Next-Generation Sequencing - Discussing Results With Patients - Bishoy Faltas

February 22, 2022

Alicia Morgans and Bishoy Faltas discuss the use of Next-Generation Sequencing (NGS) and how to use it in practice and communicate results to patients. Dr. Faltas gives a deep background on how NGS works and how it can be used to improve patient care. They also discuss why clinicians need to get familiar with the nuances of this sequencing to maximize the benefit of NGS. Because there are multiple layers of information in genomic or transcriptomic data, a multi-discplinary molecular tumor board is essential to interpreting results and deciding how they may be applied to a patient. These tumor boards should ideally consist of all the providers who have input into the care of a patient.
ASCO and the College of American Pathologists have released consensus recommendations for interpreting and reporting sequence variants in cancer. It divides the actionability of tumor variants into four tiers based on how relevant they may be from either a diagnostic, prognostic, or therapeutic perspective.


Bishoy M. Faltas, MD, Director of Bladder Cancer Research, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York City, New York

Alicia Morgans, MD, MPH, Genitourinary Medical Oncologist, Medical Director of Survivorship Program at Dana-Farber Cancer Institute, Boston, Massachusetts

Read the Full Video Transcript

Alicia Morgans: Hi, my name is Alicia Morgans, and I'm a geo medical oncologist at Dana-Farber Cancer Institute. I'm so excited to have here with me today, Dr. Bishoy Faltas, who is an assistant professor of medicine and cell and developmental biology at Weill Cornell. Thank you so much for being here with me today.

Bishoy Faltas:Thank you so much, Dr. Morgan. It's always a pleasure to talk to you.

Alicia Morgans: Wonderful. Well, thank you. I wanted to really talk to you about a really practical and important talk that you gave at GU ASCO 2022, thinking about Next-Generation Sequencing and how we think about that in our practice and communicate those results to our patients. Can you share a little bit about that talk and guide us through your thought process.

Bishoy Faltas:Thank you again. Next-Generation Sequencing or high throughput genomic sequencing is expanding. It has expanded over the past few years, and now it's really in almost the mainstream of clinical practice. I wanted to give this talk as someone who has had some experience with this over the years to try to offer my thoughts and some guidance on how to interpret these results and how to discuss them with patients. The main points that I wanted to make are that mainly understanding the test is critical for discussing the results. I know we oftentimes think about tests as a binary yes or no, thing. Sometimes that's not true for these complex genomic tests where it's not necessarily a yes or no answer. Sometimes there's a spectrum, and there are some nuance and inner complexity there. I feel that it's important to start talking more about that. Learning more about that in order to have a good understanding of those tests before starting to make decisions or discussing those results with patients.

I think very important to understand the basic makeup of the test. What's being sequenced? Is it a targeted panel? Is it whole-exome? Is it whole genome? Very important to understand if are we just sequencing the tumor DNA or are we also sequencing the germline DNA? Is the germline DNA directly sequenced, and are germline mutations directly called from that germline DNA or are they inferred from the somatic DNA? Important to know which genomic regions are covered and what's the coverage? What's the limit of detection. Again, these may sound like they're really technical things. They're important to have some idea of that to have a good concept of false positives and false negatives and what alterations may be there, but they're below the limit of detection and so on and so forth.

It is also important to understand that Next-Generation Sequencing goes through this intermediate step of computational analysis. The properties and the design of the computational pipeline can make a whole world of difference for what comes out at the other end, which we see in the report. Very important to also be aware of sequencing artifacts, although most computational pipelines are very good at excluding these. Finally, for making clinical decision, it is important to understand the difference between a clinical-grade versus a research-grade test and what's a CLIA environment? What's CLIA certification? What does that mean for the quality of the test and what it doesn't mean for the results as well?

Alicia Morgans:I think all of that is so important as we think of some of the highlights and the key points that we need to think about as clinicians. Let's focus first on CLIA certified tests. I think it would be recommended for clinicians who are thinking about doing sequencing for their patients. We should be doing this in urothelial carcinoma also in prostate cancer at this point in time. I imagine people are doing this pretty frequently in kidney cancer too, so really across the GU spectrum CLIA certification is really important. Can you just confirm and clarify what does that mean and why is that an important part of this step?

Bishoy Faltas:CLIA certification is a type of certification that essentially ensures that the quality of the test is reliable that there's reliability when it comes down to the limits of detection. When the test is repeated multiple times, that it's essentially a clinical-grade test where a lot of these processes, their standard operating procedures for the sequencing, standard operating procedures for the interpretation, so that's very important. It's also very important to know which aspects of the test have been CLIA certified. For example, one can have a whole-exome sequencing test where a certain number of genes are the genes that were actually used for CLIA certification, but it doesn't apply to the rest of the test. In other words, some parts of the test may be CLIA certified, but some other parts may not. Again, that may sound like it's a subtle distinction, but it's important to really start asking those questions.

There are other processes as well. There is FDA approval for certain tests. Where I live, there is New York State approval for certain tests. All of these processes have some common things and also some different aspects. I think it's worthwhile understanding these differences in order to make the most sense of the technical reliability and the validity of the test.

Alicia Morgans:Perfect. Know your test. Know that it's certified so that you know it's a good test. Garbage in garbage out is the way that I think about this. You just have to make sure that it's a good test. You can trust the results. Now you also mentioned the concept of whole-genome sequencing, whole XM sequencing versus targeting certain genes. What are your thoughts there for the average clinician who's just trying to integrate this into his or her clinical practice?

Bishoy Faltas:Well, that's an excellent question. I think in this space, the technology is really outpacing our ability to adapt to a certain extent, and the sequencing capabilities are only going to advance. I think we just have to catch up. I think in the near future, it's likely that clinical whole-genome sequencing is going to be the standard at some point. The computational analysis and the computational pipelines will adapt. That would be the next stage. We'll adapt to a certain point to try to reduce the complexity of all of this information into the actionable information that would be relevant to a clinician. As I discussed and as I'm sure we'll touch on today, actionability is a bit of a dynamic concept and a lot of factors, including our knowledge of disease biology, goes into that.

The other point that I would like to make is the next step after that, is that not just the computational aspects of it, but also the annotation, which I think is really what a clinician is looking for. Because again, while a general understanding of the principles of testing is critical. In my opinion, I don't think it's practical that for every report that one would go in and try to interrogate every single genomic alteration or try to understand what is the read count or the [inaudible 00:08:01] frequency are all of these things for every single genomic alteration. I think annotating this information in a way that's user-friendly, clinician-friendly, and that lends itself to our busy clinical schedules I think is very important, and that's evolving and will continue to evolve. I don't think we're there yet, but it's something that's definitely happening.

Alicia Morgans:I agree. I think it's important for that clinician who's getting the results into his lap, her lap. How do they know that the mutation that's being identified is actually a driver mutation or a mutation that we can target in a way that not just that we have a drug for it, but that we actually expect that there's a good probability that targeting this mutation will actually affect the cancer?

Bishoy Faltas:That is a fantastic question. Again, that gets to the question of actionability. I think the first step is annotation. In my talk, I'm talking about this a little bit. Over the past few years, there are these wonderful databases that have proliferated that are searchable. I would encourage. That's certainly, what I did during my postdoc and fellowship. I spent a fair amount of my time doing that, which is just to look up some of these alterations on... We have our own internal database at Weill Cornell called PMKB. There's another fantastic database across the street by our colleagues at Memorial Sloan-Kettering called OncoKB. There are many publicly available databases. What they'll do is they'll show the distribution of that particular variant. They'll provide some computational predictions of how likely this variant is to affect protein function. They'll show you whether there assigned these interpretations two tiers based on confidence and based on aggregation of data from the literature as to whether this is an alteration that can be targetable or not. There's another wonderful database called My Cancer Genome that I'm sure that you're very well aware of.

It's actually fantastic and accessible to patients as well, and it will show you the clinical trials that are available for a given genomic alteration. All of these options are available, and I think that's the first step. That being said, it's only one step, and that's why this could be a little bit nuanced because as I heard someone say, the DNA just tells us what the cell can do. The RNA tells us that what the cell intends to do, and the protein tells us what the cell is actually doing. The DNA is great but sometimes, for example, we don't have a sense of whether a particular genomic alteration is being transcribed or translated, and how is that rewiring the signaling in the cell?

For example, we've published a case report for a bladder cancer patient or a patient with bladder cancer who had metastatic disease in an ERBB two genomic alterations, so an amplification who had an exceptional response to trastuzumab, and a attack stay. We think that the reason that patient had this exceptional response was really gained from looking at the RNA and showing that there was a severe degree of oncogenic addiction of the cancer cell to the ERBB two, based on the RNA sequencing analysis. Sometimes exome or DNA sequencing is not enough. I think I predict that in the future, we're going to be looking into transcriptomics and proteomics. I mean, we're already looking into them. What I meant is that they will be integrated more into our thinking about what's actionable and what's not as clinicians.

Alicia Morgans:That's great. I so appreciate you helping us look a little bit further into the future. We know that you and other labs have been looking into these things actually for some time now, but all the epigenetic modification and all of the other factors that go into what is actually being done. What is actually being transcribed translated, as you said, is what actually the cell can actually do. We are several steps away from that in terms of clinical practice, but we'll get there. I love that you help us look through that lens as we think about where we'll be in the future. If you had to sum up your talk and the way that we think about this data and communicate it to patients, what would it be?

Bishoy Faltas:I think if I have to summarize, I would say that understanding that the nuances of Next-Generation Sequencing is a good investment in time for clinicians who are or planning to use this information for treating patients. Actionability is a function of test properties computational analysis, kown biology, which is always changing expertise and also patient access. I would recommend having a multidisciplinary team approach and a molecular tumor board where we have expertise from clinicians, genetic counselors, social workers, scientists, and everybody to try to integrate that information into patient care. I would advocate for referral to genetic counseling for germline variants that either are specifically tested for by the oncologist or that arise or discovered, incidentally, through testing of cancer genomes.

Finally, in terms of discussing these results with patients, I think we want to follow the model of assess the patient's understanding and belief system about genetics, genomics, and cancer assist with decision making. That's where other members of the team come in, try to streamline the process. Then check-in. Offer support after communicating these results to make sure that they are well understood and taking into proper consideration by the patient when they're making their decisions about their care.

Alicia Morgans:Wonderful. Well, this like so many other aspects of cancer care in GU oncology and beyond. It's a team sport. I so appreciate you giving us some guidance that can be helpful to us as clinicians, to patients, to other members of the team, and even reminding us to think about access because we can't actually help a patient with a certain treatment if we can't get that treatment to the patient. Thank you so much for sharing your expertise with us today, Dr. Faltas. I really appreciate your time.

Bishoy Faltas:  Thank you so much. Always a pleasure to talk to you.