المؤلفون: Ansari, Morad, Faour, Kamli N. W., Shimamura, Akiko, Grimes, Graeme, Kao, Emeline M., Denhoff, Erica R., Blatnik, Ana, Ben-Isvy, Daniel, Wang, Lily, Helm, Benjamin M., Firth, Helen, Breman, Amy M., Bijlsma, Emilia K., Iwata-Otsubo, Aiko, de Ravel, Thomy J. L., Fusaro, Vincent, Fryer, Alan, Nykamp, Keith, Stühn, Lara G., Haack, Tobias B., Korenke, G. Christoph, Constantinou, Panayiotis, Bujakowska, Kinga M., Low, Karen J., Place, Emily, Humberson, Jennifer, Napier, Melanie P., Hoffman, Jessica, Juusola, Jane, Deardorff, Matthew A., Shao, Wanqing, Rockowitz, Shira, Krantz, Ian, Kaur, Maninder, Raible, Sarah, Dortenzio, Victoria, Kliesch, Sabine, Singer-Berk, Moriel, Groopman, Emily, DiTroia, Stephanie, Ballal, Sonia, Srivastava, Siddharth, Rothfelder, Kathrin, Biskup, Saskia, Rzasa, Jessica, Kerkhof, Jennifer, McConkey, Haley, Sadikovic, Bekim, Hilton, Sarah, Banka, Siddharth, Tüttelmann, Frank, Conrad, Donald F., O'Donnell-Luria, Anne, Talkowski, Michael E., FitzPatrick, David R., Boone, Philip M.

المساهمون: Medical and Molecular Genetics, School of Medicine

المصدر: PMC

مصطلحات موضوعية: Cornelia de Lange syndrome, SMC3, Loss-of-function, Cohesin, CdLS3, LoF

الوصف: Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only ...

وصف الملف: application/pdf

العلاقة: Human Genetics and Genomics Advances; Ansari M, Faour KNW, Shimamura A, et al. Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features. HGG Adv. 2024;5(2):100273. doi:10.1016/j.xhgg.2024.100273; https://hdl.handle.net/1805/41518Test

الإتاحة: https://doi.org/10.1016/j.xhgg.2024.100273Test
https://hdl.handle.net/1805/41518Test

المؤلفون: Zhang, Hanmeng, Daheron, Laurence, Cerna-Chavez, Rodrigo, Place, Emily M., Huckfeldt, Rachel M., Pierce, Eric A., Garita-Hernandez, Marcela

المصدر: Stem Cell Research ; volume 74, page 103280 ; ISSN 1873-5061

مصطلحات موضوعية: Cell Biology, Developmental Biology, General Medicine

الإتاحة: https://doi.org/10.1016/j.scr.2023.103280Test
https://api.elsevier.com/content/article/PII:S1873506123002660?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S1873506123002660?httpAccept=text/plainTest

المؤلفون: da Palma, Mariana, Igelman, Austin, Ku, Cristy, Burr, Amanda, You, Jia, Place, Emily, Wang, Nan-Kai, Oh, Jin, Branham, Kari, Zhang, Xinxin, Ahn, Jeeyun, Gorin, Michael, Lam, Byron, Ronquillo, Cecinio, Bernstein, Paul, Nagiel, Aaron, Huckfeldt, Rachel, Cabrera, Michelle, Kelly, John, Bakall, Benjamin, Iannaccone, Alessandro, Hufnagel, Robert, Zein, Wadih, Koenekoop, Robert, Birch, David, Yang, Paul, Fahim, Abigail, Pennesi, Mark

المصدر: Investigative Ophthalmology and Visual Science. 62(7)

مصطلحات موضوعية: Adult, Alagille Syndrome, Diagnosis, Differential, Eye Diseases, Hereditary, Female, Fluorescein Angiography, Genetic Testing, Humans, Jagged-1 Protein, Male, Medical Records, Mutation, Optic Disk, Optical Imaging, Retina, Tomography, Optical Coherence, Visual Acuity, Visual Field Tests

الوصف: PURPOSE: The purpose of this study was to characterize the phenotypic spectrum of ophthalmic findings in patients with Alagille syndrome. METHODS: We conducted a retrospective, observational, multicenter, study on 46 eyes of 23 subjects with Alagille syndrome. We reviewed systemic and ophthalmologic data extracted from medical records, color fundus photography, fundus autofluorescence, optical coherence tomography, visual fields, electrophysiological assessments, and molecular genetic findings. RESULTS: Cardiovascular abnormalities were found in 83% of all cases (of those, 74% had cardiac murmur), whereas 61% had a positive history of hepatobiliary issues, and musculoskeletal anomalies were present in 61% of all patients. Dysmorphic facies were present in 16 patients, with a broad forehead being the most frequent feature. Ocular symptoms were found in 91%, with peripheral vision loss being the most frequent complaint. Median (range) Snellen visual acuity of all eyes was 20/25 (20/20 to hand motion [HM]). Anterior segment abnormalities were present in 74% of the patients; of those, posterior embryotoxon was the most frequent finding. Abnormalities of the optic disc were found in 52%, and peripheral retinal abnormalities were the most frequent ocular finding in this series, found in 96% of all patients. Fifteen JAG1 mutations were identified in 16 individuals; of those, 6 were novel. CONCLUSIONS: This study reports a cohort of patients with Alagille syndrome in which peripheral chorioretinal changes were more frequent than posterior embryotoxon, the most frequent ocular finding according to a number of previous studies. We propose that these peripheral chorioretinal changes are a new hallmark to help diagnose this syndrome.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/43p780wzTest

المؤلفون: Ansari, Morad, Faour, Kamli N. W., Shimamura, Akiko, Grimes, Graeme, Kao, Emeline M., Denhoff, Erica R., Blatnik, Ana, Ben-Isvy, Daniel, Wang, Lily, Helm, Benjamin M., Firth, Helen, Breman, Amy M., Bijlsma, Emilia K., Iwata-Otsubo, Aiko, de Ravel, Thomy J. L., Fusaro, Vincent, Fryer, Alan, Nykamp, Keith, Stühn, Lara G., Haack, Tobias B., Korenke, G. Christoph, Constantinou, Panayiotis, Bujakowska, Kinga M., Low, Karen J., Place, Emily, Humberson, Jennifer, Napier, Melanie P., Hoffman, Jessica, Juusola, Jane, Deardorff, Matthew A., Shao, Wanqing, Rockowitz, Shira, Krantz, Ian, Kaur, Maninder, Raible, Sarah, Kliesch, Sabine, Singer-Berk, Moriel, Groopman, Emily, DiTroia, Stephanie, Ballal, Sonia, Srivastava, Siddharth, Rothfelder, Kathrin, Biskup, Saskia, Rzasa, Jessica, Kerkhof, Jennifer, McConkey, Haley, O'Donnell-Luria, Anne, Sadikovic, Bekim, Hilton, Sarah, Banka, Siddharth, Tüttelmann, Frank, Conrad, Donald, Talkowski, Michael E., FitzPatrick, David R., Boone, Philip M.

المساهمون: Medical and Molecular Genetics, School of Medicine

المصدر: PMC

مصطلحات موضوعية: Cornelia de Lange syndrome (CdLS), Cohesin, Loss-of-function

الوصف: Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 13 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated a milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, some instead having intriguing symptomatologies with rational biological links to SMC3 including bone marrow failure, acute myeloid leukemia, and Coats retinal vasculopathy. Analyses of transcriptomic and epigenetic data suggest that SMC3 pLoF variants reduce SMC3 expression but do not result in a blood DNA methylation signature clustering with that of CdLS, and that the global transcriptional signature of SMC3 loss is model-dependent. Our finding of substantial population-scale LoF intolerance in concert with variable penetrance in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of ...

وصف الملف: application/pdf

العلاقة: Ansari M, Faour KNW, Shimamura A, et al. Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features. Preprint. medRxiv. 2023;2023.09.27.23294269. Published 2023 Sep 28. doi:10.1101/2023.09.27.23294269; https://hdl.handle.net/1805/39578Test

الإتاحة: https://doi.org/10.1101/2023.09.27.23294269Test
https://hdl.handle.net/1805/39578Test

المؤلفون: Shah, Nidhi, Gold, Nina, Adelson, Sophia, Williams, Shardae, Bick, Sarah, Gold, Jessica, Strong, Alanna, Ganetzky, Rebecca, Roberts, Amy, Walker, Melissa, Holtz, Alexander, Sankaran, Vijay, Delmonte, Ottavia, Tan, Weizhen, Holm, Ingrid, Thiagarajah, Jay, Kamihara, Junne, Comander, Jason, Place, Emily, Wiggs, Janey, Green, Robert

المصدر: Genetics in Medicine Open ; volume 1, issue 1, page 100444 ; ISSN 2949-7744

الإتاحة: https://doi.org/10.1016/j.gimo.2023.100444Test
https://api.elsevier.com/content/article/PII:S2949774423004442?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S2949774423004442?httpAccept=text/plainTest

المؤلفون: O'Connell, Kaitlin, Borchert, John, Comander, Jason, Huckfeldt, Rachel, Pierce, Eric, Place, Emily

المصدر: Genetics in Medicine Open ; volume 1, issue 1, page 100287 ; ISSN 2949-7744

الإتاحة: https://doi.org/10.1016/j.gimo.2023.100287Test
https://api.elsevier.com/content/article/PII:S294977442300287X?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S294977442300287X?httpAccept=text/plainTest

المؤلفون: Hauser, Blake M., Luo, Yuyang, Nathan, Anusha, Al-Moujahed, Ahmad, Vavvas, Demetrios G., Comander, Jason, Pierce, Eric A., Place, Emily M., Bujakowska, Kinga M., Gaiha, Gaurav D., Rossin, Elizabeth J.

المصدر: NPJ Genomic Medicine; 5/27/2024, Vol. 9 Issue 1, p1-11, 11p

المؤلفون: Wojcik, Monica H, Lemire, Gabrielle, Berger, Eva, Zaki, Maha S, Wissmann, Mariel, Win, Wathone, White, Susan M, Weisburd, Ben, Wieczorek, Dagmar, Waddell, Leigh B, Verboon, Jeffrey M, VanNoy, Grace E, Töpf, Ana, Tan, Tiong Yang, Syrbe, Steffen, Strehlow, Vincent, Straub, Volker, Stenton, Sarah L, Snow, Hana, Singer-Berk, Moriel, Silver, Josh, Shril, Shirlee, Seaby, Eleanor G, Schneider, Ronen, Sankaran, Vijay G, Sanchis-Juan, Alba, Russell, Kathryn A, Reinson, Karit, Ravenscroft, Gianina, Radtke, Maximilian, Popp, Denny, Polster, Tilman, Platzer, Konrad, Pierce, Eric A, Place, Emily M, Pajusalu, Sander, Pais, Lynn, Õunap, Katrin, Osei-Owusu, Ikeoluwa, Opperman, Henry, Okur, Volkan, Oja, Kaisa Teele, O'Leary, Melanie, O'Heir, Emily, Morel, Chantal F, Merkenschlager, Andreas, Marchant, Rhett G, Mangilog, Brian E, Madden, Jill A, MacArthur, Daniel, Lovgren, Alysia, Lerner-Ellis, Jordan P, Lin, Jasmine, Laing, Nigel, Hildebrandt, Friedhelm, Hentschel, Julia, Groopman, Emily, Goodrich, Julia, Gleeson, Joseph G, Ghaoui, Roula, Genetti, Casie A, Gburek-Augustat, Janina, Gazda, Hanna T, Ganesh, Vijay S, Ganapathi, Mythily, Gallacher, Lyndon, Fu, Jack M, Evangelista, Emily, England, Eleina, Donkervoort, Sandra, DiTroia, Stephanie, Cooper, Sandra T, Chung, Wendy K, Christodoulou, John, Chao, Katherine R, Cato, Liam D, Bujakowska, Kinga M, Bryen, Samantha J, Brand, Harrison, Bönnemann, Carsten G, Beggs, Alan H, Baxter, Samantha M, Bartolomaeus, Tobias, Agrawal, Pankaj B, Talkowski, Michael, Austin-Tse, Christina, Abou Jamra, Rami, Rehm, Heidi L, O'Donnell-Luria, Anne

المصدر: N Engl J Med ; ISSN:1533-4406 ; Volume:390 ; Issue:21

الوصف: Genetic variants that cause rare disorders may remain elusive even after expansive testing, such as exome sequencing. The diagnostic yield of genome sequencing, particularly after a negative evaluation, remains poorly defined.

العلاقة: https://doi.org/10.1056/NEJMoa2314761Test; https://pubmed.ncbi.nlm.nih.gov/38838312Test

الإتاحة: https://doi.org/10.1056/NEJMoa2314761Test
https://pubmed.ncbi.nlm.nih.gov/38838312Test

المؤلفون: Lemire, Gabrielle, Sanchis-Juan, Alba, Russell, Kathryn, Baxter, Samantha, Chao, Katherine R, Singer-Berk, Moriel, Groopman, Emily, Wong, Isaac, England, Eleina, Goodrich, Julia, Pais, Lynn, Austin-Tse, Christina, DiTroia, Stephanie, O'Heir, Emily, Ganesh, Vijay S, Wojcik, Monica H, Evangelista, Emily, Snow, Hana, Osei-Owusu, Ikeoluwa, Fu, Jack, Singh, Mugdha, Mostovoy, Yulia, Huang, Steve, Garimella, Kiran, Kirkham, Samantha L, Neil, Jennifer E, Shao, Diane D, Walsh, Christopher A, Argilli, Emanuela, Le, Carolyn, Sherr, Elliott H, Gleeson, Joseph G, Shril, Shirlee, Schneider, Ronen, Hildebrandt, Friedhelm, Sankaran, Vijay G, Madden, Jill A, Genetti, Casie A, Beggs, Alan H, Agrawal, Pankaj B, Bujakowska, Kinga M, Place, Emily, Pierce, Eric A, Donkervoort, Sandra, Bönnemann, Carsten G, Gallacher, Lyndon, Stark, Zornitza, Tan, Tiong Yang, White, Susan M, Töpf, Ana, Straub, Volker, Fleming, Mark D, Pollak, Martin R, Õunap, Katrin, Pajusalu, Sander, Donald, Kirsten A, Bruwer, Zandre, Ravenscroft, Gianina, Laing, Nigel G, MacArthur, Daniel G, Rehm, Heidi L, Talkowski, Michael E, Brand, Harrison, O'Donnell-Luria, Anne

المصدر: Am J Hum Genet ; ISSN:1537-6605 ; Volume:111 ; Issue:5

مصطلحات موضوعية: CNV, GATK-gCNV, copy number variant, diagnostic yield, exome, variant classification

الوصف: Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and, with new innovative methods, can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the Genomics Research to Elucidate the Genetics of Rare Diseases consortium and analyzed using the seqr platform. The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb. The causal CNVs consisted of 140 deletions, 15 duplications, 3 suspected complex structural variants (SVs), 3 insertions, and 10 complex SVs, the latter two groups being identified by orthogonal confirmation methods. To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework. We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.

العلاقة: https://doi.org/10.1016/j.ajhg.2024.03.008Test; https://pubmed.ncbi.nlm.nih.gov/38565148Test; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11080278Test/

الإتاحة: https://doi.org/10.1016/j.ajhg.2024.03.008Test
https://pubmed.ncbi.nlm.nih.gov/38565148Test
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11080278Test/

المؤلفون: Bleicher, Isaac D., Garg, Itika, Hoyek, Sandra, Place, Emily, Miller, John B., Patel, Nimesh A.

المصدر: RETINAL Cases & Brief Reports ; volume 18, issue 1, page 80-86 ; ISSN 1935-1089

الوصف: Purpose: To describe novel clinical and angiographic findings in Wagner syndrome. Methods: A retrospective case series of three related patients with Wagner syndrome. Patients underwent standard optical coherence tomography (OCT), B-scan ultrasonography, and fluorescein angiography in addition to wide field swept-source OCT angiography (WF SS-OCTA) (PLEX Elite 9000, Carl Zeiss Meditec Inc). Patients underwent genetic testing for a panel of hereditary vitreoretinopathies. Results: Three related patients with Wagner syndrome were identified. All were found to have prominent vitreous strands, abnormal vitreoretinal adhesions, peripheral retinal holes, and varying degrees of myopia. A mid-peripheral tractional ridge was identified in all six eyes. All patients were positive for a known pathologic intron variant in the VCAN gene (4004-5T-A). Wide field swept-source OCT angiography (12 mm × 12 mm) was performed in two patients and demonstrated perivascular capillary loss in the superficial capillary plexus along the arcades bilaterally. One patient demonstrated associated retinal atrophy within the area of capillary loss. The capillary loss extended beyond the margin of retinal atrophy. Conclusion: The unusual finding of a mid-peripheral tractional ridge of the retina associated with myopia led to a genetic diagnosis of Wagner syndrome. Widefield swept-source OCT angiography demonstrated a novel feature of perivascular loss of the superficial retinal capillary plexus. This result suggests that vitreous traction may cause localized microvasculature dysfunction and subsequent retinal atrophy in Wagner syndrome. This is the first known evaluation of Wagner syndrome using OCT angiography.

الإتاحة: https://doi.org/10.1097/icb.0000000000001307Test