Ask the Mito Doc – September 2024 Q&A
All answers today are based on personal experience of the participants. As always, please consult your personal physician prior to taking any action.
Understanding Genetic Testing
Clinical Trial Readiness: Understanding Genetic Testing
Clinicians:
Austin Larson, MD, Children’s Hospital of Colorado, Aurora, CO
Eva Morava-Kozicz, MD, PhD, Icahn School of Medicine at Mount Sinai, New York, NY
Ibrahim Elsharkawi, MD, Icahn School of Medicine at Mount Sinai, New York, NY
Q: How come whole genome sequencing doesn’t report every single mutation found instead of just reporting mutations that could be related to symptoms?
A: Eva Morava-Kozicz, MD: This depends on the company, who is offering the test. Many companies report out all pathogenic variants, others only report out the ones related to the symptoms. When they consent you for the WGS test, the geneticist or counselor will ask you, whether you want to learn about all your disease causing variants, or include variants which are not related to your current symptoms.
Q: How does urine testing compare to cheek swab results in m.3243 A/G?
A: Ibrahim Elsharkawi, MD: Cheek swab and blood tend to be similar. Urine gives us a different idea on what heteroplasmy level is from renal cells, which is a different non-invasive tissue we can look at. With the m.3243 mutation in particular, we know that blood heteroplasmy level diminishes over time, and so urine may certainly offer a different number/context to think through.
Q: Would urine tests be the metabolic?
A: Austin Larson, MD: That’s correct. Usually urine testing would be looking at organic acids or maybe other metabolites. You can also do targeted testing for mtDNA variants in urine.
Q: Why does RNA sequencing take so long to get results back?
A: Eva Morava-Kozicz, MD, PhD: The number of variants which get tested is enormously high. Besides the individual data analysis, the findings are also aligned with the genetic (DNA) findings and interpreted together.
Q: When it comes to patients with negative WES and/or WGS, how to patients go about bridging the gap with discrepancy in care between confirmed and clinical diagnosis?
A: Austin Larson, MD: At that point, you would meet with a clinician to see how high the index of clinical suspicion is for a specific diagnosis. Dr. Morava will talk about some alternative testing strategies that can be used in the scenario of nondiagnostic genetic testing with still a high clinical suspicion.
Q: What can you tell us about long read repeat studies? What kinds of patients might benefit from long read repeat studies?
A: Austin Larson, MD: Great question. Long read sequencing is not yet clinically available, but it is being used in research studies. It does have the ability to detect genetic variants that are missed by short read sequencing. The difference in yield between short read and long read sequencing will depend on the gene, but for most genes, we think that the majority of pathogenic variants are detectable with short read sequencing.
Q: My neurologist is pushing for a muscle biopsy as opposed to genetic testing. I would prefer to start with genetic testing as it is less invasive and the medical literature recommends this; however my neurologist is telling me that a neuro geneticist (which she says is what I need) will not see me as an adult. How do I go about getting into a medical geneticist?
A: Ibrahim Elsharkawi, MD: I am sorry to hear this. In the USA, our recommendations are certainly to start with genetic testing over invasive procedures. I would start by googling medical genetics providers near you, or inquiring at academic centers near you. If all else fails, the American College of Medical Genetics or American Board of Genetics and Genomics may be able to help you identify a provider. Your PCP should be a valuable resource, too.
Q: If one were to go for an open biopsy, does the lab automatically run all the appropriate tests on the muscle and skin or does my physician have to order specific tests? My fear is that I would go for a biopsy and the correct testing wouldn’t be completed because it wasn’t ordered.
A: Ibrahim Elsharkawi, MD: In general, it is safest to have your provider know exactly where the sample is going and who is analyzing it, to make sure nothing gets missed. It is not necessarily about ordering a specific test, but just knowing which labs/pathologists are examining the tissue, so everyone knows what to expect from interpretation/results.
Q: Do you ever consider synergy between 2 or more genes in diagnosing mitochondrial disease, for example, if they’re in the same pathway, or have a similar function?
A: Ibrahim Elsharkawi, MD: Generally, no- this is a very interesting question, but in general mitochondrial diseases are what we can monogenic (one specific gene is associated with each type of disease). It is possible than in the future, once we learn more about polygenetic modes of disease, or how different genetic changes/variants interact with each other, this will change.
Q: What if there is a homoplasmy result?
A: Austin Larson, MD: Homoplasmic results mean that all of the mtDNA has a specific variant present. Outside of LHON, most pathogenic variants are heteroplasmic and not homoplasmic.
Q: Would plasma testing be done to test for proteins present in the plasma that would present mitochondrial disease? Do you know if these untargeted proteomic tests are using antibodies or protein binding affinity reagents such as SOMAmers?
A: Austin Larson MD: Yes. Untargeted proteomics is a test that is available on a research basis and does have some potential to be a clinical test in the future. I think that there are several different methodologies, but most of them are based on tandem mass spectrometry.
Q: Kaiser Neurology ordered 2 types of genetic testing, and no diagnosis was revealed. Stanford neurology took a muscle biopsy and I was diagnosed via that. Is there any benefit to have more genetic testing?
A: Eva Morava-Kozicz, MD, PhD: The common genetic testing offered is WES (testing the nuclear DNA) and mtDNA sequencing (testing mitochondrial DNA). Usually these two tests are sufficient to find a mitochondrial diagnosis. If these are negative, and the biochemical (functional testing) in muscle is abnormal, one can do a test called whole genome sequencing, which includes also not coding regions of the DNA, hidden between coding regions. Although this is rare, still can explain a few patients’ mitochondrial disease. The test is called WGS.
Q: What NPV do you quote to patients? The stat that only 20-60% of “mito patients” can find a genetic answer with WES is well referenced in the literature (% changing based on inclusion criteria), but everyone is hesitant to quote an NPV range.
A: Austin Larson, MD: We don’t know the true NPV without a gold standard to compare to, but I do think that the concept that the NPV of genetic testing is increasing with time as sensitivity increases is helpful.
Q: I had a muscle biopsy in late 2021. A genetic test was never done as the lab was shut down due to Covid. My Mito Dr. says that he can’t use another lab. My sample is currently in a deep freezer. Any suggestions for this situation?
A: Eva Morava-Kozicz, MD, PhD: The problem is probably reimbursement, and your physician should get a preauthorization for testing. If the plan is to do genetic testing in muscle and compare to the blood results, first DNA should be isolated from muscle at your hospital. If that is possible, then the DNA could be sent to any commercial laboratory upon preauthorization. If your center can not isolate DNA from tissue, you could see a different specialist at another center (second opinion) and that center could request transfer of your muscle sample from “lab to lab” and isolate DNA and send out testing.
Q: What’s the Best choice for having a VUS mutation “fully” described on ClinVar? Is there any chance that ClinVar or any bigger organization/agencies pays that extra work to the doctors, so the databases are fully linking phenotype and genotype? Which could be the Best organization/agency to recognize that work of doctors worldwide so databases are more comprehensive in the linking phenotype/genotype issue?
A: Austin Larson, MD: Great question. There are some great research groups that are working hard to accurately characterize as many genetic variants as possible, but it is a huge task and will take time and resources. The website findageneticcounselor.org is a great resource for finding a GC who can see patients in your state for those who are having trouble finding genetics help. You can sort by location, specialty (adult versus child for example), and telehealth versus in-person.
Q: How common is it to have more than one genetic abnormality?
A: Ibrahim Elsharkawi, MD: It is rare, but it certainly happens.
Q: What % of heteroplasmy is considered frank MELAS MT-TL1? Is urine, blood, saliva make it more frank MELAS or is a positive a positive?
A: Austin Larson, MD: While higher heteroplasmy is certainly correlated with more severe clinical symptoms, the correlation is rough and there are not clear cutoffs that will indicate MELAS vs other clinical syndromes. Heteroplasmy will generally be higher in urine than saliva and blood and that difference will get larger with age.
Q: I am heterozygous for a nuclear DNA mutation (CoQ8A). I have myopathy on EMG, and fatty infiltration and atrophy in multiple proximal muscles on muscle MRI – Is it possible to be a manifesting carrier with this type of mutation?
A: Ibrahim Elsharkawi, MD: In the vast majority of cases, carriers do not manifest symptoms. It is possible, although rare, that there is a second hit on the other copy of the gene- making you more than just a carrier- that our tests aren’t good enough to detect just yet.
Q: Is there any chance that UMDF database could be linked / given to ClinVar to get any approach of patient reported symptoms and the variants detected?
A: Austin Larson, MD: I like the idea of crowdsourcing some information. ClinVar does have a different methodology with careful vetting of expert sources, but I think that there will be a role for crowdsourcing as well in some way as a complement.