Christopher Klein, M.D.
Professor of Neurology
Department of Neurology
Mayo Clinic, Rochester, Minnesota
Zhiyv (Neal) Niu, Ph.D.
Assistant Professor of Laboratory Medicine and Pathology
Division of Laboratory Genetics and Genomics
Mayo Clinic, Rochester, Minnesota
My name is Denise Harpster. I am a senior product manager for Neurogenetics, and I'm here today with Dr. Klein and Dr. Niu to talk about the neuropathy and neuromuscular gene panel updates. Their disclosures: Dr. Klein, CMTA Therapeutic Advisory Board Member; and Dr. Niu, ACMG Therapeutics Committee Member. Today, we will be reviewing the clinical utility of neuromuscular gene panels, describing phenotype directed Mayo Clinic neuromuscular testing, and describe enhancements of the neuromuscular gene panel update.
Thank you, Denise. I'm Dr. Klein, and I'm a neuromuscular physician seeing patients on the floor. And I'm very excited to be with you today to talk about how the Mayo genetic panels have greatly enhanced my care of patients. So as a neuromuscular physician, it's kind of simple, but it's complicated. I see patients who largely have three problems: They have weakness, they have sensory loss or pain, and they have autonomic involvements that might mean problems in blood pressure, GI control, and they commonly will have pain. And so, when we see patients having the phenotypes shown here on this slide, we're largely trying to sort out, to begin with, whether it's an acquired or inherited condition. And there are certain clues about the inherited presentations, which generally means they are slowly and insidiously progressive. They tend to be symmetric, and they may or may not have a family history.
So for instance, in the slide shown here, a person who had this phenotype, with mostly ankle and hand weakness, might be of the category we refer to as Charcot-Marie-Tooth, also known as hereditary motor and sensory neuropathy. Versus the person here has what looks to be a systemic neuropathy that includes both their heart, kidneys, and the nerves. And this might be more characteristic of a type of neuropathy called transthyretin amyloidosis. So, we can band patients, once we sort out whether they're inherited, into different categories, whether it's CMT, whether it's metabolic neuropathies like TTR, or whether it's forms of primary sensory neuropathy, or ataxic neuropathies, where the cerebellum and the sensory nervous system might be predominantly affected. So, when we originally started considering these gene panels back in 2016, we really did a very specific phenotype focused approach, so CMT, metabolic neuropathies, ataxic neuropathies. But since 2016 and the advent of next generation sequencing, we've learned quite a bit.
And so, for instance, we would've previously thought of CMT as a very discrete group of genes within this sort of orange box. But as time has progressed, we've learned that CMT genes actually can overlap with some of the other phenotypes I just mentioned. And I've shown that here in this cartoon. And sometimes the differences in phenotype can be dramatic, so same gene, very different phenotypes. And I'd like to highlight one particular gene that's not on this list that was just recently discovered, which is the gene serine palmitoyltransferase 1, which most commonly causes hereditary sensory and autonomic neuropathy, but we now know that certain mutations actually cause ALS, something we would've never imagined previously in our very focused phenotype specific panels. So, in fact, we now have a biochemical confirmation assay that can help us sort out whether any variants in the gene are actually truly responsible. So, we can take the lab report, which might mean a variant of unclear significance, and push it into a definite pathologic cause. So, this experience has allowed us to revisit and update our panels through help of our laboratory geneticists and laboratorians.
So, for instance, in the space of hereditary neuropathy, we favor not ordering a Charcot-Marie-Tooth evaluation, but a much larger evaluation that includes up to 186 genes. And then we realized that there's some patients who have distal weakness that looks like CMT, but, in fact, can have a myopathy. And for doctors, unless they have access to really good EMG-ers, it may be hard to sort that out. So, we have this panel where there's uncertainty whether the weaknesses at the ankles are primarily from a neuropathy or a distal myopathy. And then, finally, for other families or individuals, we have the ability to combine gene panels. So, we might have a patient where congenital myasthenia is in the differential as well as a neuropathy. So, utilizing this custom gene panel approach, we can tailor the testing to the individual person. And sometimes we make the panels bigger, but sometimes we actually truncate the panels. For instance, if we know that someone's in a family with a specific gene, we may even just want one gene. So, this panel approach and specialty design, physician based, can be very powerful in helping us.
So, I'd like to just share with you a couple cases that illustrate here the power of this approach. So, this is a young man I saw that, for all the world, looked like Charcot-Marie-Tooth. He had very weak ankles and hands, not much sensory involvement, and was otherwise doing well in school apart from the weaknesses at his ankles and hands. So, when he went through his nerve conductions, he had a very classic finding that we see in demyelinating Charcot-Marie-Tooth. Where, if you look at the ulnar and median studies, he had marked conduction slowing here in the forearm at 27 meters per second. So, this would make it a demyelinating inherited neuropathy, which is supported by this part of the study, with no family history to give us a clue about what gene might be responsible.
So, in the earlier times, we would've probably just ordered the Charcot-Marie-Tooth eval and found nothing. But, however, utilizing the expanded approach, which included the 194 genes I just mentioned, we learned that he actually has a very rare metabolic myopathy in a mitochondrial associated protein TYMP. And so, the variant was known and has been previously been published, but we were able to confirm with even greater certainty that in fact this is truly the causal formed by utilizing a biochemical genetic assay for this enzymatic defect. So, in his case, we're absolutely able to increase our certainty by finding in his biochemical genetic test that he has a very high thymidine level, the protein that's not processed properly when this enzyme is defective.
So another example, this is a young man also referred to us for Charcot-Marie-Tooth, having the classic champagne inverted bottled below knee segments, it's very thin shin, and atrophy of his intrinsic hand muscles. And in his case, his sister was affected, but, as far as we knew, his parents were not. So, this really does, again, look like Charcot-Marie-Tooth. But, once again, by utilizing the expanded panel and, in this case, the distal weakness evaluation, we were actually able to figure out that this was not a Charcot-Marie-Tooth. In fact, this was a distal myopathy. So, he actually has a pathogenic mutation, as does his sister, a compound heterozygous mutation, in the GNE gene. And so, by finding this and not just utilizing a CMT or a directed panel, we're able not only to give him a definitive diagnosis, but end the diagnostic odyssey for him. So, this young man had been to no less than three tertiary care centers in the United States before this diagnostic possibility was made. And that's not an uncommon scenario in my clinic. So, I have many patients who've already completed genetic testing, but when they come and we do the Mayo test, we're able to get them to a diagnosis. And the advent of the biochemical conference has been very helpful in many of my patients. And so, in his particular case, both he and his sister entered into a clinical trial for a drug to treat this disorder that has now been approved in Europe and is currently being evaluated at the FDA.
So this just summarizes our new approach for getting patients to the right test who have a neuropathy, but we have similar algorithms for myopathy, ataxia, and other forms if we can get the phenotype nailed down. So, we start off sorting out if this is a very demyelinating condition. And if it is, and we're suspicious that it is CMT, we might just simply start with PMP22 duplication analysis, which accounts for about 70% of demyelinating CMT. And if that were to be unremarkable, then we could expand to the larger panels that I've just discussed. And then we do, in the Mayo test environment, have the ability, if things still remain uncertain, to expand to an exome. So, the ability to get patients the right test is greatly afforded by the information available on the Mayo test catalog shown here. So not only can you find the test that we have to offer, but there are many educational videos, webinars, and other things that you can listen to as either a senior physician or a junior doctor trying to learn about these disorders. And I personally find them very helpful when I'm teaching or when I'm trying to actually help patients get to the right test.
Thank you, Dr. Klein. My name is Zhiyv Niu. I'm one of the lab directors at Laboratory Genetics and Genomics and the consultant lead for neurogenetic testing. So recently, our neuromuscular testing algorithms were updated along with the neurogene panel update. During this improvement, we continued our phenotype focus philosophy and designed the test based on integrated experiences from genetics, neurology, and pathology. We considered more than 20 clinical practice guidelines in this update, especially for those diseases with a treatment option. Our technical design included a thorough review on more than 1,000 recent literatures on new genes and a new phenotype, and about 100,000 mutations that cataloged in public and private databases for inclusion. Certainly, we looked into key intronic mutations and challenging mutations and testing them by either NextGen sequencing or a targeted supplemental assay. Our assay validation demonstrated full gene coverage, high sensitivity for both small mutations, and a copy number variants on all genes included.
Here is the list of comprehensive and focused panels from this updated launch. When appropriate, SMN1 exon 7 testing is included, and a few new tests on Parkinson's diseases and ataxia are available now. Additionally, the genes and the panels can all be selected and customized using the CGPH system for any special need.
Our inclusive phenotype-based design is meant to simplify neurogenetic evaluation. I also like to share one example with the peripheral neuropathy panel called PEPAN. Here is the Venn diagram of PEPAN and gene content compared to several neuropathy panels available. We can see that this panel included 60 more unique genes, all of which were carefully vetted by neurologists and the geneticists. As discussed earlier, we included beyond CMT genes and included genes associated with metabolic and mitochondrial neuropathy and systemic neuropathy. When we look at a retrospective cohort, these 60 more genes included improved the diagnostic yield for more than 10% based on our experience. Additionally, our laboratory also offer a comprehensive biochemical testing manual. In fact, more than 30 genes on this PEPAN panel have complementary functional testing available. And this testing is super helpful to address uncertain findings in the practice.
I hope you enjoyed listening and learning about our updated neuropathy and neuromuscular genetic testing. Thanks for listening today.
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