Diagnostics Decoded by ZeptoMetrix
Diagnostics Decoded explores the science, technology, and innovation transforming the field of diagnostics. Through in-depth conversations with scientific and industry leaders, we uncover the discoveries and advancements shaping laboratory medicine.
Diagnostics Decoded by ZeptoMetrix
Genomics, Oncology, and the Future of Diagnostics
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What happens when engineering, genetics, and medicine converge?
Dr. Elena Repnikova joins Diagnostics Decoded to explore the rapidly evolving world of clinical genetics and molecular diagnostics. From her research background in genetics to her leadership role at Children’s Mercy in Kansas City, Missouri, Dr. Repnikova discusses how laboratories support prenatal, pediatric, and oncology patients through advanced genetic testing.
The conversation covers diagnostic workflows, whole genome and exome sequencing, bioinformatics, diagnostic stewardship, actionable cancer mutations, and emerging technologies like rapid intraoperative nanopore sequencing. Dr. Repnikova also shares her perspective on the future of genetic testing, the challenges behind rare disease diagnosis, and why precision medicine continues to transform healthcare.
Hello, and welcome to today's episode of Diagnostics Decoded. We are joined by Assistant Director of Cytogenetics and Molecular Diagnostics at Children's Mercy Hospital, Associate Professor of Pathology and Pediatrics at UMKC Med School, Go Tigers, and Program Director of Laboratory Genetics and Genomics Fellowship, Dr. Elena Repnikova. Thank you so much for joining us.
SPEAKER_02Thank you so much for having me today.
SPEAKER_00Yes, we're so excited to chat with you. So you have such an interesting background that I feel like we could have an episode just completely around. But could you tell our listeners a little bit about yourself, your background, your education, and kind of where you got how you got to where you're at today?
SPEAKER_02So first, I got my bachelor's and master's degree in engineering physics from St. Petersburg State Polytechnical University in Russia. And at that time, I was involved in many different research projects besides completing my degree. For example, my master's degree project included creation of a computer-simulated modeling of various types of radiation interaction with biological tissues prior to oncology treatment involving radiation. And I've been always fascinated with medicine, and given my interests, I decided to pursue a doctoral degree in genetics. So following completion of master's degree, I was admitted to Texas AM University, and I joined a research laboratory of Doctor of Lab Panin in the Department of Biochemistry Biophysics at AM, where the primary focus of my dissertation was to understand the role of cellulation in Drosophila melanogastrum. So it's interesting that at that time when I joined the laboratory, Dr. Panin found that fruit flies have a sequence that codes for cell transferase. It's an important enzyme that is capable of transferring salic acids to some glycosylated proteins. However, at that time, we did not know what types of cells express this enzyme, what its role, and whether mutant flies have any associated phenotypes. During my dissertation, I utilized a lot of approaches to answer many of these questions. They included from biochemistry, molecular biology tools, and even electrophysiology. And the primary outcome of that research was to demonstrate that cell transferase plays an important role in regulating sodium voltage-gated channel properties during propagation of action potential. This work was also published in the Journal of Neuroscience at that time, and it also involved analysis of important behavioral phenotypes in mutant flies, such as seizures and motor deficits and et cetera. And then about 18 months prior to my graduation, I realized that there are many different genetic conditions that are interesting on the molecular and genetic level, which overall led me to continue my clinical American Board of Medical Genetics and Genomics Fellowship training in clinical cytogenetics and molecular genetics at Nationwide Children's Hospital in Columbus, Ohio. So at that time I joined, after my graduation, I joined a diagnostic laboratory to continue this fellowship, to actually pursue this fellowship, led by Dr. Julie Gasai Foster at that time, the director of the laboratory. And I also completed a significant amount of training learning adult oncology and adult genetic conditions at the Ohio State University. So this fellowship is specifically designed to train doctoral and medical degree graduates to become directors of the clinical diagnostic laboratories. After completion of my fellowship and successful passing of the board certification exams in both cytogenetics and molecular genetics, I decided to join Children's Mercy Hospital in Kansas City, Missouri, as a board-certified cytogeneticist and molecular geneticist. Because at that time, Children's Mercy Hospital was set to emerge as a first pediatric genomic medicine center led by Dr. Stephen Kinsmore. Also, at that time, it had a high-volume cytogenetics laboratory led by a very well-known cytogeneticist, Dr. Linda Cooley, who provided cytogenetic testing both for pediatric and adult cancer patients. So overall, joining this laboratory would have allowed me at that time to utilize my knowledge and skills obtained in both clinical cytogenetics and molecular genetics diagnostics. Additionally, Children's Mercy Hospital provided me with the opportunity to give back to the community by developing a training program for PhD and MD graduates that I completed at that time. And essentially the program that would allow to train individuals who are interested to become laboratory directors.
SPEAKER_00That's awesome. Cool. Well, thanks for sharing your story.
SPEAKER_01Like Jess said, we we we probably could have an episode just and elaborating on all of that because there's a lot there in your history and background. Fascinating stuff. So thank you again for going through that.
SPEAKER_02Thank you.
SPEAKER_00Yeah. Okay, so now that you're at children's mercy, can you share like a little bit about your lab, the types of patients that your lab supports?
SPEAKER_02Yes, sure. So as I mentioned before, we offer genetic testing to different types of patients. We service adult, pediatric, prenatal patients. Essentially, our testing includes genetic testing from prenatal stage. So testing would include amniotic fluid, chorionic villi sampling for possible genetic conditions. We also test products of conceptions. We service pediatric patients with suspected genetic conditions, as well as pediatric patients with cancer and adult patients with hematological malignancies.
SPEAKER_00Quite a bit. Okay, so some for someone that might not be familiar with this space, how would you describe the role of a genetic testing lab in clinical decision making today?
SPEAKER_02Yes, this is a very interesting and important question. Today, genetic testing laboratories, of course, are the foundational engine of precision medicine. And testing that is done in the genetics testing laboratory has shifted clinical care essentially from reactive one-size-fits-all treatment to proactive individualized strategies. And I can give you a few examples. Yeah. So one of them, for example, prior to a during pregnancy, labs can evaluate a couple's risk for passing on genetic disorders. So this allows families to make informed reproductive and family planning decisions, including pre-implantation genetic testing through IVF to avoid transferring hambers with known genetic abnormalities. And then another example could be for pediatric and rare diseases. Laboratories now often utilize genomic sequencing, for example, whole exoma, whole genome sequencing to diagnose conditions in newborns well before irreversible symptoms appear. That all allows clinicians to initiate life-saving treatments immediately. And then finally, in oncology, we're now doing somatic testing as standard of care for tumors, leukemias, to understand the molecular drivers of cancer and also to see if we can bypass a traditional broad spectrum chemotherapy, essentially in favor of precision therapy, to attack cancer on the molecular level. So this overall allows to significantly improve the efficacy and minimize side effects. So overall, I think that early diagnostics allows us to initiate treatments early, manage pregnancies. In oncology, we can choose targeted treatments and role in specific clinical trials.
SPEAKER_00Yeah, absolutely.
SPEAKER_01Thank you. Um, kind of switching gear here to your genetic testing kind of ideal patient. I know the last time we talked, I I did bring up and just and discuss my my daughter had to go through some genetic testing. But we she had her own kind of symptoms and triggers that we picked up, but maybe you could discuss some of the more common clinical signs and triggers that you see in genetic disorder patients.
SPEAKER_02Yeah, sure. So doctors typically order genetic testing when they face a medical mystery, like a child who is missing major milestones, or for example, someone who is born with unusual physical traits or birth defects. Another huge trigger for genetic testing is the family trees itself, especially when you see a pattern of rare diseases, or for example, when relatives are getting hit with cancer or heart disease at an unusually young age. We also see it a lot in reproductive medicine. Doctors will call for testing if a pregnant mom is over 35, if a routine ultrasound performed and then it finds some abnormalities, or if a family is dealing with a heartbreak of repeated miscarriages. So ultimately, genetic testing is about looking beneath its surface, looking at the DNA, and to explain severe, sudden symptoms like unexplained seizures in a baby or rapid muscle weakness and turning to our DNA blueprint to finally get some concrete answers and clear path forward. In cancer world, on the other hand, it's pretty much any type of cancer is primarily driven by genetic changes. And therefore, genetic testing is now incorporated into a standard diagnostic workflow to later correlate with pathological findings, determine treatment plans, and establish prognosis.
SPEAKER_00So once that test is ordered, what does the workflow look like from sample to result? Yes. I know it's a big question.
SPEAKER_02Yes, it's uh it's a it's a great question. And the clinical genetic testing workflow from sample collection to final diagnostic result operates through a very standardized series of pre-analytical, analytical, and post-analytical steps. First, usually in the doctor's office or in the phlebotomy laboratory, patient provides a biological sample. Typically, it's a blood sample, but over COVID, we also evolved by allowing collection of saliva and chick swabs. Those kids are typically sent homes and the samples can be collected at home. Upon arrival at the laboratory, the samples get accessioned by the laboratory accessioning team. We verify the provider's test requisition form, quality of the sample. We'll make sure all patient identifiers are accurate. After that, depending on what type of testing is ordered, the sample is then routed to different areas of the lab. So it could be a cell culture setup area or an inside two area if we're talking about tumor, or a DNA extraction for any subsequent molecular tests.
SPEAKER_00So for that test, how do you decide which technology you guys are going to use? I know there can be different platforms to test for the same thing.
SPEAKER_02Sure, yes. And the short and simple answer to this question is that the choice of technology very much depends on the patient's clinical presentation and how confident the clinician is about a certain diagnosis. So, in other words, if a patient presents with classical sort of textbook features of a genetic condition, clinicians can order a test targeted to that specific gene that causes a disease. This could be, for example, fluorescent and seizure hybridization testing for trisomy 21 associated with Down syndrome, or trisomy 13, for example, in Patau syndrome, or a targeted gene testing for things like Duchenne muscular dystrophy. However, if a patient clinically presents with features of a disease that can be associated with many genes, like for example, autism or seizures, then it is generally advisable to utilize whole genome analysis approaches, for example, whole genome sequencing or microarray to start with. So it's interesting that if we lived 40 or 50 years ago, the answer would have been very simple. Clinicians would order just simple karyotyping or chromosome analysis. However, these days, genetic testing has significantly evolved over time. And we have many testing options. Therefore, we just have to understand that each test comes with its own benefits and limitations. And understanding those limitations is going to be very important to establish accurate diagnosis. Most importantly, we need to understand there's currently no single test that can detect every genetic abnormality, which makes it sometimes difficult for the clinicians to decide which option to choose.
SPEAKER_00Yeah. So how do you maintain diagnostic stewardship with that? Do you have to work with your clinicians and say, okay, maybe that we're not getting the anticipated results? Or do you make that decision to combine different technology to reach that diagnosis?
SPEAKER_02So it depends. That's why in the laboratory we often have a team that is triaging samples. When we get the requisition form, we thoroughly review the reason for genetic testing. And if we think that the testing or different testing modality should be offered to the family, then we definitely give a call back and discuss it with the ordering provider.
SPEAKER_00Okay, could you maybe walk us through an example on how you've had to combine different testing methods to reach that diagnosis?
SPEAKER_02Sure. Recently we had an interesting case where a newborn was admitted to our ICU unit for management of lower urinary tract obstruction. Additionally, this patient had coarse facial features. There was no family history of any kidney concerns or urinary tract issues, and our neonatologist wanted obviously to rule out a genetic disease. However, the clinical phenotype the patient presented with can be seen in many genetic conditions. And therefore, our neonatologists ordered a symptom-driven exome sequencing analysis with copy number variant analysis to start with. So we're first ran next generation sequencing test and noticed that their signal on the X and Y chromosomes looked different from what we would expect from a normal controlled male or female patient. However, we could not get the definitive explanation for what is going on with those two chromosomes. So we subsequently asked the provider to send us a fresh blood sample and look at chromosomes on the individual cell level. At that time, interestingly, we noticed that this patient has mosaicism for three different cell lines. So some cells were missing the X chromosome and only had the Y chromosome. Interesting. Some cells had one copy of the X chromosome and an abnormal Y chromosome called an isodiccentric Y, so with two centromeres and essentially double the amount of Y chromosome material. And then the third cell line had an X chromosome and two copies of that isodicentric Y chromosome. Overall, the presence of X and Y chromosome mosaicism, in fact, explained that interesting luto phenotype our patient presented with. And in fact, patients with this kind of abnormality can present with features of short stature, ambiguous genitalia, urinary tract abnormalities to even phenotypically normal males with infertility. So as we can see, while next generation sequencing detected the abnormality, given its bulk methodology approach, it was unable to distinguish multiple cell lines, and we had to implement a single cell traditional testing methodology to establish accurate diagnosis.
SPEAKER_01Thank you so much, Elena, for that. I just want to switch gears to some oncology platform-specific questions. So I'm interested to hear in terms of oncology, does genetic testing platforms differ from cancer testing platforms? Are you using similar sequencing for both? Could you maybe go into detail on how that relates to your lab?
SPEAKER_02I have to say that there's, of course, a lot of overlap in the testing technologies that we use for cancer testing and inherited genetic conditions. However, for cancer testing, the choice of testing method is very much guided by the established treatments and surveillance guidelines and recommendations such as National Comprehensive Cancer Network or World Health Organization or any other specific clinical trials. So, for example, for the patient with acute myeloid leukemia, the standard testing to start with will include chromosome analysis of the bone marrow cells, to map out the exact genetic fingerprint of the cancer cells, fluorescent and seizure hybridization, targeted testing for the important abnormalities associated with better and worse prognosis, sequencing analysis of certain genes like FLIT 3 tyrosin kinesis, TBFT3, YDH1 and 2. And all this data will pinpoint the specific type of acute myeloid leukemia and determine the best course of treatment.
SPEAKER_01And regarding treatment decisions, you've mentioned multiple different types of platforms and technologies specifically for confirmatory testing. How do the results directly impact the different treatment decisions?
SPEAKER_02As I mentioned before, we in an oncology we're very much guided by the guidelines. And therefore, we would utilize essentially methodologies that would help us to find those targets that are used for treatments.
SPEAKER_01So, Elena, you mentioned tools like fish and other ways for confirmatory testing. How do those results directly impact the treatment decisions that are made?
SPEAKER_02Yeah, great question. And as I previously mentioned, every test comes with its limitations, such as resolution and limits of detection. And when we see abnormality using whole genome approaches, but either unable to determine what genes are impacted or whether we need to later monitor the disease using techniques with a faster turnaround time or much cheaper, we will use targeted testing such as fluorescent and seizure hybridization or targeted molecular testing such as RNA fusion analysis. So all of these tests will be directed to a specific genetic abnormality driving the disease.
SPEAKER_00What are those actionable mutations and how do they help guide the therapy selection?
SPEAKER_02Yeah, so rather than like a one-size-fits-all chemotherapy, actionable mutations allow oncologists to utilize precision medicine. For example, these days, patients with EGFR mutations and non-small cell lung cancer receive targeted tyrosynkinase inhibitors rather than standard chemotherapy. Or, for example, tumors with an untracked gene fusion can be treated with specific tyrosine kinase inhibitors, regardless of whether cancer started in the lung or the soft tissues. Another example, as I mentioned before, in acute myeloid leukemia, FLIT III internal tandem duplication mutations are a classic high-stakes example of actionable mutations. They occur in about 20 to 25% of AML patients, driving rapid cancer cell proliferation and historically carrying a very high risk of early relapse. And currently there are multiple FDA-approved targeted treatments designed specifically to treat FLID-3 mutated acute myeloid leukemia.
SPEAKER_00Interesting. Okay, so I'm gonna go back months. So we originally met you at AMP last year in Boston. That was a fun conference. And during our conversation, we were talking about a little bit on rapid intraoperative diagnostics available using nanopore sequencing. Could you share a little bit about that and kind of where that's going in the future?
SPEAKER_02Yes. And this is actually a total game change. So rapid intraoperative diagnostics using nanopore sequencing essentially represents a paradigm shift in oncology and particularly in neurosurgery. So essentially, we're moving from microscopic cell analysis to molecular genetic sequencing while the patient is still asleep on the operating table to get accurate diagnosis of a tumor.
SPEAKER_00That's crazy.
SPEAKER_02It is, yeah. So using lawnry technology developed by Platforms like Oxford NANO4 Technologies. Pathology teams can bypass days of laboratory processing. They can return a precise molecular classification of a tumor in essentially as little as 30 to 90 minutes. Wow. And several hospitals in Europe have already started utilizing this approach, and now several hospitals in the US will be adopting this methodology. So, in a nutshell, in the patient with brain tumor, the surgeon resects a small piece of tumor biopsy, and at the start of the operation, then the tissue undergoes a highly streamlined PCR-free DNA extraction and library preparation that only takes a few minutes. After that, DNA gets sequenced and the data is analyzed instantly using machine learning algorithms such as widely studied sturgeon and robin pipelines. They match the tumor's epigenetic fingerprints against global databases to confirm the exact tumor subtype and return the results to the surgeon.
SPEAKER_00That's crazy. I can't even imagine what that's doing kind of for the patient and even the costs associated with patient care and just the whole infrastructure.
SPEAKER_01So, uh Elena, just switching gears to some challenges that have been seen over multiple decades, but still today, literature kind of suggests that only about 35 to 40% of cases receive a definitive diagnosis. Why today is that number still low? And do you see that improving in the next couple of decades?
SPEAKER_02Yeah, sure. And I have to add that 35 to 40% of cases get the definitive diagnosis when we're talking about inherited genetic conditions. And cancer, I think we already have reached a very high diagnostic yield overall. But for inherited genetic conditions, there are still a lot of reasons for why we're not reaching a very high diagnostic rate. One of the primary reasons is, of course, probably about half of the genes in the genome still have no clear disease association or well-characterized function. Also, a lot of diseases have multifactorial bases, and so it's difficult to understand how genes interact with each other. There are a lot of epigenetic changes that occur in the genome, and we don't know how overall they change the function of the genes. Several genes that undergo epigenetic changes, but in order to understand how they impact the gene function, we need to obviously do some functional studies and do some research and model organisms, etc. Some genes and proteins still have unclear mutational mechanisms and the penetrance could be reduced. And then now we're also entering into the area where we're discovering a lot more patients with mosaicism, like a case I described earlier. And a lot of bulk methodologies have limitations of detecting that type of mosaicism. So we have to develop single-cell molecular-based technologies to detect and to differentiate genetic abnormalities on the single cell level. So overall, I think it's still contributing to overall 35-40% diagnostic yield, even though we have increased that over the last few years from essentially 10-15% to almost 40%.
SPEAKER_01So definitely still some major challenges there. Do you see any kind of new and exciting research or technologies come up that can help fill that gap or at least help get over some of those challenges?
SPEAKER_02Yes, definitely. Basic research is absolutely essential for us to understand the role of the genes, the role of epigenetics, the role of even glycosylation, protein glycosylation is also very important, but we are not even there yet to understand how glycode shapes our proteins and post-translational modification. This will be the next step overall. Many genes and humans have homologs and modal organisms, and we can learn a lot from work in cell culture, in modal organisms, and then extrapolate that knowledge to humans. Additionally, we can study how specific mutations affect proteins and cell culture, or by studying those in modal organisms such as fruit flies or mice, and subsequently provide more diagnosis for our patients.
SPEAKER_00Absolutely.
SPEAKER_01Thank you so much. So I'm curious to hear, and this is kind of a loaded answer, but I'm going to skip to kind of the data interpretation and bioinformatics part, if that's okay. So I I know you receiving all of this data and bioinformatics and data software is huge to interpret what you're seeing. Could you maybe talk about more on the bioinformatics side, general testing? What how are you and how does bioinformatics help you turn what the testing and data into meaningful insights?
SPEAKER_02Yes, sure. So bioinformatics plays a very important role. It acts as the computational bridge that translates millions of raw, unreadable DNA fragments into a clean, prioritized list of medically useful findings. And essentially, without bioinformatics, a genetic sequencer would only produce terabytes of text files containing letters A, T, C, and G. Bioinformatic pipeline transforms this massive data load into clinical insights through essentially five critical phases. First one is raw data quality filtering and control, and then alignment and mapping. Then the next one would be variant calling. The fourth stage would be annotation and clinical curation, and then finally algorithmic variant prioritization, deciding which variants are pathogenic, likely pathogenics or benign or likely benign, et cetera. Or some of them may come up as variants of unknown significance.
SPEAKER_01So, Elena, what role do software platforms and informatics teams play in your workflow on a day-to-day basis?
SPEAKER_02Yeah, so this is a great question. And software platforms and informatics definitely play a huge role in every clinical genetic testing. For example, for next generation sequencing, it is a crucial part of testing, as well as for other tests. In NGS workflow, software platforms and informatic teams act essentially as a digital blackbone, transforming terabytes of unreadable raw genetic data into secure, structured, and essentially medically actionable insights. And obviously, we're utilizing software platforms for different kinds of tests, whether it's carryotyping analysis, fluorescent and seizure hybridization, targeted sequencing tests, or optical genome mapping, loan read sequencing. So everything utilizes software.
SPEAKER_00So when you're using the software, what goes into ensuring the accuracy and reliability behind those results?
SPEAKER_02So obviously, for any clinical testing that will be offered by the laboratory, we have to do extensive validation. And that includes not just the validation of the test itself, but it also includes validation of the software, ensuring that it performs to the highest of standards and can pick up all the abnormalities we're looking for.
SPEAKER_00So I assume you have to follow CAP and CLIA guidelines. How does that kind of shape your everyday workflow?
SPEAKER_02Ensuring the accuracy and reliability of genetic test results, and especially next generation sequencing, because it's a highly complex test, it requires a multi-layered framework of laboratory standards, data science, and clinical governance. Because clinical decisions dictate cancer therapies or diagnose genetic disorders, every step from blood draw to final report is heavily standardized under regulatory bodies like College of American Pathologists or and clinical laboratory improvement amendments, CLIAR. So CAP and CLIAR strictly regulate what we do in the diagnostic laboratory.
SPEAKER_00So how do the CAP and CLEAR regulations shape your day-to-day operations?
SPEAKER_02CLEAR regulations and CAP accreditation standards dictate every action in a molecular and cytogenetics laboratory. And reliability is established and maintained through essentially three core domains. The first one is pre-analytic quality control, so the actual physical sample collection before it gets to the diagnostic laboratory. The second domain is analytical step. That's when the actual sample is processed in the laboratory. And then the finally is the post-analytical core domain. That's when we generate the report and provide diagnosis to a clinician. Clinical diagnostic laboratories must meet CAP and CLEAR requirements to ensure highest standards of care. Under CAP guidelines, we must accurately follow all procedures to minimize sample failure rate and maximize the diagnostic yields.
SPEAKER_01So, Elena, this kind of wraps up the questions that we have. Is there anything else that you'd like to mention to our listeners or any shout-outs that you'd like to make on your behalf?
SPEAKER_02Sure. I would like to say that genetics is fascinating. And when I stepped into this water almost 20 years ago, I didn't realize that it will go through this rapid evolution. Essentially, in 2002 and 2003, I do remember when my advisor showed me Nature magazine and screaming loud, the human genome sequenced sequence has now been published. This was a beginning of a new exciting era. And every day now at work, we are facing a lot of interesting diagnoses, a lot of interesting challenges, and this is what makes my job very exciting. And I encourage everybody to just learn about genetics and see how genetics can be incorporated into medical care. I would like to thank everyone in the diagnostic laboratory at Children's Mercy. We all solve a lot of diagnostic challenges every day. Our team is wonderful. I would like to thank all patients who are trusting us to deliver highest care and waiting anxiously for their results. And obviously, I would like to thank all the mentors who shaped my career up to this point, from my engineering to biology and diagnostics.
SPEAKER_01Perfect. Thank you so much, Elena. So I I I agree with you, and I want to echo that over the last couple, two, three decades, this industry has just evolved so rapidly and dramatically in a good way. And honestly, you and us, we are lucky that we are able to be a part of that industry and because ultimately it helps patients and patients' lives and quality of life. So I I agree with you, and I I think it's fantastic that you do what you do and help uh patients on a day-to-day basis. At this point, Elena, we've kind of wrapped up our QA. So I just want to take a second to thank you for being uh involved in this podcast. We have had such a blast talking to you over the last couple of weeks.
SPEAKER_00And learning all about you.
SPEAKER_01All about you. So extremely knowledgeable, but also a pleasure to talk with. Always with a smile on your face. So we really appreciate you being on here.
SPEAKER_02Yes, thank you so much for having me today. Of course. It's always a great pleasure to share knowledge with you.
SPEAKER_00Thank you for joining us for today's episode of Diagnostics Decoded. We'll be back each month with new conversations diving into the science, challenges, and innovations shaping diagnostics.
SPEAKER_01If you'd like to learn more about Zeptimetrics and the resources we offer, visit us at www.zeptometrics.com. Until next time, thank you so much for listening. Toodles.
