Welcome to the ACMG Genomics Case Conference. The series has been planned by the ACMG Educational Committee. Each month, the conference will rotate among laboratories that perform genome-scale testing and the clinicians involved in the cases. Use of all case materials that will be presented have been formally consented for with patient or guardians. So I'm Dr. Ingrid Holm, and with me is Dr. Ozge Bershoi, who's representing this together. So this activity is supported by an educational fund. This is the disclaimer. This is intended for only for educational purposes only. So I'm Dr. Holm, and Dr. Bershoi is with me from Memorial Sloan-Kettering. We have no disclosures. The planning committee has no disclosures. This session is approved for one CME. Those who paid for CME will receive an email with questions and a certificate. So these are the overall learning objectives of the Genomics Case Conference. And these are the session learning objectives. So to ask a panel a question, you type your questions into the Q&A box in the lower left corner of your control panel, and they'll be answered verbally by us, the panelists, at the end of the presentation. So to start off, this talk is about a project that we're involved with. It's called the Genomic Sequencing for Childhood Risk and Newborn Illness, which we fondly call the Baby Seat Project. And the Baby Seat Project is one of four sites that are part of what's called the N-Site Consortium. This is a group of four grants that are studying the integration of newborn sequencing into newborn screening. And so we are one of the four sites. The others are the University of North Carolina, and then the site that started off at Children's Mercy and is now at Rady's Children's in San Diego, and UCSF. And the goals of our project, and again, just to reiterate the projects are all different, but our goals of our project are to determine if parents who receive genomic results struggle with this information in a way that could produce anxiety or distress. So really looking at the, you know, potential harms and benefits, and to critically evaluate the positioning of genome sequencing as a resource that can positively impact the care of healthy and sick children early on in life. So the Baby Seat Project is a randomized trial, and so we're randomizing children either from one of the NICUs, Neonatal Intensive Care Units, or any of the other intensive care units that have infants. So it's been mostly the Cardiac Infant Care Unit at Children's. So both at Children's Hospital and Brigham and Women's Hospital, and then a separate cohort of healthy children born at the Brigham and Women's Hospital. And so within each cohort, patients are randomized either to receive the standard of care, newborn sequencing, and family history, which they both receive. And then in the genome sequencing cohort, they also undergo genome sequencing, get a genome report, and if there's a particular indication for more in-depth analysis, they get indication-based results. They're enrolled in the beginning, they do surveys, and then the study physicians and genetic counselors meet with them after the results and the reports are done, and disclose the results. And so we meet both with the control group and the sequencing group. We also discuss the results in the family history and the standard newborn screening, and then the results go into the medical record, and we review the medical records over a period of about a year. And we do patient and-or physician and patient, or really family surveys, and look at outcomes over that period. So we have two reporting strategies in the BabySeq. All babies in the sequencing arm of the project, both babies in the VAL newborn nursery and in the NICU cohort, receive a screening report, which is our newborn genomic sequencing report, which returns risk for childhood onset disease, carrier status for childhood onset disease, and pharmacogenomic variants relevant to pediatrics. In addition to that, babies in the NICU and babies in the VAL newborn nursery who later develop an indication that may prompt a genomic-targeted analysis, receive an indication-based analysis where we look more closely at genes associated with the infant's clinical features, and we also have the option to query pharmacogenomic variants related to the infant's care. We have very specific criteria for including a gene in a BabySeq report. In our screening reports, we are very conservative, so we only include genes that have strong evidence to be associated with a highly penetrant childhood onset disorder. Whereas in our indication-based analysis, we can also include genes that may have moderate evidence to be associated with the infant's clinical features or may have moderate penetrance or may typically be associated with a later onset as long as the gene is associated with the reported features. And if we are suspecting a specific disorder, we may actually return genes that may have limited evidence to be associated with that specific disease or may have lower penetrance. This is just to give you an idea of the number of conditions that we are testing in BabySeq. So in the recommended universal newborn screening panel, 34 conditions are tested, and ACMG recommends return of incidental findings in 59 genes associated with 27 conditions from genomic sequencing. Whereas in BabySeq, we are testing and may return results in more than 1,000 genes that have been associated with pediatric conditions that meet our criteria. We also have specific criteria for including a variant in a BabySeq report. So in our screening report, we only return variants that we classify as pathogenic or likely pathogenic because we want to only include variants that we are confident to be disease-causing. Whereas in our indication-based analysis, similar to any other diagnostic test, we also return variants of uncertain significance in genes that are associated with the infant's clinical features so that we can allow follow-up studies such as segregation studies or clinical follow-up that may help clarify their significance. So I just want to give an overview of our exome filtering and analysis approach for our screening report. We start with about 40,000 variants, and we first filter variants that are in HGMD or in ClinVar with an allele frequency of less than 5% and novel loss of function variants in disease genes, which we call as the medical exome, with a minor allele frequency of less than 1%. This leaves us with 200 to 300 variants, which we then take through a few exclusion steps. So first, we exclude variants that we have seen in more than 10% of our genome sequencing cases, which excludes common technical false positives, but we keep common disease variants such as Factor V Leiden or HFE variants. Then we exclude variants in genes that we have previously curated and found no evidence to be associated with disease, and genes that have only been associated with non-medically relevant phenotypes. We then exclude variants that we previously classified as benign or only had GWAS associations, which we would not report in the BabySeq. This leaves us with 10 to 25 variants, which we then manually curate. We first look at the genes level of evidence for disease association, age of onset, penetrance, and inheritance pattern to make sure that the gene meets our reporting criteria, and if it does, we then further classify the clinical significance of the variants. On the other hand, for our indication-based analysis, we take a phenotype-driven filtering approach. So, again, we start with about 40,000 variants, and we create lists of genes that have been associated with the different phenotypes that are present in the infant, and we create these lists by looking at the literature or databases like HGMD, OMIM, or using tools like Phenomizer, which leaves us with about 300 to 800 variants. We then exclude variants that have a minor allele frequency that is too high to be associated with the disease of interest, and variants that we previously classified as benign. This leaves us with 20 to 40 variants, which we then again first curate the gene and make sure that the gene is indeed associated with the feature that we are interested in, and we further classify the clinical significance of the variants. So, today we are going to tell you about two interesting cases we came across in the BabySeq. So, the first case is a female newborn enrolled in the NICU cohort, and the phenotype that was discovered by the clinical team included an anteriorly displaced in perforated anus. So, we performed our regular screening and indication-based analysis. For our indication-based analysis, we looked at 45 genes that had been associated with anorectal malformations, which was negative. So, we did not find any variants that could explain this feature. On the other hand, in our expanded screening analysis, we found a truncating variant in the ANKRD11 gene, which was a four base pair deletion that leads to a frame shift and a truncation in the protein. So, this variant came from our novel loss of function variant in a disease gene filter. So, loss of function variants in ANKRD11 gene have been associated with autosomal dominance, KBG syndrome, and this particular variant is absent from population databases. It has not been reported in the literature. It was predicted to lead to truncated and absent protein, and several other loss of function variants have been reported downstream of the variant and in the same exome. So, based on these information, we classified the variant as likely pathogenic for KBG syndrome in an autosomal dominant manner. So, in the baby, we do not do trio sequencing. We only sequence the newborn, but for any monogenic disease risk variants that we identify in the infant, we also test parental samples to clarify the significance of the variant and also the risk of disease. So, when we tested this variant in the parents, we found that it occurred de novo in our patients. So, then the question was whether this variant could explain the anorectal malformation that was reported in our patients, and because anorectal malformations were not reported within the phenotypic spectrum of KBG syndrome at the time of our analysis, and there was a question regarding the penetrance of this gene and whether there was variable aggressivity, we decided to first report the variant under the monogenic disease risk. So, we reported the monogenic disease risk section of our report, not under our indication-based results, so that we could allow further clinical studies that could help identify if there are any additional features in the infant. Okay. So, this just kind of a phenotype in the case, and so, at the time when the baby was kind of first seen in the genetics clinic, the baby was fairly young, I think a few months old, and had this imperfect anus with erectile vaginal fistula, had mild hydrodiphrosis and vesicle ureteral reflex. There was a small ASD. There was a tethered cord. There was mild strabismus, and then she had kind of mild craniofacial dysmorphisms, including a flaccoxiput, and initially, the possibility, mostly kind of related to the tethered cord, was that maybe she had a vactral association. So, that kind of was the initial thought about potentially what her diagnosis might be. So, just to remind you with the KBG, so I have to say, I keep saying KGB, but it's KBG. It's easy to get confused, but it's a KBG syndrome, and the four cardinal features are facial dysmorphisms, and I think you can kind of see some of these pictures here on the bottom right of older individuals who have this syndrome, and one of the hallmarks is kind of a triangular face, and then there's a somewhat flaccoxiput. Another kind of cardinal feature is this macrodontia, the upper central incisors, which you can see on the photo on the upper right, and some of the photos on the bottom, and so that's fairly characteristic, and of course, our patient didn't have teeth yet because the patient was so young. So, that was not something that we could really look at. You can see skeletal, mainly costovertebral anomalies, and then a fairly significant piece of the KBG syndrome is these neurodevelopmental issues, so delays in gross motor and in speech, and then mild to moderate intellectual disability. There's a number of other features that one can see, and which are listed here as a short stature. You can have an abnormal EEG or seizures, abnormal hair implantation, syndactyly, a short neck, hearing loss, palate abnormalities for business, and congenital heart disease. So, that's kind of what the features are of KBG syndrome. So, because these, as you can see on that list, that anorectal malformations were not part of that, we didn't able to look at the child's teeth because she was young, you can see why we weren't really convinced that this was part of, that she fit into that syndrome, and then we, kind of looking, I think, a little bit more deeper into the literature, we came up with a publication that reported an anorectal malformations, specifically an anteriorly displaced anus, in a patient with KBG syndrome, with a similar deletion to ours. So, our patient had the C2409 to 2412 deletion, and the patient reported in this publication was a 2408 to 2412 deletion. So, that finding led us to kind of go back and say that we thought that maybe, indeed, that this variant was actually considered to be diagnostically relevant. And I think the next is yours. So, this brought up some interesting considerations regarding our analysis approach. So, because the NKRD11 gene was not associated with anorectal malformations at the time of our analysis, we did not include the gene in our indication-based analysis list. And we discovered this likely pathogenic variant through our loss-of-function variant filter. And the further phenotypic analysis, in light of this finding, helped diagnose the patient with KBG syndrome. So, the variant was discovered because it was a truncating variant in a disease gene. So, if it was a missense variant, for example, that was not previously reported, we would not have filtered the variant in, and we would not have reported the variant. Therefore, if it was a VUS in this gene, we would have missed the opportunity to let the clinical team know about this variant so that further targeted analysis could be done. So then, it's an interesting consideration for any laboratory who does diagnostic exome and genome analysis, how comprehensive should we be when reporting quote-unquote incidental findings, and how close the phenotype must be to the patient's reported indication when returning VUSs. So then, given a lot of this uncertainty that we've been talking about, made it somewhat difficult to counsel, and I thought we'd just kind of go over some of the considerations, and I think these are typical considerations for other conditions where you're not talking about potentially phenotype expansion or question of penetrance. So, there was no definitive genotype-phenotype correlation in this case, and as we've talked about, there was limited evidence of an association between anal atresia and the child's other features and the KBG syndrome. So, it really was just one report that we found, and we've continued to look for other reports and haven't found them, but it was just this one report where the anteriorly displaced anus was reported, and so that's kind of not a lot to go on. It was also unclear what this finding kind of meant for the child's future neurologic development, and here, again, the gene was identified in 2011, and these variants have not been really followed or defined or followed prospectively, so there's just not that much information in the literature and not much known about what kind of the long-term implications are for patients, and again, the penetrance is not entirely clear. The gene has a high PLI score in EXAC, but there is a presence of three individuals out of greater than 6,000 with truncated mutations kind of leaving open, at least at theoretical possibility, of incomplete penetrance. So, we disclosed these results to the family at four months of age, and I think we kind of talked about this molecular finding and this connection to the neurodevelopmental issues. We talked about the incomplete understanding of penetrance, the lack of a clear genotype-phenotype correlation given that she's young and there's not really good prospective studies. You know, kind of that said, we emphasize the importance and efficacy of screening with developmental pediatricians and early behavioral interventions. There's, of course, no specific targeted treatments for this disorder, but certainly, as in any disorder where there's developmental issues, early behavioral interventions and followings carefully are important. And then we discussed that there are researchers studying KBG syndrome and related disorders, and there are also patient advocate groups that can be in this area, and so these are really the types of things we discussed, and clearly a lot of it is kind of us saying to them that there's a lot that we don't know, and we're kind of providing them the best information that we can. So, in terms of kind of the family response, I think it really kind of took them by surprise. This really were kind of now new implications for future neurodevelopment that they hadn't really considered. They really had been focused on her GI malformations and really had not thought about a broader syndrome with potentially neurologic considerations, and so this was, I think, a surprise and kind of a difficult encounter for them, you know, kind of thinking their child just had these malformations, and now it might be something broader that affected her development. They accepted the recommended follow-up with a clinical geneticist, which they have followed through with, and the child is now 20 months, and the KBG syndrome is still felt to be the unifying diagnosis. The family has also connected now with the KBG syndrome community, and she is receiving early intervention as she's less than three years of age, and so far meeting her developmental milestones. All right, so we'll go on to the next case. So just as a background to the next case, the initial BabySeq protocol was just returning the results for childhood onset conditions, excluding the return of actionable adult onset conditions, and there were several reasons for this. At the time that the protocol was going through the IRB, it was still kind of a lot of emphasis on protecting the autonomy of the child. We also felt that including adult onset conditions that might have immediate benefit for other family members may cloud a family's decision when deciding about whether or not they should participate, and we felt that excluding these actionable adult onset conditions would keep the focus of the participation and potential benefits on the child as opposed to on the parents. At the time when we went through the IRB, they did question our decision to exclude adult onset conditions. I think they kind of recognized that there could be potential benefits to that, but in the end, they did agree with our decision. In addition, this project ended up being scrutinized by the FDA and came under the purview of the FDA, and in the end, they decided that the clinical investigation that we were doing was a non-significant risk device based on three factors, and one of the factors was that we were only gonna report variants associated with pediatric onset conditions and not adult onset conditions. So between kind of the FDA and the IRB, that was kind of finalized that decision. So the case that I'm just gonna talk about is that we had a newborn male that was enrolled in the study. He was in the cardiac intensive care unit due to complex congenital heart disease. In the family history, it was notable in that both the mother and his brother had congenital heart disease. This child was randomized to a sequencing arm and an indication-based analysis, as Ozge has discussed, that was performed for the heart disease and there was no genetic findings discovered to explain the heart disease. So Ozge, yep. So in the NGSR, in the general screening analysis of this case, we found a truncating variant in the BRCA2 gene. It's being reported in multiple individuals with breast and ovarian cancers. It is present in four chromosomes in EXAC and five chromosomes in NOMAD. It was classified as pathogenic by Enigma and multiple laboratories in ClinVar and it is predicted to lead to truncated and absent protein. So based on these reasons, we classified it as pathogenic for hereditary breast and ovarian cancer syndrome in an autosomal dominant manner. So... Oh, hold on a second, that's... There we go. So let me just double check, okay. So there we go. So this was the kind of the ethical dilemma that we had. So we had a BRCA2 heterozygous known pathogenic variant in the child and of course, as I think most of you know, these variants are associated in the BRCA2 with a 45% risk of breast cancer and 11% lifetime risk of ovarian cancer in adult females. There's also an elevated risk of other cancers in both females and males. And this is the hereditary breast and ovarian cancer syndromes are considered adult onset conditions because there are, although there are pre-symptomatic screening preventive measures that really performed in adults and not in children. Yet again, are highly actionable because there is screening and measures that you can undertake. So as mentioned earlier, we do the whole exome sequencing on the probands and then we have findings we can do Sanger confirmation. And we did this in this case and it revealed that this variant was inherited from the mother. So here we had the situation, we had a three generation family history that was negative for cancer. And the child unfortunately passed away during the first few months of life and was deceased by the time we had this finding. So we called to consult with the IRB. And I think the kind of here I've listed the three main questions that the IRB came back with us were first of all, were there additional adult onset highly actionable genes or disorder? How many other outstanding cases are there where this is a possibility? And how are we going to avoid similar circumstances in the future? Which are all very good questions. And they felt very strongly that this family should be given the option to receive this result or this class of results. And that of course, they wanted us to notify the IRB as well as the FDA with the results of disclosure. And they should note that they felt that the family should have the option to receive it, not that we should just give it to them, but we should abide by their preferences. So the study PIs, so myself and one of the other PIs met with their parents and their pediatric cardiologist. And the reason for including the cardiologist was just that they had a longstanding relationship with the cardiologist as one of the other brothers had also had heart disease. And they felt that it was, the IRB actually really wanted us to do that because they felt it would be better for the family to be with someone that knew them well and knew us. So we gave the parents the option of learning about this condition and both the parents agreed to hear about it. And as soon as we told them about this finding, the mother's first words were, oh, so that explains it. And so basically what happened is that it triggered her to recall that there were additional family members of more distant female relatives on her father's side of the family who had a history of breast and ovarian cancer. And we had done a three-generational family history, but we hadn't kind of gone beyond the grandparents. And so we didn't kind of pick up on our history that this more distant history of cancer. So then we recommended follow-up at a local cancer genetics clinic. And the other thing we did as kind of answer some of the questions about the IRB was we changed our protocol to allow the return of highly actionable adult onset conditions. So kind of just thinking about the ethical considerations and as I think most of you probably know, there is a high, often with these highly actionable adult onset condition, there's a high likelihood of disease risk in the family as a lot of these conditions are autosomal dominant. And of course, genetic information about future risk could be relevant for family members. And traditionally, medical genetics practice has been to withhold risk for adult onset-only conditions in children, but this has generally been in the setting where families have a known genetic risk. And so children are then kind of prompted to decide in adulthood if they want to learn about this risk or not. So it's something that's kind of known in the family. And this allows children to predict their future autonomy to decide if they want to learn about it, yet it doesn't kind of fall off of their radar screen because this is something that's known in the family. And when we're doing screening like we're doing with in BabySeq, it's a little bit sort of different situation because if there's something that's not known in the family, if you don't report it, it may prevent families from knowing that they have a risk and enable their children to then act in their own best interest when they reach adulthood. So the screening piece of kind of what we're doing I think is very different than a traditional medical genetics where it's a known condition in the family. And this kind of gets to, you know, there's kind of different models for thinking about these kind of processes. So there's kind of the best interest model and then there's this family interest model. And I think that this kind of case in genetics fits well into this family interest model. So family interest model is, we think of family interest as not being the sum or just the function of individual family members' interest. And that holistic medical management for the entire family really often is in the best interest of the child. And so in this case, the mother's at risk of breast cancer and she doesn't know it and she develops breast cancer and then passes away. That's not in the best interest of the child. So it's really having healthy parents and a healthy family is in the best interest of the child. And this is really kind of what is the basis of the cascade testing because results in one family member may be relevant to other family members. The fact that this infant passed away made it kind of more clear that the ethical decision really was in the best interest of the family because the child had passed away. And so that's, these are just some of the references that we've used for this study. And the first one being the one that was the article that had the KBG cases that had anorectal cancer malformations or anterior displaced anus. And this is just to acknowledge the BabySeq team which is a large team of investigators from Brigham Women's Hospital, Boston Children's Hospital and the Baylor College of Medicine. And that is the end of our presentation and we'll go on to the next, is just the question and answer period. So if you, I think people have already been doing this, type their questions into the Q&A box in the lower left corner of your screen. We can go on to answer any questions. So how should we do with questions? Should we read them and answer them? I'm not quite sure what the best way to do. Someone from the ACMG can tell me how to do it. If you want to read the questions and then let me know. Okay. All right, so the first question here, is the sequencing raw data files available to parents upon request? So the answer is that we have had a few parents who have asked for the sequencing data files and once the study is over and we've done all the surveys and it's kind of finished, it ends when the children are about a year of age, we can go through another kind of consenting process to if they want to have the actual data. So the next question is, we recommend doing TRIO, polyxome sequencing analysis on pediatric newborn cases or just confirming the variance by parental targeted testing? So the reason that we did it the way we did it was because it was less expensive. We couldn't afford to do whole exome sequencing on the TRIOs. So that's why we chose this method. I think that if you're, I mean it's kind of a good question. It depends on what you're doing. If you're doing something like as a screening method, it makes on a particular individual, I think it probably makes sense to focus the whole exome sequencing on that individual. And if you want to confirm something to confirm parents with targeted testing, but I suppose it kind of depends on what the use is. Nadia Ozge, if you have any comments about that question. Yeah, so basically in our cases, we had a lower yield from our NICU cohort. In our NICU cohort in terms of having positive findings compared to some other studies that looked at that sequenced babies in the NICU who were suspected of having a genetic condition. So one reason was that our NICU cohort was not enriched for babies who were suspected of having a genetic condition and the phenotypes we had were not expected to have a high yield. But one other reason I'm guessing is that most of those studies, the TRIO sequencing, including the parents, and we only did the proband. So it is possible, of course, that we could have additional positive findings if we did the TRIO. So TRIO approach is, of course, more likely to give you a better result. There's another question here. Is it possible to include a registry to collect long-term clinical data on VUS patients identified? Do you want to say something about that, Ozge? Yes, 24. Long-term clinical data on VUS patients identified. I mean, that's a good point. I'm sure it would definitely help clarify significance of some of those variants. So I'm not sure if you're asking this specific to BabySeq. So I mean, of course, all of our, you know, we will publish our results and hopefully we're hoping to continue getting more clinical data on our patients. So we hope to publish, you know, if we've reported any variant of uncertain significance in an indication-based analysis, also report additional features that we identified. So another way this could be done is I assume just adding more of our clinical information, internal clinical information that we have into our interpretations that are submitted to ClinVar, which I'm sure would be helpful for everyone. So the next question is for adult-onset cases, can children opt to receive the, well, I can think we, so we are giving these adult-onset back to the families. I think, I'm just gonna mention something about the results at 18. We are set up so if we are able to, if we do get funding to continue to follow these people, we have put in that we would, you know, potentially consent children at 18 if we still kind of follow up with that, but they've kind of now received the results so we aren't keeping any of the results from them. Okay. Can you describe a case where we identified a reportable pathogenic variant in a healthy newborn? Well, we found, I don't have the data right here and we're actually in the process of publishing it, so we did find variants that we returned to both healthy newborns and children in the NICU. I should say the children in the NICU were not ascertained for likelihood of having a genetic condition. That wasn't really the idea. The idea was kind of all comers were able to join and so most of the kids even in the NICU just had prematurity or didn't have any congenital abnormalities, so we did find other pathogenic variants. I think we found one with hearing loss. We found cardiomyopathy, some other things. I don't have the data here, but that is gonna be coming out, I think, hopefully reasonably soon we'll be publishing that. There's a question, is it ethical to withhold the information if the child survived? I mean, we weren't going to withhold the information. We were returning it, so if the child had survived, we would have still returned information. Now we're able to do that for all, you know, subsequently that we're able to do that for all people enrolling in the study. So there's a question, do we envision a whole exome sequencing newborn screening be incorporated and replaced by standard newborn screening? I mean, that, so I'm not sure. I mean, I don't know. I mean, I think that's not really what we're, necessarily we're doing this because we thought it would replace newborn screening. I don't think it will. It's possible that a whole exome sequencing would be, you know, kind of an adjunct in certain cases, but at this point, I certainly don't think that's, I think we feel that it's something that would be recommended at this point. Okay, so don't you think that these two cases give great juxtaposition regarding the utility and ethics of return of results? Regardless of how a BRCA2 mutation is found, it is relevant, whereas the KBG diagnosis, even if it's definitive, barely helps anybody. Why are we still in the search of an ethical model for the return of clinically useful results? I'm not quite sure how to answer that question. I think, you know, the goal of this was to return things that, you know, we felt that had fairly high penetrance and, you know, pathogenic, likely pathogenic in an adult, in a childhood onset condition. That's kind of what we were looking at and studying, and then looking at the benefits and harms of that. So there certainly are, you know, kind of ethical issues that are, you know, kind of still there. So, Asge, there's one here. The slide about, yeah, you wanna? Yeah, in the slide of VEST filtering for NGSR analysis, in the initial filters, what are medical exomes and what are the 5% and 1% filters based on? So the medical exome is basically, you know, a list of genes that we generated that have been associated, you know, genes that have been associated with any disease in various databases, like HGMD, OMIM, ORFANET, et cetera. And the frequency filters were basically based on just, you know, we are only aiming to return highly penetrant variants for Mendelian disease genes, so that's why we chose those allele frequency filters. There's a couple questions kind of related to, you know, going back, kind of revisiting variants that we've seen. I think it's basically going back to see if we, you know, relook at the exome to see if anything new has come up. Do you want to comment on that, Asgei? Kind of the idea of going back to, you know, past exomes and, you know, looking, yeah, go ahead. We do not have a really definitive plan to go back and do the analysis, you know, reanalysis of the genomes, but that's something we are considering. I think, as I was going to say, we have to consider that the grants have ended, or kind of are ending, so I think that's the other piece of it is just, you know, funding to support that, and so I think that's always a problem when you're doing research is that, and we have written for another grant to continue following the participants, but that also makes it a little bit complicated, you know, the funding issues, too, and kind of keeping up with the families. Okay, I know that considering KBG is a conservative approach to managing the baby, but in your discussion with the family, did you elaborate on the concept that this may only be allelic to KBG and might not actually have any additional features of that diagnosis? So I wasn't actually in on the counseling session, but I think we did talk a lot about kind of how little we, you know, but how little we know, and how this baby at the time didn't have all the features, and so I think we tried to convey, you know, the fact that we weren't completely certain, or there was some level of uncertainty, in this finding. All right, so someone asked, hemoglobinopathy-specific genes included in baby seq. Do you want to answer that? Okay. I'm not sure if the question is hemoglobin, no. I assume the question is, are they on the list? Oh, so I mean, so for example, if you're asking about HBA, you know, we're not, we do exome sequencing, so we're not able to reliably detect, you know, HBA deletions, so we would not be able to test it. I'm not sure if I understood your question right, but. So then next, how many variants on average do you go on to report for healthy baby? So that's a good question. So in terms of monogenic findings, most don't have monogenic findings. I think we had 11% that had, I think about maybe 10 or 11% that had a monogenic finding, so most of them did not. We are, we did report on carrier status, and about 90% of the babies had a carrier status finding. We did not say or confirm those in the parents, so we gave them the information and, you know, told the parents if they, something they wanted to follow up on, they would have to do it on their own because we didn't go and, we didn't have the kind of ability to, or the, that's just not what we did. We didn't look at the carrier status in the parents because they were just carriers, and it didn't, we really only Sanger sequenced the parents if there was something that informed the ability to understand the finding in the child, and so most people had carrier status, and most people did not have a monogenic finding. So someone's asked about the platform for sequencing the kit used for library preparation, that I would have to refer to you. Sure, so it was, we did HiSeq, and the kit was the Illumina content, the Illumina ice exome probe. And I think you have, the next is, oh, were you gonna say something, or? Yeah, I was gonna say, I think the next question, we kind of talked about the reanalysis protocol. I think we kind of talked about already. Oh, so the parental follow-up, was there blood drawn initially, or were they recontact? No, we got everything, all the blood initially. We got blood from the parents and the child when they enrolled, so we weren't going back and recontacting, because it was part of the analysis, so as soon as we did analysis, we found something, we needed to have the parental blood available, otherwise it would have taken us a long time to go get it. So we obtained the blood initially, and then if we used it, we extracted DNA, and we collected, it was either blood or a salivary DNA kit. So I think, I think that's it. There's a couple other, I'm trying to go to the next. Here we go. So this is just thanking QIAGEN Bioinformatics and the Ingenuity Clinical Decision Support Platform for their support, and a recording of this will be available at the ACMG Genetics Academy. This is just a reminder for Call for Abstracts for the ACMG meeting in Seattle in April with a deadline of November 30th. And the final thing just to mention is that the Undiagnosed Diseases Network has their Grand Rounds, it's an open Grand Rounds tomorrow at one o'clock Eastern time, and I was just asked to let people know about that. That is also a CME, get CME credits for that, also though I don't have the information for that. And I think that's it. So if there's nothing else, then thank you very much for joining.

ACMG Genomics Case Conference

monthly event

genome-scale testing

BabySeq project

genomic results

genetic findings

implications

genetic counseling

Q&A session