Next-Gen Sequencing in Genetic Medicine with Dr. Lina Ghaloul-Gonzalez

Plain Community Translational Medicine Program and Clinic at UPMC Children's Hospital of Pittsburgh

Genetics Homepage | CHP.edu

Genetic Disease in Amish | CHP.edu

Amish and Plain Communities | The University of Pittsburgh School of Medicine Department of Pediatrics Translational Research

Genetics, medicine, and the Plain people | NIH National Library of Medicine

Improving access to genetic services for underserved populations: Amish, Mennonite, and other Plain communities | Centers for Disease Control and Prevention

Next Generation Sequencing (NGS) - An Introduction | Applied Biological Materials YouTube

What is next generation sequencing? | NIH National Library of Medicine

Whole genome sequencing | CDC

What are whole exome sequencing and whole genome sequencing? | NIH MedlinePlus

TANGO2-Related Metabolic Encephalopathy and Arrhythmias | NORD

TANGO2 Research Foundation

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Voiceover: This podcast is for informational and educational purposes only. It is not medical care or advice. Clinicians should rely on their own medical judgements when advising their patients. Patients in need of medical care should consult their personal care provider. Welcome to "That's Pediatrics", where we sit down with physicians, scientists, and experts to discuss the latest discoveries and innovations in pediatric healthcare.

Dr. Amanda Poholek: From UPMC Children's Hospital of Pittsburgh, welcome to That's Pediatrics. I'm your cohost, Amanda Poholek, Assistant Professor of Pediatrics.

Dr. Arvind Srinath: And I'm your co-host, Arvind Srinath, Associate Professor of Pediatric Gastroenterology.

Dr. Poholek: Today, our guest is Dr. Lina Ghaloul-Gonzalez, and she's here to discuss genetic disorders affecting the Amish communities and how learning from the Amish communities can help communities at large. Dr. Ghaloul-Gonzalez is a geneticist at UPMC Children's Hospital of Pittsburgh and an assistant professor of Pediatrics in the Division of Genetic and Genomic Medicine with a secondary appointment in the Graduate School of Public Health. During her fellowship, she became interested in translational research, including implementation of Next-Gen sequencing and bioinformatics analysis to diagnose genetic disorders in a modern approach to medicine. And this interest became more focused on studying genetic disorders in the plain communities in western PA. Thank you so much for joining us today.

Dr. Lina Ghaloul-Gonzalez: Thank you for having me.

Dr. Poholek: Can we just start by you sharing your path to UPMC Children's and how you became interested in a specialty in genomic medicine?

Dr. Ghaloul-Gonzalez: Sure. I'm actually an internist different probably than many people here at UPMC Children's. I did my internal medicine residency in Buffalo, New York, but I always had in mind that I want to do genetics. I did interview in very few places for medical genetics and UPMC actually was one of the places that I really liked because of the research opportunities. And there were so many clinical trials there here, with the Division of Genetics. I chose to do my fellowship here and did the fellowship in medical genetics and biochemical genetics, did also post-doc afterwards, became interested during my postdoc and fellowship with interest in novel genetic disorders. I remember the first patient we had with whole exome sequencing, was during my fellowship, that took almost a year to get the results back. And this is why I decided during my research to focus on doing Next-Gen sequencing, translational medicine and started from there.

Dr. Srinath: For us pediatricians that I apologize if these questions are very basic, they're basic to me, is what is Next-Gen sequencing. And can you tell us how this process came about and what its utility is for?

Dr. Ghaloul-Gonzalez: Yeah, sure. Next generation sequencing, when we talk about it in general, we are talking more towards whole exome sequencing and whole genome sequencing. It also includes other technologies like RNA Seek, but for people that they're not much into the genetics and this technology. When we talk about and explain to our patients about whole exome sequencing is really reading through the letters that they compose our genes. Whole exome sequencing is more focused into the exonic regions that they get translated into proteins while whole genome sequencing, it sequence everything, exons, introns, also mitochondrial DNA. And from whole exome and whole genome sequencing, then you can look for specific genetic disorders based on the phenotype of the patient. You look for genes that they are implicated with specific phenotype. Sometimes when we do whole exome or whole genome sequencing, and we have a specific phenotype, sometimes it's easy. We can find the answer quickly. And sometimes, we are looking for something novel, that's not discovered previously.

Dr.Poholek: I'm glad you asked that question, Arvind, because that was going to be my next question. But actually I want to jump off that and ask, can you share a little bit about how NextGen sequencing has really changed the field of genetic medicine or maybe even helped make it what it is today?

Dr. Ghaloul-Gonzalez: Enormously. And I can tell you, so I started my fellowship here at UPMC Children's in 2010. And I can tell you from when I started my fellowship to now, we changed things dramatically in our practice in genetics. The way that it used to be in the past is, we see a patient in the clinic, then we have to think about differential diagnosis. We still encourage all fellows to do that. And then, depending on the differential diagnosis, you think which one is the highest in my differential diagnosis and you do single gene testing for that genetics orders, that's high in your differential. If that comes back negative, then you go for the second one in your list. If that's negative then to the third. Ten years ago, so this is how we used to do it with single gene testing.

And we had sometimes gene panels, but those gene panels included two or three genes. Now we have gene panels that include maybe 100 or 150 genes. And we have the ability to do whole exome sequencing. In 2010, it took a year to get results back for the patients. Now we can do whole exome sequencing and get results in a clinical lab in two to three months. We can do rapid exome sequencing and get results in 10 days. We have the whole genome sequencing where we can get results in 72 hours, which its dramatic for our patients because it changes the management, it's really huge change from over these past 10 years-

Dr. Poholek: Yeah, it's amazing.

Dr. Ghaloul-Gonzalez: Now actually, when we see patients, so even if we do single gene testing and that's negative, our second approach, no more single gene testing go directly to whole exome sequencing.

Dr. Srinath: You're reading my mind in terms of the next set of questions is, what prompts you to go beyond single gene testing, if that is negative? What scenarios, what situations or what prompts you there?

Dr. Ghaloul-Gonzalez: We always want to find the answer for our patients because finding the genetic diagnosis, then you do precise treatment for that specific diagnosis. For example, if we have a patient in the clinic with seizures, let's say, it's a common thing that we can see. Seizures get treated with anti-seizure medications. But as a geneticist, we know we have to think about different things. Seizures can be due to, just a patient will have only seizures. It can be part of a syndrome where patient can have seizures and other things related to that like GM3 Synthes deficiency. Patients have seizures with developmental delay.

Propionic acidemia for example, in the Amish population, it's much milder than the general population. And sometimes they present only with seizures and the treatment for propionic acidemia is totally different. It's diet management, protein restriction, there's specific amino acid restricted that we have to do. We have to think about seizure as long QT, for example, can cause arrhythmia and seizures. If you see the patient and you really did single gene testing, you didn't find the answer, the next thing you will... Well, I have all these differentials. It can be anything, what's the best next step? Best next step in many cases, is whole exome sequencing.

Dr. Srinath: That's super helpful.

Dr. Poholek: I know you recently got another grant, congratulations on the TANGO2 Study, I believe. And I was wondering if you could just tell us a little bit about some of the things you've been studying specific to the plain communities, the Amish and the Mennonites in western PA and how that has really helped you understand these disorders at large. And then maybe a little bit about TANGO2.

Dr. Ghaloul-Gonzalez: I actually didn't have, at the beginning, have the interest specifically in Next-Gen sequencing in the Amish and Mennonites. I started just applying this for the patients that we used to see in the clinic that we didn't have diagnosis on them. But then I remembered during my postdoc, so we have an Amish female with the MELAS Syndrome, which is mitochondrial DNA mutation. And we did research study related to that and went to the community, tested other family members and found there are other members with the MELAS mutation and thinking about that and then about other patients, I saw in consult and inpatient or outpatient, we realized that the Amish and Mennonites in western Pennsylvania, we don't know much about their genetics. We know that Amish and Mennonite immigrated from Europe in the 1700, but then they settled in different areas.

We know a lot about the genetics of the plain community, plain meaning Amish Mennonite in eastern Pennsylvania, Lancaster. But we know that the genetic disorders are different between the different communities. They share some genetic disorders, but they also, each community have their own genetic disorder. And since we didn't know much about western Pennsylvania, thinking about that MELAS patient and how we diagnosed so many members with MELAS, then came another immune deficiency disorder, which was not seen in other communities. The need, that to learn more and do more studies in this community.

Dr. Poholek: That's amazing. Can you tell us a little bit about TANGO2?

Dr. Ghaloul-Gonzalez: Yeah. TANGO2 is actually a very interesting disease. It's relatively new disorder. TANGO2 mutations just discovered in 2016. We don't know anything about the exact function about the disease. We know a little bit, we know that there were several studies looking for mitochondrial dysfunction. And the reason is these patients have... Some of them present with lactic acidosis, some of them with hyperammonemia, others with developmental delays and rhabdomyolysis, things that you can see with mitochondrial disorder, but not exactly and the phenotype is very different, so it can be from mild to severe. There were some different studies in Canada, Europe, here in the US and looked for mitochondrial dysfunction and there was controversy. Of course, TANGO2 is seen in the general population, and it's also seen in the Amish. This is why it's more interest for me because I'm seeing it in both populations and looked more in depth into mitochondrial dysfunction.

And indeed we did find that we know that there's chondrial mitochondrial dysfunction in these patients. There is some hints that there is abnormalities in transportation between ER and golgi, but we don't know much about that. And there is still a lot to learn. We are working actively actually in the lab to learn more about the pathophysiology about the disease. The one thing which I would say that is really fascinating about TANGO2, is you can see patients with the same mutations, severe mutations with no protein when you tested and it can be very mild or severe. There is something else having a role, whether it's epigenetic, environmental, we don't know exactly.

Dr. Poholek: Fascinating.

Dr. Srinath: How do you hope the understanding of TANGO2 for example, and many of these other conditions you've described, which this Next-Gen sequencing is revealing. How do you hope understanding the pathophysiology will affect treatment modalities and where are you at certain conditions that you've basically learned about?

Dr. Ghaloul-Gonzalez: Related to TANGO2 or in general?

Dr. Srinath: In TANGO2 first and perhaps in general?

Dr. Ghaloul-Gonzalez: In TANGO2, yeah. We actually working extensively on supplements that can affect that. It's not published yet, but it's going to be hopefully soon. Natural history study in Baylor that I'm collaborating with them. And also in Canada, looking for specific vitamins that they are having benefit on patients and they tested it on fibroblast, fruit flies that they have TANGO2 deficiency. There is a specific vitamin B that it's remarkable to see that a B vitamin that's on the shelves in the pharmacies. You can see that the phenotype of the fruit flies almost reversed completely. And the fruit flies, you can look at their neurodegeneration because these patients, they progress normally, but then they have neuro regression. And one of the things you look at the eyes of the fruit flies, it's so fascinating with the control.

You have the normal red eyes, the TANGO2 deficient, completely wide, and those fruit flies that they're treated with this B vitamin, recover completely. Their movement, it's remarkable. It's something we did not think about. And also the natural history study, following these patients with a TANGO2, they also found that patients with TANGO2 deficiency, that they are on some of these B supplements, also have less admissions with rhabdomyolysis or metabolic crisis. This is one of the things that we really want to confirm looking at skin fibroblasts, IPS aligns, and cardiomyocytes and IPS align neuron, wants to see whether it's so good to be real, to make sure that our results, we trust these results and this will be translated to the patients, with diet recommendations, what kind of supplements.

We know with mitochondrial dysfunction, these patients are on supplements that we give for patients with mitochondrial disorders, but they don't really work much. We have, actually, this is one of my aims to look for, other compounds that they are on clinical trials, affect the function of the mitochondria. We will be testing also to see if they have any positive effects. This is ongoing work.

Dr. Poholek: That's exciting.

Dr. Srinath: Fascinating.

Dr. Poholek: I have a question sort of as a non-clinician, which is, there are so many patients that have potentially broad and difficult to define, differential diagnoses. They maybe have fatigue or they maybe have joint pain or they maybe have... Sometimes it's clear, they have a clear immune deficiency or something. But sometimes it's not so clear and they can go for some time seeing doctor, after doctor, after doctor, trying to figure out what's going on. At what point does it sort of become clear that this is a candidate for genetic testing, that maybe they don't fit into any of these boxes for diseases that we know about, for polygenic diseases that we know about. And you can actually say, "We don't know what's going on with you. Let's try and see if there's a gene deficiency here that we can see and potentially even describe a novel disease."

How does that decision come about?

Dr. Ghaloul-Gonzalez: We get so many patients that they're seen probably by six or seven subspecialties. And what we try to do in genetics is to connect these dots together and see, is there something common that would lead to all these different things that we're seeing in the patient. Sometimes we think, "Oh, maybe yes, this is what's causing this, all these different kind of symptoms, patient with propionic acidemia not treated, this is why he's having cardiomyopathy, he's having seizures. He's having the fatigue, the lactic acidosis, hyperammonemia." Connect all these together. But sometimes we don't know, we just have these random clinical manifestations. And in these cases where we don't have clear differential diagnosis, we tell the patient, "We don't know if this is genetic or not."

Sometimes there is more dysmorphism with major organ involvement, you think more about genetics, but if it's non-specific maybe, fatigue, headache, joint locations here and there. Maybe we're not sure, but there are some clinical features more suggestive of other of genetic disease. We give all the patients really that we... We take very good family history because that also very good component of our genetic evaluation and see if there are hints also from the pedigree and a family history about genetic disorder. If there is nothing specific that we go for a panel, in this case, we either go for whole exome sequencing or if we are not sure or less suspicious of having genetic disease, we tell the patient, "If there's something else develop, let us know and we can reevaluate you and think about genetic testing based on the new clinical manifestations."

Dr. Poholek: Interesting. Can you describe a little bit of what it's like to sort of have a patient and define a new gene for that diagnosis? To say, "Okay, we did whole exome sequencing. We found something and it's something no one's really seen before." What do you do next?

Dr. Ghaloul-Gonzalez: We have to do functional studies. Next-Gen sequencing is awesome, but I always say it's for discovery. After discovery, so you have candidate genes and with the candidate genes, or sometimes it's even novel variant that was not seen in a gene that we know that cause a genetic disorder, but even whether it's novel gene association to a disease or novel variant in a gene that we know is linked to specific disease, we have to go for functional studies. This is why I always say Next-Gen sequencing cannot function alone. You really need the basic lab wet range to complement each other. It depends on the candidate genes or variants, we either look for pathways where this gene is in specific pathways, say, "Okay, does this gene based on this pathway make sense that it can cause immune deficiency or other specific disorder," and go from there.

Dr. Srinath: And that's a great segue. A, can you define functional studies and then B, talk about just future technologies you anticipate utilizing over the next few years as geneticists.

Dr. Ghaloul-Gonzalez: Yeah, sure. Functional studies when we say, we think about lab studies and that can include either quantitative PCR or depending on the pathway, let's say it's a gene that cause mutation in guanylate cyclase, which increases cGMP, for example. We do studies related to measuring cGMP and look at that pathway, cGMP, now it's increased. What other receptors or other genes is affecting and depend on those, then we do specific studies related to the gene, the protein and the function that is known, or sometimes it's completely novel. You start with something and start to see if it leads you to somewhere else.

Dr. Srinath: Thank you so much.

Dr. Poholek: Do you often feel yourself pulled in a variety of different scientific and clinical directions given the breadth of this topic that you're researching?

Dr. Ghaloul-Gonzalez: Oh yes. It's exciting though. I'm involved with several Next-Gen sequencing with a NICU seek rapid whole genome sequencing, then there is a consortium, different institutions also putting the genomic and the EHR data, the clinical studies. You always learn something different from the different directions. And yes, even with my own studies, just on the Amish, with the Next-Gen sequencing, sometimes yes, you can feel you're pulled in different directions. Now I have these interesting variants, which one that they can be candidate. I can't do functional studies on all, so I have to choose which ones are more reasonable and to start with and go from there.

Dr. Poholek: You're in such an amazing position, having started this career at a phase when they were just a few panels of single gene testing and seeing the revolution of Next-Gen sequencing, what do you thinks next? Where do you see this going? And can you comment a little on whether you think this is part of what we talk about when we say precision genomic medicine?

Dr. Ghaloul-Gonzalez: I really envision that we will be... It's like how we do the CBC and check for anemia, this is how I envision whole genome sequencing will be. We'll get result, go to your primary care physician and you'll be able to order whole genome sequencing and we'll get results quickly. Our role as a geneticist, I think, will change over time. We see more and more services, more comfortable with doing a single gene testing, whole gene panel. We still, as a geneticist, I think we are the only one that we are doing whole exome sequencing, now at UPMC Children's at least here in our institution. But I see this is moving and more people will be more comfortable with it, more education for physicians and new doctors that will be graduating from medical school. They should be really more teaching about all these technologies, because I think they will be doing them more frequently and in the future.

Dr. Poholek: Yeah. I certainly think that's an exciting venture. I imagine that part of this then also is a discussion of privacy and how that plays a role and can you comment a little bit about some of the ethics and the privacy in sort of having these kinds of levels of sequencing of patients?

Dr. Ghaloul-Gonzalez: Yes. There is the GENE Act, which a federal law to protect the privacy of patients where we do whole exome or any genetic testing and protect them from discrimination, from healthcare insurance based on their genetic testing. We do our best definitely, to protect the privacy of these patients. On a clinical basis, this all goes to their medical records. But on a research basis, what we usually do is only the research team is aware of the names of the participants and actually not everyone, even the ones that they are in the lab doing functional studies, they don't know the name of the patients, so it's mainly me, program coordinator, two or three other persons. We try our best to have this private. And we always discuss this with our patients, so this is one of the main things, and we discuss the research, we have to talk about privacy.

Dr. Poholek: Yeah. It's important.

Dr. Srinath: And along those lines, do you ever encounter situations where patients and families just say, "No, I don't want testing done."

Dr. Ghaloul-Gonzalez: Oh, absolutely, yes.

Dr. Srinath: And how do you approach that?

Dr. Ghaloul-Gonzalez: I see that more frequently. We see it in different kind of patients, but just because of my research now is more with the plain community. I definitely see it. I see it more with the Amish compared with the Mennonite. Probably research is a little bit scary for them to go with that. But many change their position regarding this, as they get to know us better. It's hard to get a yes for research from the first visit. But once we see these families multiple times and you build this trust with these families, they can definitely change their position, whether to get involved in research or not. The treatment will be the same, so we'll continue the same treatment that will provide to any patient. But yeah, time and trust.

Dr. Srinath: That's super helpful.

Dr. Poholek: Thank you so much for joining us today. This work is just so fascinating and we really appreciate you coming here and sharing a little bit about your work.

Dr. Ghaloul-Gonzalez: Thank you.

Dr. Srinath: I echo Amanda. This has been absolutely fascinating and learned a ton just talking to you today. Thank you.

Dr. Poholek: Thank you.

Dr. Ghaloul-Gonzalez: Thanks.

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