Automating FFPE sample preparation for faster diagnostics and greater accessibility: Webinar Q&A

08 October, 2020

Recently Nick Collier, Sagentia Medical CTO has been considering how easy to use cartridge-based instruments could be developed for the testing of tissue samples for companion diagnostics in oncology, to speed up and inform treatment decisions.

“In a recent webinar I have looked to answer questions such as: What techniques and technologies are involved? What are the challenges and barriers to innovation? How could the core challenges of the techniques, such as FFPE nucleic acid extraction and amplification, be overcome? What are the pro’s and con’s of different testing locations, pathology labs v’s molecular lab? Is it commercially viable?”

Watch the webinar and read the answers to the questions that were asked by attendees throughout the webinar. 



Q: Will FFPE still be required with liquid biopsy becoming available?

A: We're hearing a lot about liquid biopsy in the news, particularly with the Grail acquisition. So, I think liquid biopsy is a very exciting technology, particularly because it's a non-invasive technique and it works across the whole treatment journey for the patient, from screening and diagnosis to, making a treatment decision. However, I don't think it will replace FFPE tissue samples that are still going to be taken, they will be the gold standard.

I think it will be more a matter of the various sample types working for different tasks. Tissue samples will still be taken e.g. for morphology, IHC etc. That method of using tissue samples is well established, and many of the therapeutics require diagnosis to come through that method, especially given uncertainties in shedding into plasma.  So, I think they will work together.


Q: The difference between the timescale of instruments, in pathology lab versus those outside, in other organizations, is interesting. Is there any evidence you've seen that the potential delay is leading to people being put onto inappropriate treatment protocols or is it simply a delay in a treatment protocol getting started?

A: Anecdotally yes, we hear that patients may not be offered those treatments, particularly in markets where the biosimilars are becoming available, but the testing isn't available. Otherwise, I think there's the delays with the resultant patient worry that we've heard before. Whether there are patients that are being put onto the wrong treatments due to the delay, would require some research. 


Q: Why do PCR testing when NGS testing is getting cheaper?

A: I think it's about where you do the test, the cost of the test, and the speed of the test. Where you have a very specific question, the PCR tests are at the right cost point, they’re quick to perform and they give a very definite answer. NGS tests can provide lots of information which could be good for the whole patient journey but may not be answering the question that needs to be answered at the time. That might be particularly relevant to the Payers' for the therapy. Will they be paying for a question that doesn't need to be answered at that time?  I think there's still a position for PCR with the simplicity, the speed and the cost advantages.


Q: The Biochartis system is clearly being adopted, the year on year growth is quite significant at the moment, you’ve shown there is a huge unaddressed market there today. Why do you think that more diagnostic firms aren’t developing systems to work with FFPE samples?

A: Well, I think that will come because in the first place many of these companion diagnostic tests are developed hand in hand with the drug therapy.

What we've seen over time is a particular approach to a test being available to more drug therapies and more biosimilars, and in 2016, the FDA, certainly changed his guidance to encourage diagnostic tests to be used for more biosimilars, to extend their labelling. I think it will come as the costs of the drugs also drop. More diagnostic players will be able to enter the market, rather than companies that formed the market at the point where drug gains approval.


Q: Is two hours of sample preparation time too long, can we speed up digest and uncrosslinking?

A: Yes, I think it is, it's unattractive in a small instrument, the faster we can make that the better. I think there's routes you can go down there. That's sort of proven by Idylla, which has time less than that, and the preparation for the Xpert system is less too. I think that's probably as much about combining paraffin separation and lysis at the same time.

Optimizing those steps within a cartridge or a particular test will allow us to see those times come down.


Q: Would this methodology work with fresh frozen tissue?

A: The process could be adapted to work with fresh frozen tissues.  The key differences are that the deparaffinization step would not be required and neither would the uncrosslinking step.  Another thing to bear in mind is what format the frozen tissue comes in, is it thin slices or will homogenization be required?  In general, it is easier to extract NA from fresh tissue.

If you have any further questions, Nick would be happy to answer them. Please contact him through

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