Running a Clinical Lab and Realizing the Potential to Make a Big Impact in Patients’ Lives
In this week’s Q&A Cofactor Genomic’s Lab Director, JT Forys, shares his experiences running a clinical lab and his passion for Next-Generation Sequencing.
Q: Why are biomarkers important for drug development?
A: I would argue that they’re not just important, but absolutely necessary for good drug development, particularly in complex diseases like cancer. Cancer is hundreds of different diseases from a histological perspective. It’s really thousands when you shine a spotlight on the molecular level, and this is why biomarkers are so important. Modern day oncology drugs are intelligently designed. They’re targeted—and for this reason we need to understand who are the patients that should be receiving these drugs and who are most likely and least likely to respond. This biomarker based stratification is a great approach to helping improve patient outcomes.
Q: Why do you think transitioning to multidimensional biomarkers is necessary?
A: Human diseases and the drugs designed to target them are each interacting with various molecular and physiological processes. If you want to know how one specific patient’s disease looks or how that disease might interact with a drug, it’s usually best to take a multidimensional approach to biomarker analysis. Take the field of Immuno-Oncology for example. The biology of a cancer cell is this mind bogglingly complex thing. Immunology is equally as complex but in totally different ways. So if you want to try to understand how the tumor, the tumor microenvironment, and the immune system are all interacting, a single-analyte approach is probably not going to do it. Looking at one specific immune cell type or one specific immune checkpoint marker is not going to tell you the whole story. We need a multidimensional analysis to be able to identify all the players involved and to understand how they are contributing to the survival of the tumor or how they’re keeping the immune system in check.
Q: What will it take to get adoption of new, innovative assays?
A: I think it it’ll take a big collaboration between pharmaceutical companies, diagnostic companies, regulatory agencies, payers, and possibly even patient advocacy groups. I think at this point most people believe that it’s a good idea to get the right drugs to the right patient. Some of these collaborations particularly between pharma and agencies like the FDA have already begun. A good example of this is from a couple of years ago when the FDA made a landmark approval for Merck’s Keytruda immunotherapy. This drug was approved for patients with multiple different solid tumor types that had a biomarker. In this case those biomarkers were microsatellite instability or defects in their mismatch repair systems. This was a big deal in oncology because it was the first time that the FDA had approved an oncology drug that wasn’t just for one specific type of disease. It was also a big deal for patients because now thousands of them had access to a drug that was showing really good results in clinical trials. This is really important for patients that are really just looking for hope, so I think part of our job as a diagnostic company is to continue to contribute stories like that. We believe very strongly that an RNA-based multidimensional biomarker approach is going to accelerate that process.
Q: Why is Next-Generation sequencing so important in developing new assays?
A: Next-Generation sequencing is obviously one of the technologies vying for space in the clinical diagnostic arena. I’m pretty heavily biased towards NGS because I spent the last five years working in that area. With that said, I think that the sensitivity of NGS, particularly using a targeted based approach, is really hard to beat. If you combine that with the scalability of modern day sequencers, I think that NGS will continue to be the first choice of people who are looking to do multi-dimensional biomarker discovery. I think another important point to make is that the flexibility of NGS instruments is incredible. Take an RNA-seq experiment for example. From one data file you can get things like gene expression isoform expression, fusion calls, you can validate DNA snaps, you can look at RNA editing events, and the list goes on. In fact there are probably things in those data files we don’t even know are important yet. This agility of NGS is going to be really important as our bank of biomarkers continues to grow.
Q: What’s it like to run a clinical lab?
A: It’s not horribly different from a regular research service lab, especially if you already have thoughtful and detail oriented people handling the samples, and we’re fortunate enough to have a team of scientists with those qualities. Now if you ask those folks I think you might get an entirely different answer. When you are bringing in samples where the data may potentially be used by an oncologist to change a patient’s course of treatment, this takes you to a whole other realm of responsibility. You know the the extra documentation, the oversight, the controls—all of those are absolutely necessary and they’re in place because we want to make sure that our assay is working in the same way it is when we originally validated it. We understand what’s at stake and I think that we’re just really excited to offer clinical products like Immunoprism™ because we really believe this type of assay is going to allow oncologists to prescribe the very best immunotherapeutics to patients.
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