Tumor-Normal Matched Sequencing and Platforms Utilized for Tumor Profiling

EP: 1.Defining Germline Sequencing and Incidental Germline Findings

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EP: 2.Tumor-Normal Matched Sequencing and Platforms Utilized for Tumor Profiling

EP: 3.Experience with Interpreting Somatic Reports

EP: 4.Identification of Patients for Germline Testing

EP: 5.Role of ctDNA in Germline Testing

EP: 6.Operational Processes and Challenges

Mark Robson, MD: I think you're exactly right about this. And this next slide, which comes from one of the abstracts that was suggested as part of the conversation this evening speaks to just how prevalent these changes are. This was one of the studies that was presented at ASCO [American Society of Clinical Oncology], this is from the MD Anderson [The University of Texas MD Anderson Cancer Center] group looking at this issue if you did both tumor sequencing and normal sequencing. How many times would you find changes in the inherited DNA and the germline that were potentially relevant? And were those findings just confined to cancer types where you already had an indication for doing germline sequencing? And as you can see, while there certainly was a greater prevalence of alterations in the cancer types that had already existing germline testing guidelines, about 11%. There is still a meaningful prevalence of genetic alterations in the cancer types that didn't have otherwise germline sequencing indications. In other words, you're finding things essentially through population screening. It's a complicated heat map type of slide looking at the different cancer types in the rows and then the intensity of the coloring shows you just how prevalent alterations are in the genes which are listed in the columns. This is YH which is a very common alteration that's seen particularly in European populations and in my view, at least as a single alteration, probably meaningless. It causes a recessive syndrome of polyposis. But the interesting thing, as you can see, that although the BRCA mutations were more common in the cancer types that you usually think of as being associated, there are fewer such alterations but still a meaningful number of such alterations in other diseases. And then the light blue background just indicates how scattered, what a long tail there is of findings in other genes. Dr Ross, with that as background, I'd like to ask you, what platform, and I'm going to ask all three of you actually, what platform do you use for tumor profiling at your institution?

Ashley Ross, MD, PhD: Thank you and thank you again for having me. At Northwestern, there's no mandate for the platform to use. Obviously, there's multiple next generation sequencing companies out there. But we tend to use or prefer partnership with Tempus. One of the reasons that we decided to partner with them is that, they do germline and somatic sequencing together and we found that to be a benefit. You touched on some of these concepts, also they offer RNA sequencing to help pick up fusions. And they try to do some data analytics as well that I think for some larger institutions can make a preferred arrangement also. To your point, I think that it's an important one and also to Dr Henson's point that finding an incidental germline mutation in a tumor that is not thought of as a typical hereditary cancer. It's crucial for cascade testing and I'm just a urologist, but I strongly believe that the way that we're going to cover the nation and figure out who's really at risk for, not just development of cancer, but development of lethal cancers is, that's going to be the way to do it. Sort of like, identify these index cases and then screen their family member. And so, I think the other minor point, and I'll give it away to the rest of the group is, some of my patients that have prostate cancer even when I talk about germline testing, the guy with metastatic disease, they're not super sold on doing germline testing. They do understand there's somatic testing. We understand that PARP inhibitors are approved, and they want to get into their somatic testing. They understand that doing germline testing is a way to make those somatic calls. And then when that gets flushed out and we tell them, you might have a germline mutation in the gene, we would like to confirm it with a very validated germline genetic test, then they're all for it. But it's been an interesting phenomenon I've seen in my practice. I saw that Dana was nodding so I'll let here speak to it as well.

Mark Robson, MD: Dana, or Ms Clark, what's the situation at Penn? How do you do tumor profiling?

Dana Farengo Clark, MS, LCGC: Ours is a little more, I'll just say challenging. So, each group, as you said Dr Ross, there's no mandate on what we have to do. So, the gynecologic oncology group generally does a Caris type test where they're getting HRD [homologous recombination deficiency]. For the most part, we do have an internal center for personalized diagnostics. So, a lot of Penn Medicine providers will use that. The only problem or challenge is that it's tumor only. So, anything identified on that, the patient hasn't been consented, so there's a whole host of different things when you're dealing with tumor alone versus tumor normal. And so, every patient that we find anything, and we can talk later maybe about how we identify who is the targets of offering germline testing. But once, as Dr Ross, I totally agree with your point that it's a tougher sell. The somatic piece, I don't even know that patients actually get the option. They're told, we're going to do this test. I don't think they really understand it necessarily, but they know it's going towards their treatment so they're OK with that. My job is to get the downstream patients. When you're doing tumor only, obviously you have to confirm anything that you find. We have no inkling whether it's germline or tumor only. It is sometimes a hard sell and we looked at our group and even of patients that their oncologist talked to them about coming in and why we were calling, still a large number of them never showed up. They didn't want to be tested. They just declined germline testing for one reason or the other. So, tumor only definitely has its own challenges. A lot of providers are going with the paired. And I think the other thing that's starting to really take off is the garden testing. That's been another interesting arena in terms of germline findings. We're just starting to deal with that now.

Mark Robson, MD: Certainly, I want to circle back to the circulating free DNA later on. Dr Henson, what are you guys doing?

John Henson, MD: We, I would say, at the moment we're probably split evenly between Tempus and Caris Life Sciences. The advantage of both of those companies, obviously, that they do offer paired testing whereas there are certain circumstances come in without a history of cancer. They're worried about it because of family history. That's a different scenario from what we're talking about tonight. But probably in a large genetic center like ours, half of the cases are more- We've actually convinced most of our clinicians now to let us manage all of the genetic testing. And so, we go to either Tempus, which has sort of been our major partner or to Caris if the clinician prefers that. And we like the ability for those two companies to get the paired germline. Those are new developments, particularly for Tempus. I think a lot of the audience will recognize that Tempus now interacts with GeneDX as their germline partner. Caris interacts now with Ambry. And historically, we would have these tumor panels that would be a germline filtering program which I used in a completely different way. Not the filter but to identify germline. And I wasn't perhaps- That's not- That wasn't the intended use for that, but it was very powerful. Now that both of those groups are partnering with bona fide germline testing companies, this is just terrific. And so, we can send one requisition to either of those companies and get tumor DNA, tumor RNA, very, very powerful germline. And so, we use both of them. Tempus is the partner that I use the most.

Mark Robson, MD: It's interesting, I don't use either of those for obvious reasons, because we have our own. Do you send a separate normal DNA? They don't take it off the tumor, right? You just send a separate one.

John Henson, MD: Yeah. In fact, Tempus, for example, they get the tumor from the hospital. You send in a paired germline test which is their standard that they've been doing for a long time. And now there's an additional tube that goes in a separate box to GeneDX. So, it's an extra tube for the patient, but, it's really not that much more for them.

Ashley Ross, MD, PhD: The nice thing too is they'll do the paired normal, but then also if you don't get enough specimen out of your FFPE [formalin-fixed paraffin-embedded] block, you can have them reflex the circulating free DNA, for Tempus at least, off that same tube. Just like Dr Henson, when I'm seeing the patient, I'm doing exactly what he's doing. Sending a tube for the XG, which is our GeneDX. Sending one for their tumor match normal XT. And then I'm saying, if you can't get enough specimen off of that paraffin, please reflex the XF, which is their circulating free tumor DNA test. It's a nice one point of contact. I think it's made things very easy. If only it would communicate with our EMR [electronic medical record] freely, but otherwise, it's made things very easy.

Mark Robson, MD: It's an interesting challenge, because the question obviously becomes, what's the gene set on the normal DNA, right?

Transcript Edited for Clarity