Good morning or good afternoon. Welcome to the ACMG Genomics Case Conference. This series has been planned by the ACMG Education Committee. Each month, the conference will rotate among laboratories that perform genome-scare testing, and the clinicians involved in the cases. This activity is intended for educational purposes only. There are three presenters in the room. I am Christy Thomas. I'm a nephrologist and a professor of internal medicine. With me are Professor Richard Smith, also a professor of internal medicine and the director of the Iowa Institute of Human Genetics, as well as Maggie Fries, a certified genetic counselor and works with me in the Renal Genetics Clinic. Our disclosures are shown on the screen. Here is the disclosures for the planning committee. This session is approved for one CME credit. Please complete the evaluation at the end of this session. The overall learning objectives of this Genomics Case Conference is well known to you. And here are the learning objectives for this particular session, which is to describe the clinical utility of targeted sequencing as it applies to renal disease, to identify clinical indications for which targeted testing would be applicable, explain the likelihood of a positive genetic diagnosis, discuss the limitations of this type of testing, and elaborate on the importance of pre-test and post-test counseling and consent. At the end of our presentation, you will need to type your question into the chat box or question and answer area of your screen, and we will attempt to get through all of the questions that we get. So to get us started, we're going to start with our case conference. We will be discussing eight case histories that are briefly outlined here, but we'll get to that at the back end of our presentation. So to start with, to frame our problem, we have to ask ourselves, why do we need to make a diagnosis? Well, it's necessary to recognize the problem, predict the cause, prognosticate and determine management. And we do this by identifying a disease pattern, selecting the appropriate diagnostic tests, assembling a differential diagnosis, and from there, moving to establish a diagnosis. So, this is also true in kidney disease, and the typical pattern of renal disease are those that are associated with a progressive decline in their estimated GFR, and it comes into one of four different broad phenotypic categories. Those that have cystic kidney disease, as an example, autosomal dominant polycystic kidney disease. Those that have renal developmental defects, such as hypoplasia, dysplasia, or renal agenesis. Those that have glomerular diseases, classically with proteinuria, hematuria, and red cell casts. Examples would be Alport syndrome and Giggs and disease Fabry. Tubular interstitial disease, classically presenting with blind urine, and a common genetic example would be medullary cystic kidney disease, given in quotes because today's name is autosomal dominant tubular interstitial kidney disease. Another broad category of kidney diseases are those that are associated with a normal GFR, and those are the disorders of tubular transport, such as Ditterman's syndrome and renal tuberous acidosis. Those that are associated with secondary hypertension, which often involve a disorder of tubular transport, but present as hypertension, and those that present with kidney stone disease, also an example of derangement with tubular transport. How do we make a renal diagnosis? Well, as with any other organ system diagnoses, we start with a history and a physical exam. We do kidney function testing, which can involve measurement of a creatinine, which tells us about global decline in kidney function, but we can also individually test for various nephron segments, such as the proximal tubule, the Henry's loop, distal tubule, and the collecting duct. We can do imaging studies looking for particular abnormalities that can give clues. We can do a kidney biopsy, and of course, we can do genetic testing, the focus of this talk. And at the bottom of the screen are three examples. The first on your left is a urine microscopy showing the classic hexagonal crystals of a genetic disease called cystineuria, where a urinalysis may be sufficient to make a diagnosis. In the middle is a CT scan of the abdomen in a patient with polycystic kidney disease, where you can see the right kidney completely replaced by cysts, the left kidney is barely visible, but also completely replaced by cysts, and the liver has a few cysts. That's a classic appearance of autosomal dominant polycystic kidney disease. And in the right setting, no further testing is necessary. And the last panel is a renal biopsy showing you the lysosomal granules of the X-linked disease, Fabry disease, in the polar sites of the glabellumus. Again, sufficient to make a diagnosis. So why do we make a genetic kidney diagnosis? Well, it doesn't really matter how we get to a diagnosis. A diagnosis is a definitive diagnosis. It may be more specific, clearly it's cost-effective, it's a simpler diagnostic test, it's non-invasive, it's safe, and in advanced CKD or ESRD, a biopsy is often unhelpful. Unless there are imaging findings, there is no other way to sometimes make a formal diagnosis. And in tubular transport disorders, biopsies have no role, and genetic diagnosis is the only way to confirm a diagnosis. We can offer prognostic information about expected outcome or progression, and that graph that you see in front of you are three survival curves derived from the PRO-PKD score, a score that includes the particular variant that causes polycystic kidney disease, and it can predict the age of end-stage renal disease and polycystic kidney disease. And you can see from these graphs that those with the lowest risk score tend to have an immediate age of onset of ESRD in their 70s, while those with the highest risk present in their 50s. They also predict the risk of post-transplant recurrence of disease, atypical pneumonic hemorrhagic uremic syndrome, there's a high likelihood of recurrence with complement factor H and complement factor I, primary hyperoximutase is an autosomal recessive disease that causes kidney failure, and there is a high rate of recurrence of disease with a kidney transplant alone. And the optimal therapies are combined with C-Stoner liver and kidney transplant. We can offer therapeutic information, for example, FabRASE. Depending on the nature of the genetic variant, you can choose to treat the patient with enzyme replacement therapy or chaperone therapy, which helps to take a trafficking defect from the ER or the oncology complex to the lysosome where it's required for its function. Eculizumab is now available for use in atypical pneumonic uremic syndrome, and one can avoid steroids or toxic immunosuppressive therapy in most generic forms of STDs. You can use this to recognize or anticipate external features or major complications, such as Wilms' tumor and nephroblastoma and gonadoblastoma in X-Y penex, where we may even need to do a prophylactical adhectin. And also of particular importance, this can be used for early screening and management of atrial saccades. There are some challenges. We may not be able to distinguish a phenotype. The phenotype may be incomplete or overlapping or phenocopy. Clinicians may not be aware of what test to order. The choice of tests may also be confusing. You could do a limited panel for a disease like polycystic herpes. Or you may need to look at 40-plus genes in a condition like FSTS. There's the issue of expense of the test. There's the issue of interpretation. There's a risk of testing. And then there's a need for genetic counseling, both before and after, and most adult internal medicine practices don't often have any genetic counseling. There are two broad varieties of genetic variants. And perhaps for this audience, I don't need to spend very much time here. The first are the single nucleotide variants and small insertion deletions that cause missense variants, nonsense variants, splice site variants, as well as frameshift variants. And then there are the small insertion deletions that can also cause frameshift variants. And the other broad category of genetic change are those that arise from copy numbers, variants where you have deletions or duplications or insertions of large tract of DNA. This is now being recognized as a common cause of genetic disease, including vaccine and nephrology. And with that, I'm going to turn you over to my colleague, Professor Smith, who will walk you through the methodology that we use. Thank you, Kristi. So approximately six years ago, seven years ago, we focused our efforts on developing a genetic test that could complement the evaluation of a kidney patient. And over the course of several years, we validated that test, and we now use it quite frequently. One of the options was to consider, for example, whole genome sequencing. And while that provides precision, it also illustrates the Achilles heel of genetic testing in that each of us carry about three and a half million single nucleotide variants, about 350,000 indels, and about 1,000 large deletions. And this is not even the small deletions, which can also be disease-causing. On this graph, you see the illustration of whole genome sequencing relative to whole exome sequencing. And what we instead focused on is a targeted capture panel, specifically looking at genes implicated in hereditary renal disease. The generation of sequence is done by obtaining genomic DNA from the person to be tested. That genomic DNA is sheared. It undergoes a simple round of PCR amplification, and then it is hybridized with complementary RNA baits, which are biotinylated. We can then capture those baits, which also capture the exons of interest using stripped avidin beads, and in the second round of amplification, we can generate our sequenced data. Broadly speaking, the process involves both the targeted genomic enrichment with massively parallel sequencing, and then the data analysis. The data analysis involves variant filtering, variant prioritization, and variant confirmation. In general, for each patient, we identify about 15 variants that we need to interpret. One of the most important parts of the bioinformatics pipeline is that we are sensitive to and look for copy number variants. Copy number variants are identified in about 20 percent of all positive diagnoses, and this type of analysis must be included in any type of comprehensive genetic testing. After generating the variant list, which again includes about 15 variants per person, in a group meeting, which includes geneticists, nephrologists, genetic counselors, biopoliticians, we go through each of these variants and assign to it a classification, either benign, likely benign, uncertain, likely pathogenic, or pathogenic, using ACMG criteria, which include about 28 evidence codes and 20 rules for combining those codes. We also aggregate that data in the renal disease variation database, which we maintain. And over the course of the past two to three years, in an analysis of over 400 consecutive patients, we've had a positive genetic diagnosis made in approximately 40 percent. In the younger age group, below the age of 15, our diagnostic rate is about 56 percent, and above the age of 15, it's about 22 percent. Importantly, most of these persons in whom a genetic diagnosis is made have a negative family history. This may reflect lack of awareness of the family that there is a kidney disease ongoing or lack of penetrance, but it shows that while the family history is important, the absence of a family history of renal disease should not preclude considering genetic testing. This shows the diagnostic rate by category, with the highest diagnostic rate in the category of bacilliopathies at 49 percent. You can also see the various types of pathologic variants. We identify missense variants, nonsense variants, canonical splice variants, large CMDs, and small endelts. Importantly, also, we diagnose persons who are heterozygous carriers for important renal conditions, and the most important of which are variants in ApoL1, the G1 or G2 risk alleles, which increase a risk for FSGS in the African American population. So, with that as an introduction to the test development and the test parameters, I'm going to turn this back over to Christy, who will go over some specific examples. All right. So, I am going to now go through each of those eight cases that were briefly outlined at the start of this case conference, and these are really meant to illustrate the power of a broad-based, unbiased, comprehensive genetic test approach. So, this is, if you will, a 12-year-old male who was found to have proteinuria on a sports physical. A nephrologist confirmed sub-nephrotic range proteinuria at half a gram a day. The family history is positive on the maternal side of the family. Kidney problems not previously defined, and the 12-year-old undergoes a biopsy, and he is shown to have focal and segmental glomerulosclerosis, a nonspecific but descriptive term used to describe a form of genetic glomerular disease. Also noted on electron microscopy were thin basal membranes. Of note, there is no family history of sensorineural defects. So, continuing with this case, then we have this patient who has FSGS and thin basal membranes by kidney biopsy. One of the standard approaches to FSGS is to try and determine what its cause is. Given that there was a positive family history, obviously, a genetic diagnosis came to mind. Given the thin basal membrane, a genetic diagnosis came to mind. He had broad-based genetic testing done, and a missense variant was identified in the alpha 5 chain of colitin 4, or COL4A5. This has not been previously reported. It has a high pathogenesis score, and in this particular family, it segregated with disease. So, the final diagnosis here is X-linked FSGS from COL4A5 variant. You could call this Alport syndrome, but as you may recall, Alport syndrome requires extra renal disease, and he did not have the presence of sensorineural hearing loss, and as far as we know, he did not yet manifest any changes in his limbs. So, this is an example, then, of an incomplete phenotype, but it turns out that the most common cause of adult-onset FSGS is the so-called entity of nonsyndromic Alport, and we will have to find a more appropriate term than nonsyndromic Alport syndrome for these patients. The second case is a 3-year-old male with bilateral multisystemic dysplastic kidneys. The family history is positive for a 6-year-old sister who also has the same phenotype, and neither parent is known to have renal cysts. The clinical diagnosis here, then, is a congenital anomaly of kidney and urinary tract. This is one of the more profound disorders of renal development, broadly called CACUT for short. The pedigree chart is shown here with the dark circle and the dark square indicating affected siblings, and the hatched parents have an unknown phenotype. On the right is an example of an ultrasound showing you what multisystemic dysplastic kidney looks like. It's a small misshapen kidney with cysts of various sizes, usually seen in very early childhood, because these kidneys tend to regress with time, tumult and may be absent by the time they become adults. So, the indication for genetic testing here is a family history of cystic kidney disease with bilateral multisystemic dysplasia, and again, broad-based genetic testing revealed two variants. One was in PKD1, the most common cause of autosomal-dominant polycystic kidney disease. It's a frameshift variant that is pathogenic. The second was a variant in PKD2 that accounts for about 15% of autosomal-dominant polycystic kidney disease. This was a missense variant, but it occurred at the first methionine, or the start of the open reading frame. Since it disrupts the start of the open reading frame, it is likely pathogenic. And as you recall, polycystic kidney disease is an autosomal-dominant disease where a single pathogenic variant is sufficient to cause disease. So, this brings up the issue whether these are both the cause of disease, and the only way to determine this is to phenotype the SIDS further and to screen and genotype the variants. And again, you will note that the presentation here wasn't the classic polycystic kidney disease, but rather as a multisystemic dysplastic-type appearance. That raises the issue whether the disease is more secure because of diagenic variants, the so-called trans-hepatocytes variants occurring in one copy of each of PKD1 and PKD2. And this is very plausible because of the current understanding of the pathogenesis of cyst formation and polycystic kidney disease. It has a two-hit model, if you will, where one inherits a germline variant in PKD1 or two, and then has a second hit, a somatic hit, in each of the cells in the corresponding allele for PKD1 or PKD2, each of the cells that go on to develop cysts. And that's because this is an unstable TCH gene that is prone to errors. And one can therefore imagine that if you had a germline mutation in each of PKD1 and PKD2, you could get to the same place, but at an earlier stage in life. And PKD typically has age-dependent penetrants. In this case, we have somebody presenting with severe disease, stage three. How common is this? Well, polycystic kidney disease is one of the most common serious genetic dominant diseases we have. It's seen in 1,000 live births. And therefore, you would expect bilinear ADPKD in about 1 in 1,000,000,000 covenants. This is then an example of an exaggerated phenotype where a single-gene-focused sequencing may not have revealed the condition. Third case is a 28-year-old male presenting with extramural disease. His ultrasound shows a large kidney with innumerable cysts. He has no family history of kidney disease. He needs a kidney transplant. His parents are ineligible to be kidney donors. And his 26-year-old sister, who has a negative renal ultrasound, wants to be the donor. So here's the background. Here's the pedigree chart. You can see the only involved person is that 28-year-old who has advanced kidney disease and wants to get a kidney transplant. His parents first step forward to be donors, but the dad has kidney stone disease, and he gets a CT scan, and there are no cysts on his CT. His mom, who's also in her 50s, has no cysts on her kidneys by ultrasound, but she's ruled out for another medical reason. And that only leaves him with his biological sister, who wants to be a donor. Now, she gets an ultrasound, which is a valid screening test to exclude polycystic kidney disease, and this shows no cysts. The only problem is that in the case of kidney donation, you need a test that has a 100% negative predictive value, and prior to the age of 30, the negative predictive value of an ultrasound with no cysts is only 90%. So the options, then, are to have a weight to which he turns 30, preferably to which he turns 40, and the negative predictive value rises from 90 to 98.6, or better yet, to consider broad-based genetic testing. And that's, in fact, what we did, and we found a missense variant in PKD1, which is a previously reported pathogenic variant, and therefore the genetic diagnosis is simple, PDPKD from a variant in PKD1. And it's well known that 10 percent of the time, polycystic kidney disease arises denormalized. So here, then, we have a 26-year-old donor who wants to donate. We've identified the genetic basis of the recipient disease, and we can go on to test the donor to see if she is at risk for polycystic kidney disease. She tested negative, and she proceeded to be a donor for her brother. So this is an example of evaluating pre-symptomatic kidney donors where the transplant center, as well as the at-risk individual, have a vested interest in determining the health of that candidate. Case number four is a 26-year-old presenting with nephrotic syndrome, and nephrotic syndrome, for those of you who don't know, consists of proteinuria greater than three grams, low serum albumin, and hematoma. Serum creatinine was elevated at 1.2. The serum albumin is low at 2.3, and the urine-protein cation ratio is very high. Seen in the middle panel is a grow-up of an electron microscopy view of the podocyte and the glomerular basal membrane, the glomerulus. And it's meant to show you diffused epithelial food process effacement, a classic finding in the entity called primary FSGS. So FSGS is diagnosed by light microscopy, but when there's diffused food process effacement with nephrotic syndrome, we believe that is primary FSGS rather than from a secondary cause. And the standard approach to treating primary FSGS today is to prescribe high-dose prednisone for 12 weeks, together with diuretics and lysinopril to treat the proteinuria. This is a nurse who then presents to the Renal Genetics Clinic, because she does not wish to take high-dose steroids, and she requests genetic testing, because she has read that genetic testing might help guide therapy. And so she, too, has a broad-based testing done. We identify a missense variant in a podocyte protein called TRIP-C6, which is likely pathogenic by ACMG criteria. And despite the absence of a family history, we call this a case of autosomal dominant FSGS from TRIP-C6. So in follow-up, then, we treat her with lysinopril and furosemide. We avoid the use of steroids. There is a gradual improvement in her nephrotic syndrome, and one year later, she has gone into spontaneous remission, avoiding the use of steroids or immunosuppression. And in many cases like this, patients will get high-dose steroids. Some of them will remit, but it may be because of the spontaneous remission rather than public therapy. Case 5 is a 29-year-old female who is referred for a second opinion for management of recurrent hemolytic urethric syndrome. And our relevant history is that she presented at age 27 in 2004 with severe thrombotic microangiopathy, microangiopathic hemolysis on a peripheral blood smear, and severe acute kidney injury. Back in the day, she was treated with plasmapheresis. Her kidney function was so poor that she needed immediate dialysis, and she never recovered from this illness and developed end-stage renal disease requiring long-term chronic dialysis. Six months later, she undergoes a living-related transplant from her father, and within two weeks of that transplant, she develops recurrent thrombotic microangiopathy within that renal allograft. And needless to say, within two years, that allograft had failed, and she returned to dialysis. And in the middle panel, then, you see an example in this case from her, from one of her transplant kidney biopsies showing you late-stage thrombotic microangiopathy. The central structure is a glomerulus, and the glomerulus has many glomerular capillaries and glomerulus groups filled with chronic fibrosing, organizing thrombi. So the transplant biopsy then shows recurrent immunodegenerative syndrome, and as her kidney was failing, she came to the University of Iowa for a second opinion. And she clearly wants a second transplant. You can see from her pedigree chart that she is the only affected individual. We do broad-based testing. We identify a missense variant in factor I, which by ACMG criteria is a variant of unknown significance. But based on the classic clinical presentation and the recurrence, we deem this as a case of autosomal dominant HUS of factor I. So back in 2006, we asked her to avoid another kidney transplant until new treatments were available. Five years later, Eclizumab was approved. We called her back to our institution. She was given pre- and perioperative Eclizumab and underwent a living, unrelated kidney transplant. And seven years later, she's doing very well with normal platelets, normal kidney function, and a normal hemoglobin with no further DNA episodes. This is, therefore, an example of team-directed therapy to prevent recurrence of atypical hemolytic urinary syndrome. I'm trying to advance the slides. So I'm now going to hand you over to Maggie Fried, our primary counselor, who's going to walk you through the last three cases and then wrap up the presentation. Thank you, Christy. So continuing on with case number six, this involves a 55-year-old male who came for an evaluation for chronic hyperkalemia. So this was first noted for the patient about eight years ago. And so he had presented at that time with HO fibrillation. He didn't really have any other comorbidities, no history of muscle aches, thyroid disease, no hypertension. But he had been on chronic treatment with sodium, polysaccharides, diurene, sulfate, and borosinide, but continued to have those high potassium levels. And as you can see from the pedigree, he also had a positive family history. So one of his daughters went in, had her potassium levels checked, and she also had high potassium levels. So based on the patient's history of chronic hyperkalemia, the positive family history, and the fact that he wasn't responding well to the treatment, it was suspected that maybe he had Gordon syndrome, which is the male hyperkalemia with hypertension. So genetic testing was ordered and used in this case. And the testing identified a missense variant within KLHL3. And by ECMG criteria, it's a likely pathogenic variant. And so it confirmed a clinical diagnosis of Gordon syndrome. So based off of that diagnosis, the patient's treatment was altered. He was prescribed chlorothalidone. And six months later, he had his lats redrawn, and his potassium was lower than it had been before. So by this case, by determining a genetic diagnosis, it also assisted in targeting therapy for the patient, because the new medication has a different mechanism of action and prevents the absorption of potassium within the kidneys. The case number seven, this involves a 15-year-old female who has delayed puberty. So she was evaluated at 15 years of age. But within her history, she has a known history of prefrontal syndrome, which was diagnosed at age one. And so at that time, she had a renal biopsy, which showed FSDS. And based on her kidney disease progression, she developed renal failure and had a transplant at age six. And she didn't have any family history of kidney disease, and no known cause was diagnosed for the patient. So at age 15, she came in for further evaluations. Due to her delayed puberty, it was actually identified that she had a 46XY karyotype. And so for this patient, additional testing was requested in order to determine if this delayed puberty, the 46XY karyotype, as well as the nephrotic syndrome were all related. And it confirmed that. The patient was identified to have a variant within WT1. It was in intron 9, which is previously reported in Frasier syndrome. So for this particular variant, it alters splicing of exon 9, and it's consistent with the diagnosis of Frasier syndrome. So you may be familiar with the features of Frasier syndrome, but it encompasses FSDS, in XY females, primary amenorrhea, and then also a risk of gonadoblastoma. So specifically for this patient, by identifying the phenotype of Frasier syndrome, you're able to counsel her on her future risk management. And she underwent a bilateral gonadectomy to reduce her risk of gonadoblastoma. So now that we've discussed some of the cases, I wanted to highlight the importance of pre-test counseling within kidney disease and discuss some of these core components of pre-test counseling. And these are shared between different specialties. It's not specific to kidney disease, but there are a couple of unique aspects that I'll mention as we go through. And so first and foremost, within a pre-test counseling session, we do promote informed choices for the patients. So we want them to be involved in their health care management, to be educated, share information with them about the kidney disease of the family, any disease-specific information they may need or need to be educated on. And then we also assess their personal and family history. So for regenerative counselors, we acquire a three-generation pedigree. And this enables us to discuss different familial implications of disease by utilizing that information. And depending on how the condition is being inherited, you can identify who in the family is at risk. For many inherited kidney diseases, patients are at risk of developing end-stage renal disease, which requires dialysis or transplant as treatment. And many patients do elect to have a kidney transplant. Because there is such a long waiting time for a kidney from a deceased donor, living donation is often discussed with these patients. And so that kind of leads into one of the unique aspects of pre-test counseling in kidney disease. You're not only evaluating at-risk relatives within the family, but that can also include potential living kidney donors. So as you can imagine, there are different motivations for patients who are at risk versus who are a potential living kidney donor. So for someone who is at risk, they're concerned about their own health. They want to know more information about what their future health looks like in regards to kidney disease. Will they develop it? Will their children develop it? And then compare that to a potential living kidney donor. They are often in the mindset of trying to help their relative, trying to help the recipient get through this time and allowing them to receive a kidney. So a lot of times, patients aren't able to move past that step and think more broadly into their future about the implications of having that genetic diagnosis. This is a unique aspect within pre-test counseling session. And so it really highlights that you have to make sure that people are aware of the implications of a genetic diagnosis for their future. So again, similar other aspects as well. So addressing other questions and overall discussing the pros and cons and limitations of genetic testing. Again, highlighting the implications of that genetic diagnosis, which, as you can imagine, is different for someone who is affected already versus someone who is undergoing pre-symptomatic testing. So this case, case number eight, is going to highlight some of those different complexities within pre-test and post-test counseling kidney disease. And so this involves a 32-year-old female. She is completely asymptomatic, no known history of kidney disease. But she does have a positive family history of autosomal dominant polycystic kidney disease. And currently, her mother is affected. She has developed end-stage renal disease. And genetic testing has previously been done, and she has a truncating PPV1 variant. So the mother is currently on the wait list for a kidney, and the patient is considering being evaluated as a possible living kidney donor. She's very motivated and wants to learn more about it and move forward in that process. Some of the unique aspects to this case is that the patient has one sibling. It's a brother. And he was recently diagnosed with ADPKD clinically as well as with confirmatory genetic testing. And so a couple of different issues that arose during our session is that the patient is the only child available to donate. She's nervous about discovering whether she has ADPKD. And currently, she's young. She's 32 years old, and she's planning to have more children. She currently has one daughter and is interested in continuing her family planning. And so all of this information could really change things moving forward for her. So we addressed all of these concerns and had a very lengthy discussion with her, and she decided to undergo genetic testing because for her, she felt that the pros for moving forward outweighed the cons in her situation. So before we get into how this case resolved, I wanted to also highlight some post-test counseling kidney disease components. So first and foremost, if genetic testing is pursued, we then communicate those testing results with the patient. So educating them on what the genetic change is, how it relates to their disease, and then again, how that impacts their health, their future medical management, if there are any recommendations that we need to change. And then also educating them on identifying at-risk family members who may benefit from genetic testing or being educated on the condition within the family. And then also discussing family planning options, making sure that there are options available. Many patients aren't aware of those testing options pre-conception, prenatally, or even doing things during childhood. And then also providing them with any additional follow-up or resources, which could range from just providing them with handouts on the condition itself all the way to providing them with a consult to a therapist or psychologist in order to talk more about different psychosocial issues. So if they're not coping very well with their diagnosis, that may be something of benefit to them. So following up with our case, as I said, the patient underwent genetic testing for that familial variant, and she ended up being negative. So when we met, we talked about those results and discussed all the implications. So I have them listed below, but since the patient tested negative, she's then not at risk to develop ADPKD based on that result, and she could not pass it on to her children, her current child or any future children. And then based on that negative result, she could then pursue living kidney donation and continue in that process. So as we talked through all these different things, one thing did come up. The patient experienced some survivorship guilt. So she felt that she didn't understand why she didn't inherit that PKD1 variant versus her brother. And so by allowing us to have this post-test counseling session and talk through those thoughts and emotions that she was having, it was a way for her to relieve those thoughts and not have to discuss them with a family member or a relative who may also have their own thoughts and personal perceptions. So having a third party discuss this with her was very beneficial. So overall, there are challenges with ordering genetic testing. So a lot of times patients and even providers will think about the expense of the test and who is going to pay for that testing. Will insurance cover the test or not? And with genetic testing, it's getting cheaper, but for some patients, it's just not a feasible option. So that is a challenge. Another thing is different risks associated with genetic testing. So as I mentioned before briefly about psychological risks, patients aren't always able to cope with understanding that something is underlying their disease, that it could be passed on to their children or grandchildren, as well as insurance risk. So we do have protections in place currently, but one loophole is life insurance. And so for a lot of younger individuals, thinking about obtaining a life insurance policy is something of concern or something they don't want to carry on in their situations. And then again with genetic counseling. So it's recommended that patients receive pre- and post-test counseling when they undergo genetic testing, but genetic counselors aren't always available in order to counsel patients in every institution. So like Dr. Thomas alluded to earlier, genetic counselors in internal medicine in the adult world isn't always prevalent, but it's becoming more and more common as there is a need. So as we've identified more of these disease-causing changes underlying kidney disease, there will likely be more genetic counselors working within those realms. And then we also wanted to highlight the limitations of the testing technology that we utilize for the testing. And obviously there are always going to be new genes identified that are associated with kidney disease. And so there's always a need to reevaluate and update our panels. There's, in addition, our limited ability for us to identify new causes of kidney disease. So again, there may be times when we just aren't able to identify the genetic cause within a particular patient. And then when you're looking at patients and you have someone that you're considering genetic testing, who may benefit the most from it, a couple of examples that we have is that any patient with a suspected or likely genetic kidney disease, spanning various sections or classifications of kidney disease, because a genetic diagnosis from that individual could provide and confirm a diagnosis, give information for their prognosis or future health, and then also disease management, and may change the management decisions specified by all those cases that we already provided. So for the Gordons and her patient, it changed their manner. And then secondly, any patient who has a genetic form of kidney disease and then has an at-risk family member who's interested in family planning, living kidney donation, or being enrolled in an early disease trial, having that initial patient affected undergo genetic testing to confirm that testing or that genetic diagnosis, and then allow that at-risk family member to be screened. So in conclusion for our talk, I hope that you learned that kidney disease expands individuals of all ages, and classically, the phenotypes for kidney disease may not always be that distinct. And so there are different phenotypes that have been discovered. And genetic testing can be very valuable, and within kidney disease, it's often underutilized, because there are other ways to make a diagnosis, but there is a very important aspect to utilizing genetic testing, as I hope you can see through our different examples. And then again, in many instances, utilizing a large panel of disease genes can be efficient, accurate, and cost-effective in the long run. We have our references listed here that will be available to you. And then we encourage you to type in your questions into the chat box or the Q&A area of your screen, and then hopefully we'll be able to answer your questions as time allows. Hello, this is Jane. I hope you can hear me. On case number two, did the parents get tested via genes and ultrasound? Do they each carry a mutation or have cysts themselves? We don't have the answer to that. The case came from the outside. We strongly encourage them to phenotype the parents. They had limited resources and limited access to their own best insurance, and so we don't really have any follow-up. We don't know if the parents were tested, but I suspect that they were not able to be tested for the reasons I mentioned. Okay, right, and that was the follow-up was do tests get insurance pre-authorization approval? That's correct. I think the children were covered by some mechanism, but the parents couldn't be. The next question is the estimated yield of exome sequencing for patients who did not receive definitive diagnosis using a gene panel? So that's a great question, and I don't know the answer to that because it really depends on how you filter the data on the patient and the robustness of the phenotype and the family history, etc. So that's a complicated question to answer, but I would suspect that it's certainly far under the 40 percent yield that we get with the panel. But that also brings up a good point because the families who we, the persons who we test, who test negative actually can be offered an opportunity to participate in research, and then depending on the pedigree and the phenotype, some of those families, either as as trios or more extensive persons can be studied using exome sequencing. But again, the yield is really low. If I may just follow up on exome sequencing. So exome sequencing is an excellent way to do unbiased testing, obviously, of the entire exome. The problem in kidney disease is twofold. One, it's not optimized to look at copy number variants, but more importantly, the most abundant genetic kidney disease we have is polycystic kidney disease, more often from variants in PKD1, and the proximal portion of PKD1 is highly duplicated and tends to be difficult to sequence by next-generation sequencing alone. And so a significant number of the most common, the commonest form of genetic disease could be missed by polyexome sequencing. It does become new genetic causes, and it does not require the need to update the weights used to pull down sequences. So I'll follow up just a little more on that. So the panel that we use, although we illustrated it as next-generation sequencing and targeted sequence capture, also has a component of Sanger sequencing that's done in parallel because of regions that are refractory to massively parallel sequencing because of duplication. Right. And the follow-up question was uncovering PKD1 by supplemental sequencing. Right. Well, thank you all very much. If you would, please advance to the next slide. I'd like to invite everybody to submit an abstract for the ACMG 2020 Annual Meeting. You can do that at acmgmeeting.net. I would like to thank today's panelists, and I appreciate everybody attending. When the webinar closes, you will have a link to do your evaluation and get educational credits. We also like to recognize the UDN. Their next case conference is November the 14th, and you can go to udnconnect.org slash Grand Rounds to find out more. Thank you very much. It's been a pleasure doing this. Thank you.

ACMG Genomics Case Conference

genomic testing

renal disease

targeted sequencing

genetic diagnosis

genetic counseling

kidney diseases

personalized treatments