ONCAlert | Upfront Therapy for mRCC

Using Next-Gen Sequencing to Select for TRK Inhibitors

Targeted Oncology
Published Online:1:25 PM, Wed February 27, 2019

Shubham Pant, MD: So tell me this. What is next-generation sequencing? We hear about it so much. What is this NGS or next-generation sequencing? What’s so next generation about it?

David S. Hong, MD: Well, I remember around 2000, I think I was a first-year fellow back then watching an announcement by President Bill Clinton, Francis Collins, MD, PhD, who is the head of NIH [National Institutes of Health], and Craig Venter, PhD. And they announced that they had whole-genome sequenced a human genome.

Shubham Pant, MD: What does that mean? The whole-genome sequencing, what is that?

David S. Hong, MD: So, they took all of a person’s genes and sequenced every genetic codon in that person’s gene.

Shubham Pant, MD: Why is that important in the context of disease?

David S. Hong, MD: In the context of disease, to a large extent, most of our diseases, and particularly cancer, are genetic diseases, genetic alterations that lead to altered proteins, that lead to altered cells, etcetera. And I remember there was a commentary about how much that cost, and that commentary was that it cost a mere $2 billion to do so.

Shubham Pant, MD: $2 billion with a ‘B’?'

David S. Hong, MD: Two billion dollars with a ‘B’. You can get online now and get your whole genome sequenced for 999 bucks. So there’s obviously been an incredible transformation in the technology, in the sequencing technology to sequence these genes. Next-generation sequencing has been really the reiteration of that technology on a massive scale. There are vendors like Foundation and others that can now do this on a routine basis with patients in the community, etcetera. But it’s able to identify—whether it’s just 100, 400, 300, 500, thousands of genes—genes that we think are truly players in oncogenesis and to identify if there are actionable alterations that we can use to target with certain drugs like larotrectinib.

Shubham Pant, MD: Tell me this. So some people, when they look at the new next generation sequencing, there is something called somatic mutations, there is something called germline mutations. What is the difference and were the NTRK fusions were all somatic or germline? What’s the difference between these 2 different mutations?

David S. Hong, MD: Those are good questions. So somatic just means that the actual mutation or alteration arose in the tumor. Germline refers to that it arose in the germline of the individual.

Shubham Pant, MD: It’s a genetic thing, like BRCA1, BRCA2.

David S. Hong, MD: Correct, such as BRCA1. That’s inheritable. To date, we do not think NTRK fusions are germline, that really they emerged somatically.

Shubham Pant, MD: In the tumor itself.

David S. Hong, MD: In the tumor itself. It’s not clear whether this is a very early event or a much later event. But, at this time, we think it is a somatic alteration that has occurred in the actual tumor itself.

Shubham Pant, MD: Tell me, when we talk about next-generation sequencing, some of them sequence tumors. And now there’s also some that sequence blood.

David S. Hong, MD: Correct.

Shubham Pant, MD: So they call it different names. They call it circulating tumor DNA, people call it liquid biopsies. There are different names for it. What’s the inherent difference between testing with next-generation sequencing—and they’re both next gen sequencing, right—on tissue and doing next- generation sequencing on blood. And, in your study, did you have any NTRK fusions detected in blood?

David S. Hong, MD: Yes. So with CF or circulating-free [cf] DNA in the blood, I’m not an expert. One of our colleagues, Dr Filip Janku, MD, PhD, is really just looking at the genetic material that is being shed by tumors into the blood, oftentimes, which correlate with the somatic mutations that occur in the tumor itself. It’s not 100% correlated, but we do think that as the technology is emerging, that there is a higher correlation and there are commercial vendors like Guardant that are already doing that in patients in the community. We did not do it in the initial datasets, we are doing it in LOXO-195, for example, looking at cfDNA, but we did not do that in the initial dataset for either the NAVIGATE study or the phase I study.

Shubham Pant, MD: So right now all of them were done on tumor tissue, right?

David S. Hong, MD: Correct.

Shubham Pant, MD: The ones that you can identify.

Transcript edited for clarity.

Shubham Pant, MD: So tell me this. What is next-generation sequencing? We hear about it so much. What is this NGS or next-generation sequencing? What’s so next generation about it?

David S. Hong, MD: Well, I remember around 2000, I think I was a first-year fellow back then watching an announcement by President Bill Clinton, Francis Collins, MD, PhD, who is the head of NIH [National Institutes of Health], and Craig Venter, PhD. And they announced that they had whole-genome sequenced a human genome.

Shubham Pant, MD: What does that mean? The whole-genome sequencing, what is that?

David S. Hong, MD: So, they took all of a person’s genes and sequenced every genetic codon in that person’s gene.

Shubham Pant, MD: Why is that important in the context of disease?

David S. Hong, MD: In the context of disease, to a large extent, most of our diseases, and particularly cancer, are genetic diseases, genetic alterations that lead to altered proteins, that lead to altered cells, etcetera. And I remember there was a commentary about how much that cost, and that commentary was that it cost a mere $2 billion to do so.

Shubham Pant, MD: $2 billion with a ‘B’?'

David S. Hong, MD: Two billion dollars with a ‘B’. You can get online now and get your whole genome sequenced for 999 bucks. So there’s obviously been an incredible transformation in the technology, in the sequencing technology to sequence these genes. Next-generation sequencing has been really the reiteration of that technology on a massive scale. There are vendors like Foundation and others that can now do this on a routine basis with patients in the community, etcetera. But it’s able to identify—whether it’s just 100, 400, 300, 500, thousands of genes—genes that we think are truly players in oncogenesis and to identify if there are actionable alterations that we can use to target with certain drugs like larotrectinib.

Shubham Pant, MD: Tell me this. So some people, when they look at the new next generation sequencing, there is something called somatic mutations, there is something called germline mutations. What is the difference and were the NTRK fusions were all somatic or germline? What’s the difference between these 2 different mutations?

David S. Hong, MD: Those are good questions. So somatic just means that the actual mutation or alteration arose in the tumor. Germline refers to that it arose in the germline of the individual.

Shubham Pant, MD: It’s a genetic thing, like BRCA1, BRCA2.

David S. Hong, MD: Correct, such as BRCA1. That’s inheritable. To date, we do not think NTRK fusions are germline, that really they emerged somatically.

Shubham Pant, MD: In the tumor itself.

David S. Hong, MD: In the tumor itself. It’s not clear whether this is a very early event or a much later event. But, at this time, we think it is a somatic alteration that has occurred in the actual tumor itself.

Shubham Pant, MD: Tell me, when we talk about next-generation sequencing, some of them sequence tumors. And now there’s also some that sequence blood.

David S. Hong, MD: Correct.

Shubham Pant, MD: So they call it different names. They call it circulating tumor DNA, people call it liquid biopsies. There are different names for it. What’s the inherent difference between testing with next-generation sequencing—and they’re both next gen sequencing, right—on tissue and doing next- generation sequencing on blood. And, in your study, did you have any NTRK fusions detected in blood?

David S. Hong, MD: Yes. So with CF or circulating-free [cf] DNA in the blood, I’m not an expert. One of our colleagues, Dr Filip Janku, MD, PhD, is really just looking at the genetic material that is being shed by tumors into the blood, oftentimes, which correlate with the somatic mutations that occur in the tumor itself. It’s not 100% correlated, but we do think that as the technology is emerging, that there is a higher correlation and there are commercial vendors like Guardant that are already doing that in patients in the community. We did not do it in the initial datasets, we are doing it in LOXO-195, for example, looking at cfDNA, but we did not do that in the initial dataset for either the NAVIGATE study or the phase I study.

Shubham Pant, MD: So right now all of them were done on tumor tissue, right?

David S. Hong, MD: Correct.

Shubham Pant, MD: The ones that you can identify.

Transcript edited for clarity.
Copyright © TargetedOnc 2019 Intellisphere, LLC. All Rights Reserved.