Join Dr. Bermeo in a conversation with Dr. Elizabeth Gerard, and Dr. Christa Habela, as they discuss the article, " Genetic Testing in Epilepsy: Improving Outcomes and Informing Gaps in Research ".
Click here to read the article.
This podcast was sponsored by Marinus Pharmaceuticals.
We’d like to acknowledge Epilepsy Currents podcast editor Dr. Adriana Bermeo-Ovalle, contributing editor Dr. Rohit Marawar, and the team at Sage.
In episode nine of the Epilepsy Currents podcast, Dr. Adriana Bermeo discusses the evolving role of genetic testing in epilepsy with Dr. Krista Habela and Dr. Elizabeth Gerard. They explore how genetic insights are enhancing diagnosis and treatment, highlighting the rapid advancements and future potential of this field.
Key Takeaways
- Technological Advances: Since the first epilepsy gene discovery in 1997, technological advancements such as next-generation sequencing have dramatically accelerated gene identification, enhancing genetic testing's accessibility and effectiveness.
- Basic Genetic Concepts Clarified: Dr. Gerard explains critical genetic components—genes, chromosomes, and exomes—and their relationship to different genetic tests, providing a foundational understanding crucial for grasping how genetic variations impact epilepsy.
- Diagnostic Yield and Personalized Treatment: Genetic testing varies in diagnostic yield based on patient-specific factors like age of onset and associated conditions. Higher yields in targeted groups underscore its role in developing precise, personalized treatment plans.
- Impact on Patient Understanding and Future Testing: Genetic testing not only aids in diagnosis but also provides patients and caregivers with valuable explanations for the conditions, reducing uncertainty and informing better treatment choices. The future of genetic testing in epilepsy includes potential advancements in gene therapy and precision medicine, aiming to develop targeted treatments based on specific genetic profiles.
- Overcoming Barriers to Integration: Challenges like insurance coverage, the availability of genetic counseling, and the need for provider education must be overcome as genetic testing becomes integral to standard epilepsy care. This integration promises to streamline diagnostics and potentially reduce the need for other invasive tests.
Adrianna Bermeo-Ovalle, MD (Host): Why do I have epilepsy? What causes epilepsy? Are my children or other family members at increased risk of developing epilepsy as well? These are some of the most frequent questions I hear in the clinic these days. In a healthcare environment which turns more and more towards personalized medicine, genetics presents a unique opportunity to answer some of our patients most pressing questions.
Today, we will explore the current indications and use of genetic testing in epilepsy and we'll take a peek into the future of epilepsy diagnosis and care. Marinus Pharmaceuticals is the proud sponsor of episode number nine of Epilepsy Currents podcast.
I am your host, Adriana Bermejo. I am the senior podcast editor for Epilepsy Currents, the official journal of the American Epilepsy Society. Let me first welcome Dr. Christa Habela. Dr. Habela is a Child Neurologist, Epileptologist, and the Director of the Long Term EEG Monitoring Program and the Epilepsy Genetics Clinic at the John Hopkins Hospital in Baltimore, Maryland.
Dr. Habela is the author of the review, Genetic Testing in Epilepsy, Improving Outcomes and Informing Gaps in Research. This article was published online first on March of 2024 in Epilepsy Currents. Dr. Habela, thank you for joining us today.
Christa Whelan Habela, MD, PhD: Thank you so much for having me.
Host: It is also my pleasure to welcome Dr. Elizabeth Zoe Gerard. Dr. Gerard is an Associate Professor of Neurology at the Northwestern Feinberg School of Medicine and the Founding Director of the Women in Epilepsy Program, as well as the Adult Epilepsy Genetics Clinic at Northwestern. Dr. Gerard, thank you for being with us.
Elizabeth E. Gerard, MD: Thank you so much for having me. It's my pleasure to be here.
Host: Dr. Habela, your review starts with a very nice historical perspective, a historical overview of the development of genetic testing in epilepsy. Can you please help us understand how did we get where we are today?
Christa Whelan Habela, MD, PhD: It has always been generally thought that epilepsy was a genetic disorder, even prior to any discovery of epilepsy genes. And the first gene associated with epilepsy was only discovered in 1997, and this was for the nicotinic acetylcholine receptor, and then from 1997 to 2007, only 10 more genes were discovered, and this was because we were using, very robust, but very slow and expensive Sanger Sequencing.
Early in the 2000s, the first untargeted genomic testing, came into clinical use, and this was the chromosomal microarray. This can be thought of as a very high resolution karyotype, and allowed us to look for deletions and duplications.
But it really wasn't until the development of next generation sequencing which is a much faster and a much cheaper way of sequencing our DNA; that we really began to have an explosion in gene discovery. And so, beginning with next generation sequencing, this allowed us to develop whole exome sequencing, sequencing the exomes of our genes, as well as whole genome sequencing. And these two studies allowed us to identify hundreds of genes,
up to a thousand genes from the years 2007 to present day.
Host: Wow. So it looks like our baby steps took a long time, but we are going on leaps and bounds these days. And I imagine that we will be advancing much faster, now and into the future. Dr. Gerard, let's start with the basics to orient our audience. Could you please explain the difference between a gene, a chromosome, an exome in a way that helps our listeners follow the conversation on genetics? And if you could please link that to which tests correspond to which concept?
Elizabeth E. Gerard, MD: So a gene can be thought of as a recipe for making a specific protein that's important to our body. And human genetic code contains about 20,000 recipes or 20,000 genes that make proteins. And so, as Dr. Habela was explaining, we had much faster understanding and ability to give back feedback on misspellings or typos in genes as we develop next generation sequencing.
The Sanger sequencing she referred to, could really process one gene at a time. But now with next generation sequencing, we can process and understand the genetic code of multiple genes at a time. So while single gene testing is still rarely used for very specific phenotypes, like tuberous sclerosis or neurofibromatosis, more often, patients with epilepsy, with or without neurodevelopmental disorders may need a bunch of genes sequenced at the same time to increase the diagnostic yield. And one of the ways to do that are epilepsy gene panels or neurodevelopmental gene panels, which use next generation sequencing to look at usually on the order between 200 and 500 genes all at the same time and look for errors in the genetic code that may affect how that recipe works or how it may affect how you make proteins.
So that's one commonly done tests now which are gene panels. The genes or the recipes we have are organized into chromosomes. So humans have 23 pairs of chromosomes, and you can think about these as like sort of cookbooks, that contain the recipes. So another genetic variation that can happen that can contribute to disease and contribute to epilepsy, are sort of rearrangements within that chromosome book.
So you can think about this as a missing page or half of a page missing. These are really deletions or duplications at the chromosomal level known as copy number variations. And these can include several genes or it can include just as small as part of one gene. And this stuff can be sometimes missed by gene panels or some next generation sequencing that's only focusing on certain parts of gene known as the exome, which we'll get to in a second.
So the chromosomal microarray was one of the early tests used to make diagnosis in epilepsy and neurodevelopmental disorders. I think Dr. Habela will talk about the yield of this test, but this looks specifically for deletions or duplications at the chromosomal level. As I mentioned, there are 20,000 genes or recipes in our genetic code.
And so we are moving very quickly away from these first two tests I mentioned to exomes. So whole exome sequencing, really sequences all those recipes, all the exonic parts of our recipes. We'll talk about the genetic code in our recipes, and can look at many, many, many genes at once. Even though they're looking at all of those genes in our genetic code; most exome analysis focuses on specific genes relevant to the patient's phenotype or the patient's symptoms. So this is really becoming one of the first tests that we're using in genetic testing for epilepsy and is thought by many to be one of the first two tests of choice. But there are still some things that exomes can miss.
So they can miss those copy number variants in some cases if those are not at the levels that affect whole genes. Okay, they can also miss particular disorders like expansion repeat disorders, such as seen in CSTB related progressive myoclonic epilepsy. And then the other thing that's really important to recognize is that our exome with all those 20,000 genes, is really only 1 percent of all of our genetic code.
So if you think about that recipe being made up of key components, like the ingredients that you need, that's really the exome. That set of instructions and those key factors that you need to make something or to make a recipe. But there's a lot of information on our genetic code in between the recipes or the small words within the recipe that actually tells us how to use it and how to make what we need to make.
And that's the rest of the genome. Until very recently, that's not something that we've been able to access on a clinical level, but it's becoming more affordable with advancing and sequencing techniques. And so now, genome sequencing, whole genome sequencing is becoming available at a clinical level.
And this allows us to look and learn more about the information between the genes. It also allows us in many cases, to identify with one test, those copy number variants that I talked about before. And in many cases, genome sequencing can also allow us to pick up other types of genetic anomalies like expansion repeat disorders, which are disorders where perhaps a word or a couple of letters are duplicated.
So those are some of the major tests that we're doing and many people now believe we should start for most of our patients with exome or genome sequencing. There's a few other things we haven't talked about without mitochondrial testing, which is another thing that can be added in and occasionally we should not forget to use karyotypes when these tests are not diagnostic.
Host: Thank you so much. Certainly a lot to go through, in order to get an overview of current really clinical use of genetics. Thank you for that. And I love the analogy of the recipes. Dr. Habela, can you tell us a little bit about what is the diagnostic yield of some of these tests? And also how do we determine which patients or which group of patients should take them or would benefit from one or the other?
Christa Whelan Habela, MD, PhD: I think that's one of the most important points is that the diagnostic yield of these tests really varies, depending on very specific patient factors. In general, right now, the recommendations are that if possible, if you have the resources in your clinic and the patient has the resources and can afford it, that exome or genome should be the first line, testing, but other tests may have just as high a yield.
So, chromosomal microarray, was the first sort of clinically useful and available broad spectrum testing that we used clinically, and it transformed the way that we could diagnose epilepsies, but was only giving a diagnostic yield of about three to nine percent, with the three percent being a diagnosis for somebody who had epilepsy and no other associated neurodevelopmental disorders, and the nine percent being individuals with epilepsy and intellectual disability in particular.
But at the time, that was the only test that we had available and as Dr. Gerard mentioned, sometimes we cannot pick up duplications and deletions on the exome, as sensitively as we can on a chromosomal microarray. So in general, if there has been a negative exome sequence, we would use a chromosomal microarray to confirm that there was no deletion or duplication.
Whole exome sequencing has a similarly a range of sensitivities, depending on the patient or a range of diagnostic yields depending on the patient. So, for individuals with no family history and no associated additional neurodevelopmental disorders or structural brain malformations or other congenital malformations; exome yields may only be 9%. But individuals with intellectual disability, structural brain malformations that may increase up to 50%. Similarly, estimates of diagnostic yields with the genome sequencing is around 48 to 50 percent. And then gene panels, on average have about a 19 percent diagnostic yield. But when used in specific patient populations, they can be just as highly effective as exome.
So in particular individuals who develop their epilepsy younger than the age of two, and in particularly on younger than the age of one, are most likely to benefit from a gene panel. Many of the epilepsies that develop in the first year of life are highly penetrant single gene disorders that we have already identified and are common enough that the gene testing companies have put them on their gene panels.
And so the diagnostic yield can be up to 40 percent for children who develop their epilepsy before the age of one. And for individuals who have an associated structural brain malformation, the gene panels can diagnose up to 50 percent of patients as well. And it's important to remember that when we think about doing genetic testing, that it's the age of onset, not necessarily the age of the patient. If an adult never had genetic testing as a child, doing genetic testing as an adult is just as likely to result in a diagnosis dependent on the factors of age of onset and associated developmental delays or intellectual disability, or other congenital changes.
And then finally, Dr. Gerard had mentioned a karyotype. There are certain, specific types of epilepsy caused by a ring chromosome that really a karyotype is the only test that will diagnose. So while there is not generally an indication for a karyotype in epilepsy, when you specifically suspect that syndrome, or, all other testing has been negative, that can be considered.
Host: So, for well chosen patients and populations, it looks like the yield is much higher than many of us know if we are not necessarily working on the field. Dr. Gerard, I find still that a lot of providers even are not sure of what the benefit is of doing genetic testing. Can you walk us through how do patients, caregivers, or families benefit from having genetic testing done in this day and age? And we just heard from Dr. Habela how even the yield is different when the diagnosis started at different age. So is there a difference between pediatric versus adult patients as you see mostly adult epilepsy patients in your genetics clinic?
Elizabeth E. Gerard, MD: I think the way you started off our podcast really speaks to an unrecognized power of making a genetic diagnosis through genetic testing. Since I've been working as an epileptologist, I've always been fascinated by how it's hard for patients to understand the diagnosis of epilepsy, especially if we can't give them a reason.
And so I think, as I answer the question, there's many layers to it, but I've found that one of the most powerful things about getting a genetic diagnosis is to finally have a reason, for why this epilepsy came to be. And a better understanding of it and a better individual understanding about why it affects this individual patient in a certain way.
For parents and caregivers, that understanding can also be really important. Because particularly for adult patients who have had epilepsy since childhood and have been unexplained to them because of the lack of the technology at the time and the clinical availability of these tests; oftentimes caregivers have had lots of reasons that have been suggested to them, such as birth injury or falls or all kinds of things as to why the epilepsy might have come to be when it's actually genetic.
And so it can be really powerful to have a why, and scale back some of that sort of guilt or rationalization that has happened over the years. I think, obviously, one of the hopes for genetic testing, and it certainly happens for some individuals, is the ability for the genetic testing to change treatment right now.
And I do like to say, particularly in my adult population, I wouldn't say that that is the majority of patients we test, but when it does happen, when you find a genetic diagnosis that has a specific treatment or certain specific treatment pathway; it is extremely valuable. It also is really important for people to know their genetic diagnoses now because we're at this point in medicine in general, where we're developing, as you mentioned, more specific interventions for specific genetic diagnoses.
And these include, but are not limited to, genetic targeted therapies. And so, patients who know their specific genetic diagnoses can be part of building solutions for themselves and for the future and being what we call clinical trial ready for when there are trials that are available for them.
Another really interesting phenomenon, and I think really important phenomenon, is the power of connection to other individuals or other caregivers who are going through the same experience. So when you can connect people to support groups, that are not just support groups for epilepsy in general or neurodevelopmental disabilities in general, but support groups for someone with the exact same genetic diagnosis as you, it can be really, really powerful to know that you're not alone.
And I think that the power of these specific groups, the caregivers and individuals with specific diagnoses are really moving the field forward as they help us define natural history studies for individual genetic diagnoses and connect with each other and advocate for research into specific genetic conditions.
To your point about adults versus peds, yes, I work specifically with an adult population, and there are, I believe, unique challenges to talking about genetics in 2024, to patients who are adults with epilepsy. One, we sort of have two major groups of patients. One group are patients who, if they were children nowadays, probably would have received their genetic diagnosis, and so these are patients often with earlier onset epilepsies, neurodevelopmental disabilities, and they just didn't have the testing available at the time.
And finally, I think when we are diagnosing adult patients, many of them, may have sort of milder phenotypes than the more severe phenotypes that Dr. Habela talked about. And so these can be in adults, less penetrant conditions, that we're diagnosing, and so that means that other individuals can have in the family or this individual's prospective children could inherit the genetic changes, but may or may not have symptoms and may have a variety range in their symptoms.
And so that concept is one we talk about a lot when we talk about patients undergoing testing before they want to have their own children. And that's another kind of unique challenge in the adult epilepsy clinic. Often because of these milder phenotypes, and these older diagnoses we're making, we're often saying to the patient that they're one of the oldest patients who has this specific genetic diagnosis.
And therefore, we don't have as much natural history or prognostic information to give them as well. So these are some unique challenges that we're learning about.
Host: Very interesting. We're certainly also building our knowledge and hopefully we will be able to inform other patients later on as we learn more about these adults that we're not testing as children. But we've a great possibility and opportunity. We know we face a lot of challenges. So, Dr. Habela, considering barriers like access to testing, availability of genetic counseling, training providers; how do you see we can better integrate genetics into our routine epilepsy care?
Christa Whelan Habela, MD, PhD: That is a great question. And it doesn't have an easy answer. But I think, the answer really comes from education. And in particular provider training. Even if not, every provider is able to explain genetic testing and the details of our genes and our chromosomes and how that interacts with the different types of testing, as beautifully as Dr. Gerard did; making sure that every provider who interacts with patients with epilepsy, whether it be an epileptologist or a child neurologist or, even, primary care physicians is aware that genetic testing is part of the standard evaluation of patients with epilepsy. And from a practical standpoint, including genetics and genetic testing in the curriculum of medical students and our residents and our epilepsy fellows, is extremely important.
And including a discussion of genetics into our conversations with patients, even from the time of diagnosis. Many of us were trained and think immediately of doing an EEG, depending on the type of seizures or the findings on the EEG, an MRI very quickly after diagnosing epilepsy in a patient or as part of the diagnosis of epilepsy in a patient.
And many of us include those results in our descriptions of our patients when we review notes. And I would argue that, genetic testing, whether or not it's been performed, what the findings are should be sort of part of the standard history and evaluation of our patients from diagnosis.
That doesn't mean that every clinic will be capable of sending an exome, but, understanding that it's part of the evaluation. And if we're not capable of doing it in our own clinic; knowing where we can send our patients to get that testing. And certain tests are relatively easy to send from clinic.
So our gene panels require a little bit less genetic counseling. And typically, for providers to understand the basics of genetic counseling, may allow them to send those tests on their own. So, being able to tell families and patients, what the testing is looking at, what the potential results are that we may find an answer. We may not find an answe. That we may find something that we're not sure whether or not it's related to their epilepsy yet. Those are the variants of unknown significance that are potentially the hardest answers to explain to patients, but are also the most common results that we get from genetic testing.
And being able to explain to patients that the testing may help us with medication selection, may potentially let us know about associated problems in other organ systems that come along with a genetic diagnosis. And they may or may not lead to sort of disease modifying treatment now or in the future.
Those general concepts can be talked about in a clinic visit provided the provider can make that time. But access to a genetic counselor is ideal, but not always possible.
Host: Certainly we have providers working in very, very different environments, but it is clear that genetics is part of the standard of care of epilepsy for adults and children nowadays. Now, I would like to invite both of you to try to think into the future. Where do you see the field of epilepsy genetics testing and epilepsy genetics treatment as well, in the near future, and what do you envision in the horizon for this rapidly evolving area? Dr. Gerard, I would love your thoughts first and then Dr. Habela.
Elizabeth E. Gerard, MD: There's so much there and I really think we're going to transform epilepsy care by increasing access to genetic testing. I like the analogy that Dr. Habela has used and also invite you to read her review, which is so thorough. I do think we're going to start thinking about genetic testing up there first, just like imaging.
And in many cases, if we can get a genetic diagnosis, early on, in a patient's care, that may actually preclude other expensive workups like repeated MRIs or autoimmune workups. So I think we're really going to move genetic testing as it becomes more affordable and more available, earlier and earlier into the workup of epilepsy.
We haven't touched on also, there's other genetic mechanisms such as polygenic contributions to epilepsy, which we think are underlying many of the cases that have not yet been diagnosed, including our genetic generalized epilepsies. And those polygenic risk scores may also become an early part of genetic evaluation.
There are a couple of important barriers, to reaching this goal of early integration of genetics in our workup, and a lot of those are sort of the resistance, particularly for adult patients, of insurance companies to support genetic testing, really at any level, whether you're talking panel or exomes, and so these tests are becoming more affordable, but we're going to have to advocate for them to be seen as essential by payers and people who support this testing. Because that's a lot of the bottleneck right now, for our patients, who don't see it as necessary or may not see it as necessary if their insurance company doesn't.
And I just want to make a final plug for the role of genetic counselors, as Dr. Habela mentioned. I do think we should further educate our providers about genetic testing, but nobody can provide genetic care and counseling better than genetic counselors. And I want to say my entire analogy, which I didn't get quite right, was stolen from my genetic counselor who I've been working with since 2011.
I think that we have to find a way as a neurology and epilepsy community to make sure genetic counselors are supported and are an important part of our practice.
Host: Thank you for that. And, for the advocacy plug and the plug for genetic testing. Hopefully, outlets like this one will get this message to a broader part of our community. Dr. Habela, any thoughts for the future?
Christa Whelan Habela, MD, PhD: I think that was really well summed up by Dr. Gerard. I would just second the plug for using the services of genetic counselors and advocating for more people to be trained in genetic counseling. And that I think we're really sort of just at the beginning of understanding how achieving a genetic diagnosis for our patients can, affect and improve their care going forward.
And there are multiple studies looking into genetic modification, but aside from that, understanding how particularly in polygenic genetic epilepsies, potentially how a polygenic profile may contribute to patients' tolerance of medications or how our genetic backgrounds contribute to single gene changes, affecting the severity of our symptoms from a genetic cause of epilepsy.
And then thinking about how we can apply epilepsy genetics to epilepsies that we don't always think about genetics in. So, patients with focal epilepsies who are undergoing surgical evaluations, more and more we find that there are genetic changes within the epileptic lesions, that are not necessarily discoverable by doing testing on our blood or our skin or our saliva and potentially may predict patient's surgical success or success to medications after surgery.
So, I think we're just at the beginning of understanding how we can help our patients with increased knowledge, and hopefully we can provide access to testing to the patients who need it.
Host: Wonderful. It sounds like there's still a lot to talk about in genetics, but it also sounds like the development, of this field will drive a hopeful future for our patients in testing and in treatment.
I want to especially thank both of you for participating in Epilepsy Currents podcast today. I want to thank our listeners. Today, I want to especially thank our sponsor, Marinus Pharmaceuticals. Marinus is dedicated to the development of innovative treatments for rare genetic epilepsies, including the CDKL5 deficiency disorder.
They are committed to collaborating with epilepsy experts to advance therapeutic options that support the work of physicians and make a meaningful difference in patients lives. You can learn more about their work at marinuspharma.com. That is M-A- R-I-N-U-S pharma.com. I want to thank Dr. Rohit Marwar and the SAGE podcast production team.
We look forward to having you at our next episode of Epilepsy Currents podcast. Please remember to subscribe to Epilepsy Currents podcast wherever you get your podcast and send us your feedback, suggestions, or questions through our website, epilepsycurrents.org and follow us in social media on X former Twitter at AESCurrents.
Until next time, everybody.