tumor content of each individual FFPE sample. Any provider that is relying on the initial pathology report cannot guarantee tumor content or percent necrosis of the sample.
At Discovery every FFPE sample is reviewed at least 3 times by a pathologist. This may seem excessive, but this attention to detail gives our customers confidence in the samples they are receiving and explains why we have a less than 2% return rate on FFPE, while the industry average is 10-15%. Following the initial pathologist review at the clinical collection site, Discovery performs a second detailed review and annotation of each FFPE block on receipt. This second review includes much more detail, such as tumor %, necrosis %, etc., to create a robust inventory report for each sample. We also perform full Aperio scans so clients can conduct their own digital pathology review, these files are available online from the Discovery website through the Discovery Biostore™ (you can register for access here) and allow clients to review and select potential samples from our extensive inventory. Finally, Discovery pathologists perform a final review of all samples selected by a client to ensure they will meet the client’s needs. These multiple reviews ensure your samples are exactly what you expect, ruling out one source of experimental error and ensuring the best data possible from downstream experiments
How do you ensure the samples will meet my specifications?
Many providers have a catalog of pre-characterized samples that clients can select from. However, if these orders are assembled and shipped without any additional checks, it is possible that some samples may not meet requirements, or are not 100% suitable for the intended studies. In an ideal world, your supplier would perform a final review of all the samples in your order to ensure that each sample individually meets requirements.
Discovery conducts a final pathologist review of each sample in a customer order to ensure that they meet requirements prior to shipment. This review is in addition to any pathologist reviews and other quality checks that a sample undergoes on receipt at Discovery and is done as a final quality check to ensure all samples within an experimental set are fit for purpose.
How big is your collection network?
The larger the network of collection centers the more samples and the greater the range of disease states a supplier has access to, both in terms of their inventory of existing samples and their ability to perform prospective collections of specific sample types to support a specific client project. Suppliers with a limited collection will have a much narrower inventory of samples to choose from and can struggle with prospective sample collections.
At Discovery Life Sciences we have a comprehensive infrastructure of collection centers across the US that we have built up in over 20 years collecting and processing samples. We also have an extensive network of collection sites in Europe that provides us with access to thousands of samples annually across a broad range of disease types. This gives Discovery access to a huge collection base for both routine samples, as well as collecting prospective samples on behalf of clients to support specific studies.
We have a comprehensive infrastructure of collection centers across the US that we have built up in over 20 years collecting and processing samples.
Do you have dedicated facilities to provide comprehensive downstream services for FFPE services?
Many times, it can be easier to have some of the analytical work you need performed by your FFPE provider, so long as they have the capabilities and expertise to do the work. Indeed, some tasks are made significantly more complicated by the fact that the samples are FFPE embedded, and having the expertise in dealing with these challenging samples can make the difference between success and failure. Even simple tasks such as DNA or RNA extraction become much more challenging and yields of DNA/RNA can vary widely simply based on the extraction protocol used. Ideally, your FFPE provider will have deep expertise in handling these sample types, enabling them to extract the most information from your samples for you.
At Discovery we offer a suite of in-house analytics for our customers including comprehensive IHC, and optimized dual DNA/RNA extraction from FFPE which dramatically increases yields and strand length compared to off-the-shelf extraction kits. A full suite of sequencing services for both DNA and RNA, and critically the ability to assist in the selection of FFPE blocks that are good candidates for sequencing. Not all FFPE blocks can be sequenced, and our in-house pathologists determine if blocks need macro dissection prior to extraction. Having these services available allows Discovery to improve success rates for clients, utilizing our expertise in handling FFPE samples to maximize the types and quantity of experimental data that can be derived from a single sample block.
Your research is important, expensive, and time-consuming. Taking the time to ask these qualifying questions of an FFPE supplier before sourcing your samples can pay huge dividends on the back end. Ensuring your data is as good as possible, and that you can perform all of the studies you need using the samples you purchase. You can learn more about the full suite of services and samples available from Discovery on this FFPE specific webpage.
To propel your projects with The Power of Discovery.™
Contact Us Today
Let us know about your project!