Making Exomes More Revealing

Standard exome sequencing, which maps the protein coding regions of the genome, will deliver a diagnosis of someone with a rare disease in about 35 percent of cases. Ambry Genetics’ ExomeReveal seeks to improve the diagnostic yield of these tests by adding RNA analysis to exome testing. That can help resolve variants of uncertain significance in about 2 to 3 percent of the cases. Ambry will also perform continuous reanalysis of the results over time to take into account new gene-disease relationships as they are discovered. This provides a diagnosis to about 5 percent of those without an answer.  We spoke to Brigette Tippin Davis, chief operating officer for Ambry Genetics, about the diagnostic odyssey for people with a rare disease, Ambry’s new ExomeReveal test, and what people can do to accelerate their path to a diagnosis.

Daniel Levine: Brigette, thanks for joining us.

Brigette Tippin Davis: Glad to be here. Thank you so much for having us.

Daniel Levine: We’re going to talk about the diagnosis of rare diseases, Ambry Genetics, and its new exome reveal test, which looks beyond DNA. Let’s start with the diagnostic odyssey though. What do people with a rare disease face in getting an accurate diagnosis today?

Brigette Tippin Davis: Families affected by rare disease often face, as you mentioned, a very long diagnostic journey before they actually are offered genetic testing. Sometimes that can take five or more years, often being referred to a number of specialists. I think the average for a rare disease patient is up to seven specialists before they actually get a genetic diagnosis, and frequently tens of thousands of dollars in healthcare costs. So, it’s not uncommon to get a misdiagnosis along the way, which complicates things even further.

Daniel Levine: Why is it so difficult for people with a rare disease to get an accurate diagnosis?

Brigette Tippin Davis: I think one of those major barriers is that most folks are living outside of a location where there’s an advanced academic center of excellence that supports rare disease diagnoses. So they’re presenting in an emergency room in a community hospital where there may not be a lot of experience from those doctors in that community that can recognize a genetic disease off the bat.

Daniel Levine: Genetic tests are not monolithic. Can you explain the basic types of genetic tests that are performed today?

Brigette Tippin Davis: The primary type of genetic testing that happens is really DNA based, and those are typically performed on next generation sequencing, which is really the high throughput, fast scale, comprehensive testing that happens. So testing can be performed on sequencing through what we call panels now, where it might be a panel of a certain subset of genes that are known to be associated with a disease like cancer or cardiovascular diseases, or it could be a larger test like an exome panel or a whole genome panel that does a comprehensive sequencing of all the genes in our body.

Daniel Levine: And what determines which test a person will get?

Brigette Tippin Davis: Typically, it’s how confident the clinician who’s ordering the test is in the suspected diseases. So for a rare disease patient, if it’s really straightforward where there only seems to be one organ system involved, usually they can order a panel that will target in and speed up the testing process and get quicker to diagnosis. For some of our rare disease patients where they may have multiple organ systems involved, there could be neurological symptoms, there could be skeletal symptoms, there could be other biochemical things happening in their body. Those are complex syndromes typically, and there you’re going to want to cast a really wide net, and that’s where exome testing typically comes in.

Daniel Levine: And is there a great difference in diagnostic yields from one type of genetic test to another?

Brigette Tippin Davis: Definitely. So, the wider net that you cast, so basically the more genes that you sequence, the higher chance you have of finding what’s underlying the issue for your patient, the yield for exome testing on average around the industry is in the 25 percent range, no matter where you get testing. But with additional tools such as what we’re doing with ExomeReveal now, you can actually increase that diagnostic yield and typically squeeze out an extra 7 percent by doing more. So that could be additional gene analysis, it could be additional types of technical analysis, which ExomeReveal does to get us up to the mid-thirties in detection rate versus if you run a panel where you’re focusing in, those detection rates range from about 15 to 20 percent on average of folks who will have a positive diagnosis from those. So a slight increase, but there is more cost and there’s more complexity and time to analyze a larger panel like an exome.

Daniel Levine: I guess to some extent you touched on this, but to what extent is a reason for a delay in diagnosis the time it simply takes a physician to recognize the need to order a genetic test, and what are the other barriers that exist in a patient getting the test they need?

Brigette Tippin Davis: Yeah, I feel like there are a couple of barriers. The first one that I mentioned was really just the awareness of the original clinician, who the patient’s presenting to. I think the second barrier would also be a mix of the physician experience historically of not being able to get genetic testing that’s comprehensive, like an exome test, covered by a patient’s insurance. But that historical trend has really changed significantly in the last few years. So most major private insurance payers and also a lot of government payers are now covering exome testing for these complex syndromes. And I think that the news really hasn’t gotten out on that across the medical community, and especially not in some of the more rural communities.

Daniel Levine: The cost of these tests has been falling rapidly. How is that affecting the access to these tests?

Brigette Tippin Davis: I actually think that the falling cost of sequencing to provide these tests is really helping insurance payers get more supportive of providing coverage for it. And it’s also allowing providers, hospitals, children’s centers and private labs like ours to be able to provide it quicker and more efficiently because the costs have come down and the plexing—basically the number of specimens we can run at once—allows us to scale and handle it because a lot of data that’s generated on a large panel, so it makes it easier for us to operationalize to actually test and sequence so many genes at once. And it also brings those costs down to make insurers more willing to pay for it.

Daniel Levine: Well, when is a genetic test indicated and is there something you would tell patients who may have a rare condition? Are there points at which they should be asking for such testing?

Brigette Tippin Davis: I definitely think so. There are a lot of resources such as with the Global Genes program, a lot of information on the internet. There are ACMG websites that you could look at to find a genetic service. And I think that patients, but typically the parents, are really empowered these days with a lot of information to be able to look up some of the symptoms on medical sites and determine whether or not it smells funny to them. Right. If you suspect that your primary physician or the specialist that you went to isn’t really hearing the symptoms that you’re experiencing and they may not be offering genetic testing, you can look up and find out where you could advocate for yourself on acmg.net, for example, to find a genetic service that’s in your region and get that third opinion and ask for it. Say, I think that my son or daughter or I might have a genetic cause to what I’m experiencing, and is there a test that might help me determine that and can you help me facilitate that process? So, it’s really about self-advocacy in some ways. If you’ve been through that diagnostic odyssey and no one’s offered you genetic testing, acmg.net has a link to find a genetic service, and I think that’s really where you have to step in and do some of the outreach on your own. Another option, which is now becoming available, is you can actually call your insurance provider and ask them, and look on your own in-network pediatric geneticist or just geneticists that are covered in your plan and ask for a referral. It might help your primary care physician if you let them know, hey, I found a geneticist that’s in my network. Can you refer me to them because I’d like to pursue genetic testing. And in some cases, your primary physician may not be comfortable ordering the genetic test because they wouldn’t feel comfortable interpreting it and explaining it to you. But if you give them the easy button, honestly, by handing them someone who’s in your network who is a specialist and they can simply refer them to without a lot of bureaucracy, they’re usually pretty willing to do that and hand you off to the expert.

Daniel Levine: It’s interesting to hear you say that because I think most people would think of payers as being the barrier. Is it sometimes the physician that becomes the barrier?

Brigette Tippin Davis: Sometimes, and I don’t think it’s intended. I think it’s out of trying to manage the patient to the best of their ability. And honestly, genetics is a newer specialty. A lot of the clinicians that are out there in the community, they got a week or a month of genetics training when they were in medical school, or depending how long they’ve been in practice, it’s still kind of foreign to them. So it may not be top of mind. And depending on that background, it may bias the comfort level of your physician to recommend it if they’re not in a large academic center where genetics is primary standard of care now for most evaluations for complex patients.

Daniel Levine: One of the things that may surprise people who are seeking genetic testing is that they may not be able to provide a definitive diagnosis even if they do have a genetic disease. What’s the diagnostic rate for these tests today?

Brigette Tippin Davis: For our tests, we’re in the 30 percent range, so it’s pretty good. Yeah. So, 25 to 35 percent will find an answer, so about one in three patients will actually get a result. And I think one of the other underappreciated aspects of genetic testing, and one of the unique things that we do at Ambry is we also will continuously evaluate for new gene discoveries. And if you have a patient tested today, what we know about the 20,000 genes and the human body, we have a disease that that’s associated with in about 5,000 of those. But every year, a hundred more genes are associated with a disease. So, if you’ve done testing in the past few years at Ambry, for example, we have a team that will look at those new gene disease associations, go back and look at all of our patients that have been tested through our patient for life program. And if there’s a new answer for your patient, your patient had a mutation in a gene that we didn’t know whether it caused disease or not, we can actually make that correlation once that gene has been positively associated and we’ll reach back out to that patient and generate a new report for that clinician. And sometimes even though two out of three may not have an answer the first time they get testing, when we reach back out because of a new discovery, we can actually provide an answer even years after having a test. And that happens quite frequently, and it gives us up to another 7 percent yield in diagnosis over the long term. So, at initial testing about one in three get an answer, but we’re keeping chipping away at those negative results as science advances.

Daniel Levine: I think many people who have had to fight for a genetic test are surprised that it doesn’t necessarily provide the answer they they’re seeking. Why is there still that diagnostic gap?

Brigette Tippin Davis: It’s really about our understanding of the human genome. We have an understanding of about 5,000 of those genes, and it takes a lot of scientific investigation to figure out what every gene in our body does, and if that gene gets mutated or is broken, will a disease happen or will it just be absorbed by the human body? And it takes animal models. It takes years of investigation by a dedicated researcher to sometimes understand what those unknown genes are doing. That’s really why we have so much more to learn. And this field is so exciting.

Daniel Levine: One of the things that’s helping patients get to a diagnosis sooner is overlaying other data with that genetic test. One of the things Ambry is doing is it’s developed a new test that it calls ExomeReveal. How does this differ from standard exome sequencing?

Brigette Tippin Davis: So standard exome sequencing is analyzing only the DNA molecules, which is basically the book that encodes our genes. But what ExomeReveal is doing is adding an analysis of RNA, which is really a communication molecule that translates DNA to protein. Som it’s the intermediary and that RNA sequence can sometimes tell us the impact of a variant we might detect on the DNA sequencing an exome. And that’s really what the ExomeReveal product is doing. Som a particular example would be you find a variant by DNA sequencing an exome, and it’s classified as what we call a VUS, or a variant of uncertain significance. Now in processing that DNA signal into protein, there are some activities called splicing that have to happen where the DNA gets repackaged into its final translated product to make the functional protein. If that variant causes an error in that repackaging process, that splicing process, you can’t tell from just reading the DNA, but if you look at the RNA sequence and you actually investigate what’s happening to the matching RNA region, you can determine that that DNA variant actually has an impact on splicing. And with that determination, you can classify that variant instead of being a variant of uncertain significance, you can actually say that’s not going to create a functional protein. It actually is causing a physical mutation in the product. And that’s something you can’t get just from DNA sequencing alone.

Daniel Levine: To what extent is that addition of RNA analysis expected to improve diagnostic rates?

Brigette Tippin Davis: So, from our pilot studies that we’ve been working on for the last couple of years, it can be up to 5 percent increase, and it will depend on the nature of the variants that are detected in the DNA in the first place. So not all variants can be resolved by an RNA analysis, so that’s why it’s not a 30 percent increase, but getting that additional yield out of the RNA analysis will solve that many more cases for patients that are already been struggling.

Daniel Levine: What type of variance can RNA analysis detect that DNA sequencing alone might miss?

Brigette Tippin Davis: Predominantly the interpretation of those splicing variants. So outside of that, RNA analysis is going to tell you exactly what DNA is, but it can tell you whether that DNA variant predicted to impact splicing, whether it actually does impact that splicing.

Daniel Levine: Have you had discussions with payers over the test? Do they cover it?

Brigette Tippin Davis: So, our RNA analysis right now is included in the reimbursement that we would get for the exome testing. There isn’t an additional charge for our insurance providers to that. We’ve packaged it into the overall price for that test.

Daniel Levine: There’s been a lot of excitement about the potential for AI to improve rare disease diagnosis. Is Ambry making use of this technology and what role do you see AI and machine learning playing in rare disease diagnostics in the future?

Brigette Tippin Davis: We actually use some elements of AI and machine learning, both in our analysis for variants right now and we’ve been doing that for about seven years. And the tools have really matured in the last few years, especially with things like ChatGPT, which can interpret natural language on medical records and help us understand the phenotype of that patient and match it to the genetic variants that we’re finding. But we also use a lot of AI to comb the literature to see if there are new gene discoveries. That’s a process that we use in our “Patient for Life” program as well—so really the ability of AI to mine massive amounts of data that are either out there in publications that are coming out at a very frequent level, as well as re-analyzing our genomic sequences from patients who’ve been tested in the past to tease out new interpretations and find other alterations that may have been underappreciated in the past that may have an impact once we combine that with new information about gene discovery. So AI is really a tool to help us re-scan that data and to find correlations and new associations that may have been missed through manual processes. It can handle way more data than the human brain can in any given setting.

Daniel Levine: What advice would you give to patients and families embarking on a rare disease diagnostic journey?

Brigette Tippin Davis: I really think it would be to persevere. And if you’re not getting an answer or a diagnosis and your initial referrals haven’t resulted in a genetic test yet to rule in or rule out, I would keep asking. I would seek out a geneticist. I would continue to ask every year, hey, has testing advanced? Do you think genetics might have a new answer for me? If you haven’t had genetic testing and if you had a negative result from prior genetic testing, I would ask for a re-analysis at least on an annual basis to make sure that your family or you or your patient have access to the latest interpretation because the field is moving so fast where we didn’t have an answer last year, we might have an answer this year. So keep asking and don’t give up.

Daniel Levine: Brigette Tippen Davis, Ambry Genetics’ chief operating officer. Brigette, thanks so much for your time today.

Brigette Tippin Davis: Thank you very much. It was my pleasure.

This transcript has been lightly edited for clarity and readability.

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