A fascinating discussion with Dr. Diana Carrasco and Dr. Nikhil Sahajpal on the role of DNA in diagnosing genetic conditions and the potential of optical genome mapping to improve diagnostic accuracy. They also delve into the importance of comprehensive patient histories and the need for equitable genetic research participation across all ethnicities.
Transcript
00:00:00
Music
00:00:04
Host Hello and welcome to this edition of Cook Children's Doc Talk. Today we're talking about diagnostic mysteries: the secrets in our DNA and optical genome mapping with Dr. Diana Carrasco and Dr. Nikhil Sahajpal.
00:00:17
Host: Dr. Diana Carrasco is a pediatric clinical geneticist here at Cook Children's. She completed her residency at Baylor College of Medicine in Houston. As the clinical genetics lead for Cook Children's precision medicine program, Dr. Carrasco is passionate about improving the diagnostic rate and time to diagnosis for genetics patients. In this role, she hopes to bridge the gap between clinical care and research so that patients can benefit from cutting edge technology.
00:00:45
Host: Dr. Nikhil Sahajpal is a laboratory genetics and genomics fellow at the Greenwood Genetics Center in South Carolina, and is a recipient of the ACMG LGG next generation Fellowship Award by the American College of Medical Genetics Foundation. Dr. Sahajpal has a keen interest in rare disorders and birth defects with a focus to understand the genetic basis of these conditions. Welcome.
00:01:11
Diana Carrasco, M.D.: Thank you so much for having us.
00:01:13
Dr. Nikhil Sahajpal: Thank you for having us.
00:01:15
Host: So let's start with what attracted each of you to the field of clinical genetics, and a little bit about your collaboration.
00:01:22
Diana Carrasco, M.D.: So when I was in medical school, my histology professor introduced my class to one of my favorite poems by Alfred Tennyson, and it's called Flower in the Crannied Wall. And I bring it up because it reminds me of why I love genetics. It reads, flower in the cranny wall, I pluck you out of the crannies. I hold you here, root and all in my hand, little flower. But if I could understand what you are, root and all and all in all, I should know what God and man is. And for me, our DNA is the flower in the cranied wall that allows us to best understand our patients. As geneticists, we see children with developmental conditions, neurologic diseases, birth defects and medical concerns that seemingly have no explanation. Our job is to look deeply into their DNA to see if we can find a genetic cause for their concerns. So in this way, a geneticist is like a detective whose job it is to solve diagnostic mysteries. The detective work is a part I enjoy the most about what I do.
00:02:23
Dr. Nikhil Sahajpal: I think for me, it was also my mentors that attracted me to this field. I think I was fascinated by the fact that there is something that we hold that is a blueprint to who we are, that realization itself led me to pursue this field as my career or a life choice, per se.
00:02:40
Host: And so how did you guys get together and form your collaboration?
00:02:46
Diana Carrasco, M.D.: I had heard about optical genome mapping as an emerging technology in our field, and it's great potential to potentially detect variants that other testing technology cannot detect. And then I saw a virtual conference that Dr. Sahajpal presented in, and I found his email and reached out to him about possibly establishing a collaboration between Cook and the Greenwood Genetic Center where we might be able to offer this technology to some of our undiagnosed patients.
00:03:21
Dr. Nikhil Sahajpal: Yeah, I think like minded people come together. Every geneticist is having a quest to find answers, and every opportunity that there might be to increase the ability to find answers or to increase the diagnostic yield in the patient population that we serve, and that's the basis of how we came together, is to advance the genetic testing that we offer to our patients and have a higher diagnostic yield.
00:03:50
Host: This is such a fascinating topic. So to orient our listeners, can you give us a back to basics introduction to genetics?
00:03:58
Diana Carrasco, M.D.: Yes, and I'm gonna go way back to basics. And this might be too basic for some of our listeners, but I always find that before we get into the nitty gritty of things, it can be helpful to do that. Our hereditary material is called DNA, and we all inherit our DNA from our biological parents. We get 23 chromosomes from our mother and 23 chromosomes from our father, and our DNA is like a recipe book. It has instructions for how our body works, but instead of being written with the 20 letters of the alphabet, it's written with four letters or nucleotides, which are adenine, guanine, cytosine and thymine. And whenever there's a change in our DNA, we call that a variant. We can compare a change in our DNA to a typo. Some variants can be compared to hold deletion or duplication of paragraphs in a book. There's many, many different types of variants. Variants are classified according to whether they cause disease or not. So a pathogenic variant is a variant that can lead to medical disease. A likely pathogenic variant is a variant that, with more than 90% likelihood, can lead to a disease. A benign variant is a variant that does not lead to disease, and those are the variants that make each of us different. And then likely benign means more than 90% likelihood of being benign. There's also a category called variants of uncertain significance, and that means that testing has detected a variant that we just don't know enough about to be able to conclusively say whether it's pathogenic or benign. And those classifications are based on the American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines that were published in 2015 and they were published by a group of experts in the field. And we hope that new, updated guidelines will be coming soon. And so when we see patients in the genetics clinic, our job is to order the genetic test that is most likely to detect the type of variant that might be causing their disease. And there's many different types of genetic tests to choose from. No one test is able to detect all variants. And then, aside from variants, there are other changes in our DNA that can cause disease, like methylation abnormalities.
00:06:19
Host; Dr. Sahajphal, can you tell us more about the types of changes in DNA that can lead to medical conditions?
00:06:25
Dr. Nikhil Sahajpal: Yes. So how Dr. Carrasco was saying, there are several types of changes that can lead to a medical condition. We can start with the largest changes, which we refer to as chromosomal changes, or aneuploidies, which is a missing or an additional chromosome. For example, there can be a loss of chromosomes, such as loss of chromosome X, that results in a condition called Turner Syndrome. And then there can be a gain of chromosome, an additional copy of chromosome 21 which we refer to as Down syndrome. Then there are copy number variations, or copy number changes, which is missing or additional pieces of DNA. An example of this would be DiGeorge syndrome, which is caused by the lesion of a portion of DNA on a specific chromosome, chromosome 22, and we refer to that region as q11.2. Then instead of the whole region, there can be just a missing gene or an additional piece of a gene. These are referred to as single gene deletion or duplications. An example of that would be duplication of the gene PMP 22 which results in Charcot-Marie-Tooth. Then, instead of a single copy, duplication or deletion of a gene, there can be spelling errors in a gene. We refer to these as single nucleotide variants. And to give an example of this, the most historic example is the variant called F508del, which is the lesion in the gene CFTR and single amino acid deletion at position 508 which results in a phenotype or a presentation of cystic fibrosis. Then, apart from these, there are repeat expansion and repeat contraction disorders. An example of this would be Fragile X disorder, which is one of the most common reason or cause for intellectual disability. Then there's repeat contraction, which would be D4Z4, repeat contractions in the gene duct score that results in the condition called FSHD. Then what Dr. Carrasco was referring to that there can be changes which are not in the content of the genomic DNA, but is how the DNA is packaged, which we refer to as the epigenome. So there can be changes in the epigenome, and we refer to these as imprinting disorders. An example of this would be Beckwith-Wiedemann syndrome, Russel-Silver syndrome and so on. Then, since we are talking more about rare disorders, these genetic changes are germline changes. They most often occur in the germline, but they can also occur in somatic cells or during post fertilization periods. And we refer to these as mosaic queries. And the most common example of these are changes in the gene PIK3CA, which would result in PIK3CA gene related disorders. And then there can be changes in the genetic composition, or the gene body, the genomic content which is not in the nucleus, which is actually in a different cell organelle, referred to as mitochondria, and the changes in the mitochondrial DNA would result in a specific set of disorders. An example is Leigh syndrome. So there's several different types of variations for which different tests might be ordered.
00:09:41
Host: So what are some of the most common genetic tests used in the genetics clinic?
00:09:46
Dr. Nikhil Sahajpal: The most common tests that are seen in a lab varies with respect to which part or which region of the world the lab is in, but I would say the most common genetics tests are routinely seen in a laboratory. Are chromosomal microarrays, then there would be specific gene panels or exome sequencing. And more recently, we have been seeing an influx or a higher order of genome sequencing orders. Then, based on the presentation of the patient, their clinical signs and symptoms, more specific tests might be ordered, which we just discussed, such as epigenetic modifications, for those sort of changes, and the conditions that result from those changes would be imprinting disorders such as Beckwith-Wiedemann syndrome, Russell-Silver syndrome or Angelman syndrome. Then for specific repeat contraction expansion disorders, there might be specific tests which are ordered to, per se, identify those specific changes. But I would say the most common test that we see are chromosomal microarrays and some form of next generation sequencing, be it from panels going up to genomes.
00:10:47
Host: And so what kind of genetic changes can each of those tests detect?
00:10:58
Dr. Nikhil Sahajpal: So if we start with chromosomal microarray, these tests look at what we call as chromosomal changes. These would be aneuploidies, a loss of a chromosome or a gain of an additional copy of a chromosome. And then these are more specific for copy number variations, LBC, again, of a certain region of a chromosome or loss of a certain region of chromosome. And they have a higher resolution than some of the historic cytogenetic tests such as karyotyping and FISH, and they can look at smaller regions of the chromosome, such as single gene the lesion, or single gene duplications. Then if we look at exome sequencing ... so just to refer back to that example of a book, if we consider we have 46 chapters, how many of those chapters actually code or there's a summary of that book?
So what we believe is that the summary is actually the coding sequence within that book, if we can refer to that analogy. So the coding sequence is only one to 2% of the entire book, of the entire genome. So exome sequencing is like just looking at that coding sequence or the summary of the book, and we would sequence or look at just one to 2% of the entire genome. Then as we go to a broader test such as genome sequencing, this would look at almost the entire genome, and it has the ability to pick what chromosomal microarray picks, and it also has an ability to pick what exome sequencing identifies. But in addition to that, it can look at what exome sequencing does not look at, which is some of the in-between lines within that summary. So it can look at changes which are in the introns, not in the coding sequence, but which might cause a change in the coding sequence. So these are the main tests. But I would like to point here, since in the introduction, we did mention the technology, optical genome mapping. What these tests do not identify is something referred to as balanced chromosomal rearrangements. So these are changes which does not cause any copy number changes. They are balanced within the genome. And the type of structural variations that would come in this category would be translocations, inversions, insertions and inverted duplications, knowing how the orientation of the duplicated material is important to identifying these balanced events. These are the variant classes which are beyond these technologies that are used regularly in the clinic. There's one technology that the most historic technology referred to as stereotyping, which is still used to pick these changes, but the resolution of that technology is five megabases and beyond, which is to say that it can look at very large balanced rearrangements, but cannot look at small balanced rearrangements. So we have been missing these smaller balance rearrangements for a long time, and we think that there are answers that we would reach when we start looking at these smaller balanced rearrangements. And that's how optical genome mapping fits into this clinical workup and in our discussion.
00:14:03
Host: So we really do come with an owner's guide or owner's manual. We just don't know how to read it all yet. So Dr. Carrasco, as a geneticist in clinic, how do you know which test to order for each patient?
Diana Carrasco, M.D.: This is a really important topic, because sometimes the way I make a decision might be by reaching out to a laboratory geneticist, and that's where the relationship between the clinic and the lab is very important, though there are guidelines. So the American College of Medical Genetics and Genomics recommends exome or genome as a first tier test in cases of developmental delay, intellectual disability and congenital anomalies. And I would say to our providers listening, if you have a patient with some of those concerns, and I would include neurologic disease in that, refer to genetics, and the earlier you refer, the better, because we want to try to find a diagnosis as quickly as possible for that patient. So exome and genome sequencing are pretty comprehensive tests. There are times when we would order a narrower or more targeted test, and we do that when we see a patient that has a readily recognizable condition. The easiest example that I can bring up is something like Down syndrome. And so Down syndrome is caused by extra material of chromosome 21 and chromosome analysis would be the best test in that situation. Other disorders that are easy to recognize are things like Cornelia de Lange, which includes terminal limb defects, or rasopathies like Noonan syndrome, where children have short stature, pulmonary valve stenosis and a broad webbed neck and other features. So in those cases, I might order a panel that only includes the genes that are most likely to be involved. Dr. Sahajpal had talked about methylation disorders like Beckwith-Wiedemann. Others are Prader-Willi, Angelman syndrome. And so when we think we have a patient with that condition, we have to order that specific test to detect it. It requires having a higher clinical acumen. And then when we talk about mitochondrial conditions, whole genome sequencing, of course, includes mitochondrial DNA, but some signs of a mitochondrial condition are things like ptosis, external ophthalmoplegia, myopathies, deafness, exercise intolerance, cardiomyopathy, optic atrophy, pigmentary retinopathy, encephalopathy, seizures, stroke-like episodes, ataxia, spasticity and chorea. And if we see that maybe in combination with elevated lactic acid levels, elevated CK levels, then we would be suspicious of a mitochondrial condition. So in summary, the type of medical concerns that my patient has tells me what kind of genetic alteration might be present in that patient, and that, in turn, helps me choose the test for that patient. There is publicly available genetic testing stewardship pathway on the Cook Children's website. If you just Google Cook Children's clinical pathways, you'll be able to see a lot of pathways, including one titled genetic testing stewardship, which might be helpful for providers.
00:17:20
Host: That's fantastic. Thank you. So Dr. Sahajpal, what are the most important things you need to know about a patient in order to have the best chance at finding a diagnosis? As a laboratory geneticist,
00:17:32
Dr. Nikhil Sahajpal: I think I'll start with a quote that comes from a book that we refer to as our Bible. The book is Genetics and Medicine, and I apologize that I don't remember the author of the quote, but the quote goes by taking incomplete patient or family history is bad medicine. So you have to remember that a lab geneticist does not see the patient, but is the person who looks at the patient's genetic data. So what we rely upon is clinicians notes, the terms that they submit that this patient has these clinical features. So you look at the genetic information, and we match that genetic information to the clinical features that are listed by the clinician. So that's the key thing that we need, or what we rely upon to reach a diagnosis. And in many instances or circumstances, what we would do is, instead of just running the patient genomic analysis, we run a dual analysis, or trio analysis, which is to say that we also run the parents. And what we look for is, if the parents are unaffected, do we see a change in the patient, which is a new change, which was not in the parents. So this is very important, having the right samples, having the right family members for doing the genetic testing. And to go back to my point of having the right history, what we would note in certain circumstances is that a change was inherited, which was listed as that the parent was unaffected. But when we go back and do a thorough clinical workup, we will find that one of the parents from which the change is coming is actually mildly affected. So that's a causal change. So having the right history, right patient samples, and the correct family members for doing the genetic testing is very important.
0019:21
Diana Carrasco, M.D.: I want to talk a little bit about that because what Dr. Sahajpal is pointing out is very important. As you can see, there are many factors that can impact the diagnostic yields of a test that happen or are provided to laboratory geneticists before any testing is done. And talking about the variant classification guidelines that a laboratory geneticist relies on to be able to tell us whether a patient's genetic variant is responsible for causing that patient's disease or not, some of the most important elements of those guidelines have to do with having very accurate patient phenotyping. And relevant medical history, relevant family history. And geneticists work with genetic counselors. Together, we obtain a three-generation pedigree for our patients and including relevant family members. So oftentimes, when biological parents are available, it's very important to include their samples. Sometimes it might be relevant to include a patient's sibling or a more remote family member who has similar medical concerns to our patient. All of that increases our chance at finding a diagnosis before any testing begins. Dr. Sahajpal was also referring to the concept of phenotypic variability, where we might see a patient's parent who has maybe a very mild symptom that wouldn't raise flags for a geneticist. But when we consider it in the context of that child's medical concerns, then it could be suggestive of Mendelian disorder that was passed on from parent to child, and in the parent, maybe that genetic condition expressed in a very mild way, but in the child it expressed in a more severe way. And providing the lab with all of that information really helps them out. So that's where I would say it's also very important to involve the genetics team in decisions related to genetic testing. Genetic testing stewardship is a very important topic. It helps us utilize our resources in the most efficient way possible, and it helps improve patient outcomes.
00:21:31
Host: So it sounds like you have a wide variety of genetic tests available using this technology, I imagine you are able to find a diagnosis for a large majority of your patients? Is this true?
00:21:42
Diana Carrasco, M.D.: Some studies have shown that, on average, pediatric patients and their families spend up to five years searching for a diagnosis, undergo five uninformative medical tests and incur $10,000 or more in health care costs before reaching a diagnosis. Using our current knowledge and technology, we are able to find a diagnosis for about 40% of our patients. That means that we have not found an explanation for the medical concerns in as many as 60% of the children we see. And the reasons for that are varied. They include technological limitations of current tests. We also know that on average, it might take up to 17 years to translate a novel research finding into routine clinical practice, and that's not just in genetics, but in medicine in general. And it takes that amount of time because new technologies need to be validated, professionals need to be educated on their use and so all of that accounts for that time lag.
00:22:44
Host: So what is the importance of finding a diagnosis?
00:22:50
Diana Carrasco, M.D.: Finding a diagnosis helps us understand why a child developed the medical condition they have. Why was a neonate born with a severe congenital heart defect? Why is a child experiencing debilitating immune dysregulation disorders, or why do they have renal function issues? It's very important for families to find an explanation about that. It helps us have a better understanding as well of what a patient might expect in the future, because if we find a diagnosis, we do a comprehensive literature review about that genetic condition, and we see what kind of information has been published about patients with that condition and their age ranges. So that helps us give parents important information. There are also clinical care guidelines that might apply. So for example, one of the multidisciplinary clinics that we have a Cook Children's is the 22q11.2 deletion clinic, and there are very updated guidelines about the specific type of medical care a child with that deletion needs throughout their lifetime. Of course, as a children's hospital we rely on the pediatric guidelines, and there are also adult guidelines, it allows families to be connected to a community as well, to establish a relationship with other families who might have children with the same genetic condition, reach out to specific foundations or societies that focus on their child's genetic condition. Parents can also have important information that helps them with family planning, they may be able to know how likely it is that if they have another child, that child will have the same genetic condition, and whether they might want to make use of seeing a fertility specialist or treatments like IVF. We learn more about rare diseases by diagnosing them. So in aggregate, a rare disease affects about 10% of the population in the United States. The more we're able to diagnose patients, the more we're able to contribute to the medical literature for those rare diseases and have a better understanding of how to manage those patients, and then, very importantly, finding a diagnosis is the first step in being able to find possibly a cure for that diagnosis.
00:25:06
Dr. Nikhil Sahajpal: I would like to add something to what Dr. Carrasco just referred to. I think finding treatment is very important, and that's where the next frontier is. But something more Dr. Carrasco referred to in her answer to this question was guidelines on management. I think those are very important. And just to give some context to that, so there have been natural history studies done, which is when we identified patients with a specific syndrome or disorder, they were followed for several years as to see how they progress, which changes or which conditions, which abnormalities would happen at specific periods of time. So that now, when a new patient is identified with a specific syndrome or disorder, we will know that these are the conditions or changes that we need to monitor for. So we would know that at age three, this individual might develop this particular clinical feature or phenotype. At age eight might develop this so the families are prepared for what is to come. So I think that's very important, even when ... for conditions where we do not have a treatment, to having these management guidelines is very important for the patients and their families.
00:26:21
Host: Very similar to the Prader-Willi clinic that we have here at Cook Children's, where the parents that are connected now, because they can share that support, and then they can also, like, start to learn what to expect at each phase. And it takes a little bit of pressure off, because it's a lot of pressure on parents to have some of these conditions. And on the family, so financially, emotionally. So, yeah. So this is fantastic. Thank you.
00:26:43
Dr. Nikhil Sahajpal: This was a really good point, because those support groups are very important. And many times we have these clinics for Angelman syndrome and more common genetic disorders where there are patients in hundreds and the families can connect. But then there are such rare disorders that do not have a common clinical presentation, they are the same disorder because of the changes that have been found in the same gene. So it's genotype first approach that the disorder is characterized from what has been found in their genetic information, rather than a common clinical presentation. And there might be just a handful, less than 10 individuals around the world, so having a connection, knowing that there's someone else out there managing the same thing, it's very important for those families to be connected and go from there. So I think that's a very important point to be highlighted over there.
00:27:33
Host: So will the Precision Medicine Program at Cook Children's help in this regard?
00:27:38
Diana Carrasco, M.D.: Yes, I hope so. And I'm really excited about the Precision Medicine Program at Cook Children's. It came about as an endowed chair that was awarded to Dr. Anish Ray. And what Dr. Ray's done is he's united the pharmacogenomics, research, clinical genetics, and oncology departments with the common goal of providing our patients with individualized care. In the clinical genetics department, we hope that we can increase our contributions to the medical literature through the Precision Medicine program resources, and build collaborations with various institutions that can allow our patients access to a wide array of testing options. Our goal is to increase diagnostic rates, decrease time to diagnoses, and connect patients with relevant clinical trials or research projects that target their genetic condition.
00:28:27
Host: What are some barriers you've encountered in reaching a diagnosis for your patients?
00:28:32
Diana Carrasco, M.D.: One of the barriers might be limited access to care. If there are any students listening, please look into pursuing a career in medical genetics, laboratory genetics, genetic counseling, it's really a very fulfilling career, I can say. And it seems like over time, the genetics caseload, the number of patients who need to see a geneticist, is increasing, but the number of geneticists is not. Another important barrier is cost. Some of the out of pocket costs for these tests can be as much as $2,500 or more, and some patients don't have access to insurance that can cover that. Sometimes insurance might take some time to extend coverage. So for example, in 2010 a chromosomal micro array was recommended as first year testing in children with things like birth defects or developmental delay. But it wasn't until 2021 that a CMA was added to the Texas Medicaid schedule. And then by that time, the American College of Medical Genetics and Genomics was recommending exome and genome sequencing as first year testing for neurodevelopmental conditions and birth defects. So those time lags can present a lot of barriers in helping us help our patients. There's been increasing literature about the cost effectiveness of things like exome and genome sequencing. These are tests that are still not covered by many payers, and many other tests that include things like genome wide methylation analysis. The Greenwood genetic Center has one called EpiSign Complete and other tests that maybe detect mosaic variants. Some of these tests are very difficult to get coverage for. And then other barriers are things related to racially and ethnically minoritized groups. So we know that these groups participate in research at much lower rates than majority populations, which means that we know less about their genetic material, less about what variants are important in causing disease in those groups. They make up a smaller fraction of cases and genomic databases. And genomic databases are some of the most important resources that clinical and laboratory geneticists rely on to decipher a patient's genetic information. For example, there was one pan assembly of the genome where 10% of African DNA sequences were missing from that reference genome. That's a very large amount, and that can lead to increased rates, also a variance of uncertain significance, which means, "We found a variant in your DNA, but we just don't know enough about it to be able to tell you whether it does not cause disease or it does cause disease." So we really need to do more as a field to advance equitable care.
00:31:23
Host: So it seems like there's extra cost to not being able to diagnose something more thoroughly, because there's constant attempts at trying to find out why your child is ill, or why your child has these certain things. So you're paying all of this money and going to different doctors and different treatments and therapies without really ever resolving what's at the cause of it.
00:31:43
Diana Carrasco, M.D.: Yes, that's exactly right. And there's many papers written on the cost effectiveness of both exome and genome sequencing and specific clinical situations for that reason.
00:31:53
Host: So, Dr. Sahajpal, talk a little bit about the reference genome. What is it?
00:31:59
Dr. Nikhil Sahajpal: So a reference genome is an accepted representation of the human genome sequence that is used by a geneticist as a standard for comparison of DNA sequence generated during testing. So you have to remember that when we are looking at a patient's genomic information, we are trying to look for a change that causes a particular disorder or the syndrome that the patient presents with. Now, if we talk about general human variation, the earlier estimates were that 99.9% of the human DNA content is similar between two individuals. So to say that the difference between two individuals is just point 1% of the genetic information, or the genetic content. What we know now is that that's not true. We know that at least 2% variation is there between two individuals. So that's just a natural variation. That's what makes us unique. And when we are looking at clinical genetics, we are not looking for that natural variation. We are looking for that variation that causes a syndrome, that is causal, for the phenotype that the patient presents with. So for that to happen, we need to know what the normal sequence is or what the reference is. So we have built a reference genome sequence which is a common representation, which is not complete in any regards. Dr. Carrasco just alluded to that, in a more recent study there was African American population where 10% of the genome was new. That was not a part of the reference. This is just because we are not sequencing enough individuals of different ethnicities. So the reference genome is not complete in any regards, but, but it does serve our needs to a certain extent. So that's what the reference human genome is, that we use it to see through the different variations and look for variations that might be causal.
To give you the context, the first human genome was sequenced back in 2003 it was a huge effort on part of several institutions. It took 13 years to complete. The cost was enormous just to sequence one human genome. It was around $3 billion. Now we can sequence the entire genome of a person in few $100 so that's the progress that we have made through these years, and that's the progress that has happened in genetics and clinical genetics. Now, if I were to say that we sequenced the entire human genome in 2003 that would be a false statement, because we only sequence around 90 to 92% of the human genome. That's because of the technical limitations. There were difficult to map regions, difficult to sequence regions in the human genome, and we could not reach 100%. More recently, we used a consortium,called Telomere-to-Telomere consortium, that made the human genome sequence more complete. Again, we did not reach 100% of the genomic content. That is because in that consortium, the Y chromosome was not sequenced. But more recently, the Y chromosome has also been sequenced to a certain extent. So we are very close to a complete genome sequence. But again, it would be inaccurate to say that we have sequenced the complete genome just because of the diversity that we have in the world that and we would need to sequence individuals from different ethnicities so as to make a more comprehensive reference genome against which we can look for causal variants.
00:35:36
Host You talked a little bit about optical genome mapping, and this is such an exciting topic and an exciting development in the world of laboratory genetics. Can you tell us more about this test?
00:35:46
Dr. Nikhil Sahajpal: Yeah, so optical genome mapping is a next generation technology we refer to as a next generation cytogenomic technology, and you can compare this to next generation sequencing. So a decade ago, we were doing Sanger sequencing, pyrosequencing, very low throughput sequencing technologies were used, and then we had this next generation sequencing technology, or massively parallel sequencing, which is very high throughput, and we could sequence, to this day, the entire human genome. So the cytogenetic field was lagging, if I can say that, it was lagging with respect to A high-throughput method which would have a higher resolution than what we are using right now. In the cytogenetics lab, we commonly use three different methods, karyotyping, FISH and chromosomal microarray to identify different classes of structural variations. But even with the use of three different methods, our resolution is limited. So what optical genome mapping provides us is, it gives us an opportunity to identify the different classes of structural variations which would be identified with these three different methods. So it ideally replaces the three different methods that are used in a lab, and it also provides a higher resolution to identify these SVs that are picked up by these different technologies. We were just referring to the cost and the time to reach diagnosis, one of the reasons for that is that we have to use multiple tests. It's more of a rule out approach, that we rule out a certain variant type, and then we move out to a different test and rule out another type and so on and so forth. So what this test would provide us is, since it's a single test that can identify different classes of structural variations, we would identify these different classes in a single test. So that reduces our cost, but even more importantly, it reduces the time to reach a diagnosis. So that's one clear advantage that I've seen of using new technology. Apart from combining these different methodologies, there's even a rare set of disorders called repeat expansion and contraction disorders, which are very specific disorders for which there are very specific tests. So one test just looks for a specific repeat in a specific gene. So one test for one disorder. What this technology provides us is, it gives us an opportunity to do a genome-wide survey of all these different repeat, expansion and contraction disorders in a single test. So we can do a genome-wide screen and look for different repeat expansion and contractions with a single test and with a single analysis, which is a huge technological advancement in our field of clinical genetics.
00:38:33
Host: That is fantastic. And that leads me to, as we wrap up, what does the future look like for genetic testing.
00:38:41
Dr. Nikhil Sahajpal: Our hope is that we will be able to increase the diagnostic yield. That is, that we would be able to provide answers to more patients and and more families, upwards of the 40% that we just referred to. Our hope is also that we would limit the time to reach a diagnosis. There's a common terminology, which we refer to as diagnostic odyssey. So, Dr. Carrasco referred earlier that the time to reach a diagnosis is, on an average, five years, which, I think, is a huge time if you think, if you're affected by a condition and you just do not have an answer. It's criminal in that regard, that you cannot reach to an answer, and then the steps that would lead from there on. So I think increasing the diagnostic yield and ending diagnostic or disease is what we strive for, and I hope that we would accomplish these two feeds in the next decade.
00:39:37
Diana Carrasco, M.D.
So we were talking about how long it took to sequence the first human genome, which was more than a decade, and how much it cost, which was close to $3 billion and how now it costs $300 to sequence the human genome. And Dr. Sahajpal, how long does it take to sequence the human genome now?
Dr. Nikhil Sahajpal 39:57
On the lab part, it takes around two to three days, at max, to sequence a human genome.
00:40:02
Diana Carrasco, M.D.: So my hope is that that trend continues, that our testing technology has faster and faster turnaround times. That the cost continues to decrease significantly, and also that as a field, we're able to do more when it comes to health policy, so that maybe when a first tier test is recommended by the ACMG that it doesn't take 11 years for health insurances to extend coverage for it. Those are my hopes.
00:40:32
Host: This has been a really fascinating topic, and I really thank you both for being here.
00:40:37
Diana Carrasco, M.D.: Thank you so much, Jan. It was great to be here, and I want to say a big thank you to Dr. Sahajpal for giving us his very valuable time.
00:40:46
Dr. Nikhil Sahajpal: Thank you so much for having me. And it was very nice talking to you both and discussing these very key points that are very critical to a lot of people out there. Thank you.
00:40:56
Host: You’ll find more information about research and genetics on our website at cookchildrens dot org. You can also access clinical pathways on the health professionals section of the website. And while you're there, sign up for our DocTalk newsletter. Want more Doc Talk? Get our latest episodes delivered directly to your inbox when you subscribe to our Cook Children's Doc Talk podcast from your favorite podcast provider. And thank you for listening.
00:42:22
[music out]
Back to Doc Talk