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Feero WG, Steiner RD, Slavotinek A, Faial T, Bamshad MJ, Austin J, Korf BR, Flanagin A, Bibbins-Domingo K. Guidance on Use of Race, Ethnicity, and Geographic Origin as Proxies for Genetic Ancestry Groups in Biomedical Publications. JAMA 2024; 331:1276-1278. [PMID: 38470200 DOI: 10.1001/jama.2024.3737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Affiliation(s)
- W Gregory Feero
- Maine-Dartmouth Family Medicine Residency, Augusta, Maine
- JAMA , Chicago, Illinois
| | - Robert D Steiner
- University of Wisconsin School of Medicine and Public Health, Madison
- Genetics in Medicine , New York, New York
| | - Anne Slavotinek
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
- American Journal of Medical Genetics , Hoboken, New Jersey
| | | | - Michael J Bamshad
- Departments of Pediatrics and Genome Sciences, University of Washington, Seattle
- Human Genetics and Genomics Advances , Cambridge, Massachusetts
| | - Jehannine Austin
- Departments of Psychiatry and Medical Genetics, University of British Columbia, Vancouver, Canada
- Journal of Genetic Counseling , Vancouver, British Columbia, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham
- American Journal of Human Genetics , Cambridge, Massachusetts
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Feero WG, Steiner RD, Slavotinek A, Faial T, Bamshad MJ, Austin J, Korf BR, Flanagin A, Bibbins-Domingo K. Guidance on use of race, ethnicity, and geographic origin as proxies for genetic ancestry groups in biomedical publications. HGG Adv 2024; 5:100282. [PMID: 38479390 PMCID: PMC11019354 DOI: 10.1016/j.xhgg.2024.100282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Affiliation(s)
- W Gregory Feero
- Maine-Dartmouth Family Medicine Residency, Augusta, ME, USA; JAMA, Chicago, IL, USA.
| | - Robert D Steiner
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Genetics in Medicine, New York, New York, USA
| | - Anne Slavotinek
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA; American Journal of Medical Genetics, Hoboken, NJ, USA
| | | | - Michael J Bamshad
- Departments of Pediatrics and Genome Sciences, University of Washington, Seattle, WA, USA; Human Genetics and Genomics Advances, Cambridge, MA, USA
| | - Jehannine Austin
- Departments of Psychiatry and Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Journal of Genetic Counseling, Vancouver, BC, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA; American Journal of Human Genetics, Cambridge, MA, USA
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Feero WG, Steiner RD, Slavotinek A, Faial T, Bamshad MJ, Austin J, Korf BR, Flanagin A, Bibbins-Domingo K. Guidance on use of race, ethnicity, and geographic origin as proxies for genetic ancestry groups in biomedical publications. Am J Hum Genet 2024; 111:621-623. [PMID: 38479392 PMCID: PMC11023913 DOI: 10.1016/j.ajhg.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Affiliation(s)
- W Gregory Feero
- Maine-Dartmouth Family Medicine Residency, Augusta, ME, USA; JAMA, Chicago, IL, USA.
| | - Robert D Steiner
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Genetics in Medicine, New York, New York, USA
| | - Anne Slavotinek
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA; American Journal of Medical Genetics, Hoboken, NJ, USA
| | | | - Michael J Bamshad
- Departments of Pediatrics and Genome Sciences, University of Washington, Seattle, WA, USA; Human Genetics and Genomics Advances, Cambridge, MA, USA
| | - Jehannine Austin
- Departments of Psychiatry and Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Journal of Genetic Counseling, Vancouver, BC, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA; American Journal of Human Genetics, Cambridge, MA, USA
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Feero WG, Steiner RD, Slavotinek A, Faial T, Bamshad MJ, Austin J, Korf BR, Flanagin A, Bibbins-Domingo K. Guidance on use of race, ethnicity, and geographic origin as proxies for genetic ancestry groups in biomedical publications. Nat Genet 2024; 56:555-556. [PMID: 38480924 DOI: 10.1038/s41588-024-01708-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Affiliation(s)
- W Gregory Feero
- Maine-Dartmouth Family Medicine Residency, Augusta, ME, USA.
- JAMA, .
| | - Robert D Steiner
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Genetics in Medicine
| | - Anne Slavotinek
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- American Journal of Medical Genetics
| | | | - Michael J Bamshad
- Departments of Pediatrics and Genome Sciences, University of Washington, Seattle, WA, USA
- Human Genetics and Genomics Advances
| | - Jehannine Austin
- Departments of Psychiatry and Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Journal of Genetic Counseling
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
- The American Journal of Human Genetics
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Ha T, Morgan A, Bartos MN, Beatty K, Cogné B, Braun D, Gerber CB, Gaspar H, Kopps AM, Rieubland C, Hurst ACE, Amor DJ, Nizon M, Pasquier L, Pfundt R, Reis A, Siu VM, Tessarech M, Thompson ML, Vincent M, de Vries BBA, Walsh MB, Wechsler SB, Zweier C, Schnur RE, Guillen Sacoto MJ, Margot H, Masotto B, Palafoll MIV, Nawaz U, Voineagu I, Slavotinek A. De novo variants predicting haploinsufficiency for DIP2C are associated with expressive speech delay. Am J Med Genet A 2024:e63559. [PMID: 38421105 DOI: 10.1002/ajmg.a.63559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/16/2023] [Accepted: 01/04/2024] [Indexed: 03/02/2024]
Abstract
The disconnected (disco)-interacting protein 2 (DIP2) gene was first identified in D. melanogaster and contains a DNA methyltransferase-associated protein 1 (DMAP1) binding domain, Acyl-CoA synthetase domain and AMP-binding sites. DIP2 regulates axonal bifurcation of the mushroom body neurons in D. melanogaster and is required for axonal regeneration in the neurons of C. elegans. The DIP2 homologues in vertebrates, Disco-interacting protein 2 homolog A (DIP2A), Disco-interacting protein 2 homolog B (DIP2B), and Disco-interacting protein 2 homolog C (DIP2C), are highly conserved and expressed widely in the central nervous system. Although there is evidence that DIP2C plays a role in cognition, reports of pathogenic variants in these genes are rare and their significance is uncertain. We present 23 individuals with heterozygous DIP2C variants, all manifesting developmental delays that primarily affect expressive language and speech articulation. Eight patients had de novo variants predicting loss-of-function in the DIP2C gene, two patients had de novo missense variants, three had paternally inherited loss of function variants and six had maternally inherited loss-of-function variants, while inheritance was unknown for four variants. Four patients had cardiac defects (hypertrophic cardiomyopathy, atrial septal defects, and bicuspid aortic valve). Minor facial anomalies were inconsistent but included a high anterior hairline with a long forehead, broad nasal tip, and ear anomalies. Brainspan analysis showed elevated DIP2C expression in the human neocortex at 10-24 weeks after conception. With the cases presented herein, we provide phenotypic and genotypic data supporting the association between loss-of-function variants in DIP2C with a neurocognitive phenotype.
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Affiliation(s)
- Thoa Ha
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, USA
| | - Angela Morgan
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Meghan N Bartos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Katelyn Beatty
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, L'institut du Thorax, University Nantes, Nantes, France
| | - Dominique Braun
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Céline B Gerber
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Harald Gaspar
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anna M Kopps
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Claudine Rieubland
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, L'institut du Thorax, University Nantes, Nantes, France
| | | | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Centre for Rare Diseases Erlangen (ZSEER), Erlangen, Germany
| | - Victoria Mok Siu
- London Health Sciences Center and Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Marine Tessarech
- Department of Biochemistry and Genetics, Angers University Hospital, Angers, France
| | | | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, L'institut du Thorax, University Nantes, Nantes, France
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | | | - Stephanie Burns Wechsler
- Departments of Pediatrics and Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | | | - Henri Margot
- Université Bordeaux, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Barbara Masotto
- Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | | | - Urwah Nawaz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, USA
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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Gangaram B, Lee V, Slavotinek A. Biallelic OTUD6B variants associated with a Kabuki syndrome-like disorder in three siblings: A clinical report and literature review. Am J Med Genet A 2024. [PMID: 38389298 DOI: 10.1002/ajmg.a.63567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
Biallelic variants in the OTUD6B gene have been reported in the literature in association with an intellectual developmental disorder featuring dysmorphic facies, seizures, and distal limb abnormalities. Physical differences described for affected individuals suggest that the disorder may be clinically recognizable, but previous publications have reported an initial clinical suspicion for Kabuki syndrome (KS) in some affected individuals. Here, we report on three siblings with biallelic variants in OTUD6B co-segregating with neurodevelopmental delay, shared physical differences, and other clinical findings similar to those of previously reported individuals. However, clinical manifestations such as long palpebral fissures, prominent and cupped ears, developmental delay, growth deficiency, persistent fetal fingertip pads, vertebral anomaly, and seizures in the proband were initially suggestive of KS. In addition, previously unreported clinical manifestations such as delayed eruption of primary dentition, soft doughy skin with reduced sweating, and mirror movements present in our patients suggest an expansion of the phenotype, and we perform a literature review to update on current information related to OTUD6B and human gene-disease association.
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Affiliation(s)
- Balram Gangaram
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, California, USA
| | - Virgina Lee
- Division of Child Neurology, University of California, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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7
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Mavura Y, Sahin-Hodoglugil N, Hodoglugil U, Kvale M, Martin PM, Van Ziffle J, Devine WP, Ackerman SL, Koenig BA, Kwok PY, Norton ME, Slavotinek A, Risch N. Genetic ancestry and diagnostic yield of exome sequencing in a diverse population. NPJ Genom Med 2024; 9:1. [PMID: 38172272 PMCID: PMC10764913 DOI: 10.1038/s41525-023-00385-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024] Open
Abstract
It has been suggested that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental/subcontinental genetic ancestry in a racially/ethnically diverse pediatric and prenatal clinical cohort. Cases (N = 845) with suspected genetic disorders underwent ES for diagnosis. Continental/subcontinental genetic ancestry proportions were estimated from the ES data. We compared the distribution of genetic ancestries in positive, negative, and inconclusive cases by Kolmogorov-Smirnov tests and linear associations of ancestry with DY by Cochran-Armitage trend tests. We observed no reduction in overall DY associated with any genetic ancestry (African, Native American, East Asian, European, Middle Eastern, South Asian). However, we observed a relative increase in proportion of autosomal recessive homozygous inheritance versus other inheritance patterns associated with Middle Eastern and South Asian ancestry, due to consanguinity. In this empirical study of ES for undiagnosed pediatric and prenatal genetic conditions, genetic ancestry was not associated with the likelihood of a positive diagnosis, supporting the equitable use of ES in diagnosis of previously undiagnosed but potentially Mendelian disorders across all ancestral populations.
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Affiliation(s)
- Yusuph Mavura
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA.
| | - Nuriye Sahin-Hodoglugil
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Ugur Hodoglugil
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Van Ziffle
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - W Patrick Devine
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sara L Ackerman
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
- Department of Social & Behavioral Sciences, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Barbara A Koenig
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Bioethics, University of California San Francisco, San Francisco, CA, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute and Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Anne Slavotinek
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA.
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Li D, Wang Q, Bayat A, Battig MR, Zhou Y, Bosch DG, van Haaften G, Granger L, Petersen AK, Pérez-Jurado LA, Aznar-Laín G, Aneja A, Hancarova M, Bendova S, Schwarz M, Kremlikova Pourova R, Sedlacek Z, Keena BA, March ME, Hou C, O’Connor N, Bhoj EJ, Harr MH, Lemire G, Boycott KM, Towne M, Li M, Tarnopolsky M, Brady L, Parker MJ, Faghfoury H, Parsley LK, Agolini E, Dentici ML, Novelli A, Wright M, Palmquist R, Lai K, Scala M, Striano P, Iacomino M, Zara F, Cooper A, Maarup TJ, Byler M, Lebel RR, Balci TB, Louie R, Lyons M, Douglas J, Nowak C, Afenjar A, Hoyer J, Keren B, Maas SM, Motazacker MM, Martinez-Agosto JA, Rabani AM, McCormick EM, Falk MJ, Ruggiero SM, Helbig I, Møller RS, Tessarollo L, Tomassoni Ardori F, Palko ME, Hsieh TC, Krawitz PM, Ganapathi M, Gelb BD, Jobanputra V, Wilson A, Greally J, Jacquemont S, Jizi K, Bruel AL, Quelin C, Misra VK, Chick E, Romano C, Greco D, Arena A, Morleo M, Nigro V, Seyama R, Uchiyama Y, Matsumoto N, Taira R, Tashiro K, Sakai Y, Yigit G, Wollnik B, Wagner M, Kutsche B, Hurst AC, Thompson ML, Schmidt R, Randolph L, Spillmann RC, Shashi V, Higginbotham EJ, Cordeiro D, Carnevale A, Costain G, Khan T, Funalot B, Tran Mau-Them F, Fernandez Garcia Moya L, García-Miñaúr S, Osmond M, Chad L, Quercia N, Carrasco D, Li C, Sanchez-Valle A, Kelley M, Nizon M, Jensson BO, Sulem P, Stefansson K, Gorokhova S, Busa T, Rio M, Hadj Habdallah H, Lesieur-Sebellin M, Amiel J, Pingault V, Mercier S, Vincent M, Philippe C, Fatus-Fauconnier C, Friend K, Halligan RK, Biswas S, Rosser J, Shoubridge C, Corbett M, Barnett C, Gecz J, Leppig K, Slavotinek A, Marcelis C, Pfundt R, de Vries BB, van Slegtenhorst MA, Brooks AS, Cogne B, Rambaud T, Tümer Z, Zackai EH, Akizu N, Song Y, Hakonarson H. Spliceosome malfunction causes neurodevelopmental disorders with overlapping features. J Clin Invest 2024; 134:e171235. [PMID: 37962958 PMCID: PMC10760965 DOI: 10.1172/jci171235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023] Open
Abstract
Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50-deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, and
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Qin Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Allan Bayat
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department for Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | | | - Yijing Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daniëlle G.M. Bosch
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Leslie Granger
- Department of Genetics and Metabolism, Randall Children’s Hospital at Legacy Emanuel Medical Center, Portland, Oregon, USA
| | - Andrea K. Petersen
- Department of Genetics and Metabolism, Randall Children’s Hospital at Legacy Emanuel Medical Center, Portland, Oregon, USA
| | - Luis A. Pérez-Jurado
- Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- Genetic Service, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Gemma Aznar-Laín
- Universitat Pompeu Fabra, Barcelona, Spain
- Pediatric Neurology, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Anushree Aneja
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Sarka Bendova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Martin Schwarz
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Radka Kremlikova Pourova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Beth A. Keena
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Elizabeth J. Bhoj
- Center for Applied Genomics, and
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Gabrielle Lemire
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Megan Li
- Invitae, San Francisco, California, USA
| | - Mark Tarnopolsky
- Division of Neuromuscular and Neurometabolic Disorders, Department of Paediatrics, McMaster University Children’s Hospital, Hamilton, Ontario, Canada
| | - Lauren Brady
- Division of Neuromuscular and Neurometabolic Disorders, Department of Paediatrics, McMaster University Children’s Hospital, Hamilton, Ontario, Canada
| | - Michael J. Parker
- Department of Clinical Genetics, Sheffield Children’s Hospital, Sheffield, United Kingdom
| | | | - Lea Kristin Parsley
- University of Illinois College of Medicine, Mercy Health Systems, Rockford, Illinois, USA
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Meredith Wright
- Rady Children’s Institute for Genomic Medicine, San Diego, California, USA
| | - Rachel Palmquist
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Khanh Lai
- Division of Pediatric Pulmonary and Sleep Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, and
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, and
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS, Istituto Giannina Gaslini, Genoa, Italy
| | - Federico Zara
- Medical Genetics Unit, IRCCS, Istituto Giannina Gaslini, Genoa, Italy
| | - Annina Cooper
- Department of Genetics, Southern California Permanente Medical Group, Kaiser Permanente, San Diego, California, USA
| | - Timothy J. Maarup
- Department of Genetics, Kaiser Permanente, Los Angeles, California, USA
| | - Melissa Byler
- Center for Development, Behavior and Genetics, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Robert Roger Lebel
- Center for Development, Behavior and Genetics, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Tugce B. Balci
- Division of Genetics, Department of Paediatrics, London Health Sciences Centre, London, Ontario, Canada
| | - Raymond Louie
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Michael Lyons
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Jessica Douglas
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Catherine Nowak
- Division of Genetics and Metabolism, Mass General Hospital for Children, Boston, Massachusetts, USA
| | - Alexandra Afenjar
- APHP. SU, Reference Center for Intellectual Disabilities Caused by Rare Causes, Department of Genetics and Medical Embryology, Hôpital Trousseau, Paris, France
| | - Juliane Hoyer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Boris Keren
- Department of Genetics, Hospital Pitié-Salpêtrière, Paris, France
| | - Saskia M. Maas
- Department of Human Genetics, Academic Medical Center, and
| | - Mahdi M. Motazacker
- Laboratory of Genome Diagnostics, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Ahna M. Rabani
- Division of Medical Genetics, Department of Pediatrics, UCLA, Los Angeles, California, USA
| | - Elizabeth M. McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics
| | - Marni J. Falk
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics
| | - Sarah M. Ruggiero
- Division of Neurology, and
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ingo Helbig
- Division of Neurology, and
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rikke S. Møller
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Francesco Tomassoni Ardori
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Mary Ellen Palko
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Peter M. Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Mythily Ganapathi
- New York Genome Center, New York, New York, USA
- Department of Pathology, Columbia University Irving Medical Center, New York, New York, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine, New York, New York, USA
| | - Vaidehi Jobanputra
- New York Genome Center, New York, New York, USA
- Department of Pathology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - John Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sébastien Jacquemont
- Division of Genetics and Genomics, CHU Ste-Justine Hospital and CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Khadijé Jizi
- Division of Genetics and Genomics, CHU Ste-Justine Hospital and CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Ange-Line Bruel
- INSERM UMR 1231, Genetics of Developmental Anomalies, Université de Bourgogne Franche-Comté, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Translational Medicine in Developmental Anomalies, CHU Dijon Bourgogne, Dijon, France
| | - Chloé Quelin
- Medical Genetics Department, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Vinod K. Misra
- Division of Genetic, Genomic, and Metabolic Disorders, Children’s Hospital of Michigan, Detroit, Michigan, USA
- Central Michigan University College of Medicine, Discipline of Pediatrics, Mount Pleasant, Michigan, USA
| | - Erika Chick
- Division of Genetic, Genomic, and Metabolic Disorders, Children’s Hospital of Michigan, Detroit, Michigan, USA
| | - Corrado Romano
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | | | | | - Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Rie Seyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ryoji Taira
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuya Tashiro
- Department of Pediatrics, Karatsu Red Cross Hospital, Saga, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Michael Wagner
- Kinderzentrum Oldenburg, Sozialpädiatrisches Zentrum, Diakonisches Werk Oldenburg, Oldenburg, Germany
| | - Barbara Kutsche
- Kinderzentrum Oldenburg, Sozialpädiatrisches Zentrum, Diakonisches Werk Oldenburg, Oldenburg, Germany
| | - Anna C.E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Ryan Schmidt
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Linda Randolph
- Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Division of Medical Genetics, Children’s Hospital Los Angeles, California, USA
| | - Rebecca C. Spillmann
- Department of Pediatrics–Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vandana Shashi
- Department of Pediatrics–Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Dawn Cordeiro
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amanda Carnevale
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tayyaba Khan
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Benoît Funalot
- Department of Genetics, Hôpital Henri-Mondor APHP and CHI Creteil, University Paris Est Creteil, IMRB, Inserm U.955, Creteil, France
| | - Frederic Tran Mau-Them
- INSERM UMR 1231, Genetics of Developmental Anomalies, Université de Bourgogne Franche-Comté, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
| | | | - Sixto García-Miñaúr
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Madrid, Spain
| | - Matthew Osmond
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Lauren Chad
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Nada Quercia
- Department of Genetic Counselling, Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Ottawa, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Diana Carrasco
- Department of Clinical Genetics, Cook Children’s Hospital, Fort Worth, Texas, USA
| | - Chumei Li
- Division of Genetics, Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Amarilis Sanchez-Valle
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | - Meghan Kelley
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | - Mathilde Nizon
- Nantes Université, CHU Nantes, Medical Genetics Department, Nantes, France
- Nantes Université, CNRS, INSERM, l’Institut du Thorax, Nantes, France
| | | | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Svetlana Gorokhova
- Aix Marseille University, Inserm, U1251-MMG, Marseille Medical Genetics, Marseille, France
- Department of Medical Genetics, Timone Hospital, APHM, Marseille, France
| | - Tiffany Busa
- Department of Medical Genetics, Timone Hospital, APHM, Marseille, France
| | - Marlène Rio
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Hamza Hadj Habdallah
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Marion Lesieur-Sebellin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Jeanne Amiel
- Rare Disease Genetics Department, APHP, Hôpital Necker, Paris, France
- Université Paris Cité, Inserm, Institut Imagine, Embryology and Genetics of Malformations Laboratory, Paris, France
| | - Véronique Pingault
- Rare Disease Genetics Department, APHP, Hôpital Necker, Paris, France
- Université Paris Cité, Inserm, Institut Imagine, Embryology and Genetics of Malformations Laboratory, Paris, France
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France
| | - Sandra Mercier
- Nantes Université, CHU Nantes, Medical Genetics Department, Nantes, France
- Nantes Université, CNRS, INSERM, l’Institut du Thorax, Nantes, France
| | - Marie Vincent
- Nantes Université, CHU Nantes, Medical Genetics Department, Nantes, France
- Nantes Université, CNRS, INSERM, l’Institut du Thorax, Nantes, France
| | - Christophe Philippe
- INSERM UMR 1231, Genetics of Developmental Anomalies, Université de Bourgogne Franche-Comté, Dijon, France
| | | | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | | | | | - Jane Rosser
- Department of General Medicine, Women’s and Children’s Hospital, Adelaide, South Australia, Australia
| | - Cheryl Shoubridge
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, South Australia, Australia
| | - Mark Corbett
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, South Australia, Australia
| | - Christopher Barnett
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, South Australia, Australia
- Pediatric and Reproductive Genetics Unit, Women’s and Children’s Hospital, North Adelaide, South Australia, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Kathleen Leppig
- Genetic Services, Kaiser Permenante of Washington, Seattle, Washington, USA
| | - Anne Slavotinek
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Carlo Marcelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B.A. de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Benjamin Cogne
- Nantes Université, CHU Nantes, Medical Genetics Department, Nantes, France
- Nantes Université, CNRS, INSERM, l’Institut du Thorax, Nantes, France
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France
| | - Thomas Rambaud
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elaine H. Zackai
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, and
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Slavotinek A, Rego S, Sahin-Hodoglugil N, Kvale M, Lianoglou B, Yip T, Hoban H, Outram S, Anguiano B, Chen F, Michelson J, Cilio RM, Curry C, Gallagher RC, Gardner M, Kuperman R, Mendelsohn B, Sherr E, Shieh J, Strober J, Tam A, Tenney J, Weiss W, Whittle A, Chin G, Faubel A, Prasad H, Mavura Y, Van Ziffle J, Devine WP, Hodoglugil U, Martin PM, Sparks TN, Koenig B, Ackerman S, Risch N, Kwok PY, Norton ME. Author Correction: Diagnostic yield of pediatric and prenatal exome sequencing in a diverse population. NPJ Genom Med 2023; 8:34. [PMID: 37872195 PMCID: PMC10593851 DOI: 10.1038/s41525-023-00382-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023] Open
Affiliation(s)
- Anne Slavotinek
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Shannon Rego
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Nuriye Sahin-Hodoglugil
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Billie Lianoglou
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Tiffany Yip
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Hoban
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Simon Outram
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Beatrice Anguiano
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Flavia Chen
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jeremy Michelson
- Institute of Human Nutrition, Columbia University Medical Center, New York, NY, USA
| | - Roberta M Cilio
- Division of Pediatric Neurology, Department of Pediatrics, University of Louvain, Brussels, Belgium
| | - Cynthia Curry
- Genetic Medicine, University of California, San Francisco, Fresno, CA, USA
| | - Renata C Gallagher
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marisa Gardner
- Department of Neurology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Rachel Kuperman
- Department of Neurology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
- Eysz, Inc, Piedmont, CA, USA
| | - Bryce Mendelsohn
- Division of Genetics, Kaiser Permanente Oakland Medical Center, Oakland, CA, USA
| | - Elliott Sherr
- Division of Child Neurology, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph Shieh
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Strober
- Division of Child Neurology, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Allison Tam
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Tenney
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - William Weiss
- Division of Child Neurology, Zuckerberg San Francisco General Hospital, San Francisco, San Francisco, CA, USA
| | - Amy Whittle
- Division of Pediatrics, Zuckerberg San Francisco General Hospital, San Francisco, San Francisco, CA, USA
| | - Garrett Chin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Amanda Faubel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Hannah Prasad
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yusuph Mavura
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Van Ziffle
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - W Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Ugur Hodoglugil
- Genomic Medicine Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Teresa N Sparks
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, San Francisco, USA
| | - Barbara Koenig
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Bioethics, University of California, San Francisco, San Francisco, CA, USA
| | - Sara Ackerman
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
- Department of Social & Behavioral Sciences, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, San Francisco, USA
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10
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Slavotinek A. Genetics in Pediatric Practice: From Baby Steps to Running Fast. Pediatr Clin North Am 2023; 70:885-894. [PMID: 37704347 DOI: 10.1016/j.pcl.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
In the last few decades, medical genetics has undergone a revolution because of the development of technologies and informatics approaches that can generate and analyze large amounts of genomic data. Pediatricians have been hugely affected by these changes. The early age of presentation for birth defects and neurocognitive disorders, together with a shortage of trained genetics professionals, has increased consultations for conditions with a genetic cause, not only in pediatric practice but also in other subspecialties. In the future, genetic testing in childhood is likely to include pediatricians, who can initiate testing in partnership with trained genetics professionals.
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Affiliation(s)
- Anne Slavotinek
- Medical Genetics, Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
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11
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Slavotinek A, Simpson B, Tam A. Genetics in Pediatric Practice. Pediatr Clin North Am 2023; 70:xvii-xix. [PMID: 37704358 DOI: 10.1016/j.pcl.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Affiliation(s)
- Anne Slavotinek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati School of Medicine, 3333 Burnet Avenue, ML4006, Cincinnati, OH 45229, USA.
| | - Brittany Simpson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati School of Medicine, 3333 Burnet Avenue, ML4006, Cincinnati, OH 45229, USA.
| | - Allison Tam
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, UCSF Benioff Children's Hospital, 550 16th Street, 4th Floor, San Francisco, CA 94143, USA.
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12
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Stallworth JY, Blair DR, Slavotinek A, Moore AT, Duncan JL, de Alba Campomanes AG. Retinopathy and optic atrophy in a case of COQ2-related primary coenzyme Q 10 deficiency. Ophthalmic Genet 2023; 44:486-490. [PMID: 36420660 PMCID: PMC10205914 DOI: 10.1080/13816810.2022.2141792] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/08/2022] [Accepted: 10/22/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE To describe a case of primary coenzyme Q10 deficiency in a child manifesting as early-onset renal failure, retinal dystrophy, and optic atrophy leading to progressive vision loss. METHODS Clinical presentation and workup including visual fields, electroretinogram, and optical coherence tomography are presented. Genetic testing was performed. RESULTS An eight-year-old female with nephropathy requiring renal transplantation subsequently developed progressive cone-rod dystrophy and optic atrophy. The patient had negative results on a targeted next-generation sequencing retinal dystrophy panel but whole-exome sequencing revealed two variants in COQ2 (likely biallelic), consistent with a diagnosis of primary coenzyme Q10 deficiency. CONCLUSIONS Primary coenzyme Q10 deficiency is a rare disorder with variable systemic and ocular findings; there is also genetic heterogeneity. Genetic testing aids in the diagnosis of this condition, and variants in the COQ2 and PDSS1 genes appear to have the strongest association with ocular manifestations. Oral supplementation of coenzyme Q10 may slow progression of disease. This case highlights the utility of whole-exome sequencing in the diagnosis of a rare syndromic form of ocular disease and reports a novel phenotypic association for this condition.
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Affiliation(s)
| | - David R Blair
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Anne Slavotinek
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Anthony T Moore
- Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Jacque L Duncan
- Department of Ophthalmology, University of California, San Francisco, CA, USA
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13
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Slavotinek A, Prasad H, Outram S, Scollon S, Rego S, Yip T, Hoban H, Foreman KM, Kelley W, Finnila C, Berg J, Murali P, Bonini KE, Martin LJ, Hott A. Information-seeking preferences in diverse patients receiving a genetic testing result in the Clinical Sequencing Evidence-Generating Research (CSER) study. Genet Med 2023; 25:100899. [PMID: 37212252 PMCID: PMC10524447 DOI: 10.1016/j.gim.2023.100899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/23/2023] Open
Abstract
PURPOSE Accurate and understandable information after genetic testing is critical for patients, family members, and professionals alike. METHODS As part of a cross-site study from the Clinical Sequencing Evidence-Generating Research consortium, we investigated the information-seeking practices among patients and family members at 5 to 7 months after genetic testing results disclosure, assessing the perceived utility of a variety of information sources, such as family and friends, health care providers, support groups, and the internet. RESULTS We found that individuals placed a high value on information obtained from genetics professionals and health care workers, independent of genetic testing result case classifications as positive, inconclusive, or negative. The internet was also highly utilized and ranked. Study participants rated some information sources as more useful for positive results compared with inconclusive or negative outcomes, emphasizing that it may be difficult to identify helpful information for individuals receiving an uncertain or negative result. There were few data from non-English speakers, highlighting the need to develop strategies to reach this population. CONCLUSION Our study emphasizes the need for clinicians to provide accurate and comprehensible information to individuals from diverse populations after genetic testing.
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Affiliation(s)
- Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA.
| | - Hannah Prasad
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Simon Outram
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Shannon Rego
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Tiffany Yip
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Hannah Hoban
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Kate M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Jonathan Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Priyanka Murali
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA
| | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa J Martin
- Division of Human Genetics Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Adam Hott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
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14
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Smith HS, Ferket BS, Gelb BD, Hindorff L, Ferar KD, Norton ME, Sahin-Hodoglugil N, Slavotinek A, Lich KH, Berg JS, Russell HV. Parent-Reported Clinical Utility of Pediatric Genomic Sequencing. Pediatrics 2023; 152:e2022060318. [PMID: 37470118 PMCID: PMC10812387 DOI: 10.1542/peds.2022-060318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Genomic sequencing (GS) is increasingly used for diagnostic evaluation, yet follow-up care is not well understood. We assessed clinicians' recommendations after GS, parent-reported follow-up, and actions parents initiated in response to learning their child's GS results. METHODS We surveyed parents of children who received GS through the Clinical Sequencing Evidence Generating Research consortium ∼5 to 7 months after return of results. We compared the proportion of parents who reported discussing their child's result with a clinician, clinicians' recommendations, and parents' follow-up actions by GS result type using χ2 tests. RESULTS A total of 1188 respondents completed survey measures on recommended medical actions (n = 1187) and/or parent-initiated actions (n = 913). Most parents who completed recommended medical actions questions (n = 833, 70.3%) reported having discussed their child's GS results with clinicians. Clinicians made recommendations to change current care for patients with positive GS results (n = 79, 39.1%) more frequently than for those with inconclusive (n = 31, 12.4%) or negative results (n = 44, 11.9%; P < .001). Many parents discussed (n = 152 completed, n = 135 planned) implications of GS results for future pregnancies with a clinician. Aside from clinical recommendations, 13.0% (n = 119) of parents initiated changes to their child's health or lifestyle. CONCLUSIONS In diverse pediatric clinical contexts, GS results can lead to recommendations for follow-up care, but they likely do not prompt large increases in the quantity of care received.
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Affiliation(s)
- Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX USA
- Precision Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Bart S. Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute, Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lucia Hindorff
- Training, Diversity and Health Equity Office, National Human Genome Research Institute, National Institutes of Health
| | - Kathleen D. Ferar
- Department of Biomedical Informatics and Medical Education, Division of Biomedical Informatics, University of Washington, Seattle, WA, USA
| | - Mary E. Norton
- University of California, San Francisco, San Francisco, CA, USA
| | | | - Anne Slavotinek
- University of California, San Francisco, San Francisco, CA, USA
| | - Kristen Hasmiller Lich
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
| | - Heidi V. Russell
- Department of Pediatrics, Baylor College of Medicine, Houston TX, USA
- Department of Management, Policy, and Community Health, UTHealth School of Public Health, Houston, TX, USA
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15
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Qu’d D, Schmitt LM, Leston A, Harris JR, Slavotinek A, Riddle I, Brightman DS, Simpson BN. Behavioral and neuropsychiatric challenges across the lifespan in individuals with Rubinstein-Taybi syndrome. Front Genet 2023; 14:1116919. [PMID: 37415602 PMCID: PMC10321757 DOI: 10.3389/fgene.2023.1116919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/06/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction: Rubinstein-Taybi syndrome (RSTS) is a rare congenital disorder characterized by developmental and intellectual disability, broadening of thumbs and halluces, and characteristic facial features. Pathogenic variants in CREBBP lead to RSTS type 1 (RSTS1) and in EP300 lead to RSTS type 2 (RSTS2). Individuals with RSTS can demonstrate a variety of behavioral and neuropsychiatric challenges, including anxiety, hyperactivity/inattention, self-injury, repetitive behaviors, and aggression. Behavioral challenges are consistently reported as one of the primary factors impacting quality of life. Despite the high prevalence and morbidity of behavioral and neuropsychiatric features of RSTS, a paucity of data exists regarding its natural history. Methods: To better understand the neurocognitive and behavioral challenges faced by individuals with RSTS, 71 caregivers of individuals with RSTS, ranging in age from one to 61 years, completed four questionnaires measuring obsessive compulsive disorder (OCD)-like symptoms, anxiety, challenging behaviors, and adaptive behavior and living skills. Results: Results revealed a high prevalence of neuropsychiatric and behavioral challenges across ages. We found specific challenging behaviors were worse in school age individuals. Scaled adaptive behavior and living skill scores differed across ages with an increased gap between typically developing peers becoming more apparent at older ages. Between types, individuals with RSTS2 had better adaptive behavior and living skills and less stereotypic behaviors but higher social phobia than individuals with RSTS1. Further, female individuals with RSTS1 appear to have increased hyperactivity. However, both groups had impairments in adaptive functioning compared to typically developing peers. Discussion: Our findings support and expand previous reports of a high prevalence of neuropsychiatric and behavioral challenges in individuals with RSTS. However, we are the first to report differences between types of RSTS. Further, age-related differences were seen with higher challenging behaviors within school-age individuals, which may improve over time, and lower adaptive behavioral skills compared to normative scales. Anticipation of these potential differential challenges across age is vital for proactive management for individuals with RSTS. Our study underscores the importance of enacting neuropsychiatric and behavioral screening earlier in childhood so appropriate management can be implemented. However, further longitudinal studies in larger cohorts are needed to understand better how behavioral and neuropsychiatric characteristics of RSTS evolve over the lifespan and differentially affect subpopulation groups.
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Affiliation(s)
- Dima Qu’d
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Lauren M. Schmitt
- Division of Behavioral Medicine and Clinical Psychology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Amber Leston
- University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Jacqueline R. Harris
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Division of Neurogenetics, Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, United States
| | - Anne Slavotinek
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Ilka Riddle
- University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Developmental and Behavioral Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Diana S. Brightman
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Brittany N. Simpson
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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16
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Slavotinek A, Rego S, Sahin-Hodoglugil N, Kvale M, Lianoglou B, Yip T, Hoban H, Outram S, Anguiano B, Chen F, Michelson J, Cilio RM, Curry C, Gallagher RC, Gardner M, Kuperman R, Mendelsohn B, Sherr E, Shieh J, Strober J, Tam A, Tenney J, Weiss W, Whittle A, Chin G, Faubel A, Prasad H, Mavura Y, Van Ziffle J, Devine WP, Hodoglugil U, Martin PM, Sparks TN, Koenig B, Ackerman S, Risch N, Kwok PY, Norton ME. Diagnostic yield of pediatric and prenatal exome sequencing in a diverse population. NPJ Genom Med 2023; 8:10. [PMID: 37236975 PMCID: PMC10220040 DOI: 10.1038/s41525-023-00353-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The diagnostic yield of exome sequencing (ES) has primarily been evaluated in individuals of European ancestry, with less focus on underrepresented minority (URM) and underserved (US) patients. We evaluated the diagnostic yield of ES in a cohort of predominantly US and URM pediatric and prenatal patients suspected to have a genetic disorder. Eligible pediatric patients had multiple congenital anomalies and/or neurocognitive disabilities and prenatal patients had one or more structural anomalies, disorders of fetal growth, or fetal effusions. URM and US patients were prioritized for enrollment and underwent ES at a single academic center. We identified definitive positive or probable positive results in 201/845 (23.8%) patients, with a significantly higher diagnostic rate in pediatric (26.7%) compared to prenatal patients (19.0%) (P = 0.01). For both pediatric and prenatal patients, the diagnostic yield and frequency of inconclusive findings did not differ significantly between URM and non-URM patients or between patients with US status and those without US status. Our results demonstrate a similar diagnostic yield of ES between prenatal and pediatric URM/US patients and non-URM/US patients for positive and inconclusive results. These data support the use of ES to identify clinically relevant variants in patients from diverse populations.
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Affiliation(s)
- Anne Slavotinek
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Shannon Rego
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Nuriye Sahin-Hodoglugil
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Billie Lianoglou
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Tiffany Yip
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Hoban
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Simon Outram
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Beatrice Anguiano
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Flavia Chen
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jeremy Michelson
- Institute of Human Nutrition, Columbia University Medical Center, New York, NY, USA
| | - Roberta M Cilio
- Division of Pediatric Neurology, Department of Pediatrics, University of Louvain, Brussels, Belgium
| | - Cynthia Curry
- Genetic Medicine, University of California, San Francisco, Fresno, CA, USA
| | - Renata C Gallagher
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marisa Gardner
- Department of Neurology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Rachel Kuperman
- Department of Neurology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
- Eysz, Inc, Piedmont, CA, USA
| | - Bryce Mendelsohn
- Division of Genetics, Kaiser Permanente Oakland Medical Center, Oakland, CA, USA
| | - Elliott Sherr
- Division of Child Neurology, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph Shieh
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Strober
- Division of Child Neurology, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Allison Tam
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Tenney
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - William Weiss
- Division of Child Neurology, Zuckerberg San Francisco General Hospital, San Francisco, San Francisco, CA, USA
| | - Amy Whittle
- Division of Pediatrics, Zuckerberg San Francisco General Hospital, San Francisco, San Francisco, CA, USA
| | - Garrett Chin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Amanda Faubel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Hannah Prasad
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yusuph Mavura
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Van Ziffle
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - W Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Ugur Hodoglugil
- Genomic Medicine Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Teresa N Sparks
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, San Francisco, USA
| | - Barbara Koenig
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Bioethics, University of California, San Francisco, San Francisco, CA, USA
| | - Sara Ackerman
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
- Department of Social & Behavioral Sciences, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, San Francisco, USA
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17
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Mavura Y, Sahin-Hodoglugil N, Hodoglugil U, Kvale M, Martin PM, Van Ziffle J, Devine WP, Ackerman SL, Koenig BA, Kwok PY, Norton ME, Slavotinek A, Risch N. Diagnostic Yield of Exome Sequencing in a Diverse Pediatric and Prenatal Population is not Associated with Genetic Ancestry. medRxiv 2023:2023.05.19.23290066. [PMID: 37293051 PMCID: PMC10246153 DOI: 10.1101/2023.05.19.23290066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Purpose It has been hypothesized that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental genetic ancestry in a racially/ethnically diverse pediatric and prenatal clinical cohort. Methods Cases (N=845) with suspected genetic disorders underwent ES for diagnosis. Continental genetic ancestry proportions were estimated from the ES data. We compared the distribution of genetic ancestries in positive, negative, and inconclusive cases by Kolmogorov Smirnov tests and linear associations of ancestry with DY by Cochran-Armitage trend tests. Results We observed no reduction in overall DY associated with any continental genetic ancestry (Africa, America, East Asia, Europe, Middle East, South Asia). However, we observed a relative increase in proportion of autosomal recessive homozygous inheritance versus other inheritance patterns associated with Middle Eastern and South Asian ancestry, due to consanguinity. Conclusions In this empirical study of ES for undiagnosed pediatric and prenatal genetic conditions, genetic ancestry was not associated with the likelihood of a positive diagnosis, supporting the ethical and equitable use of ES in diagnosis of previously undiagnosed but potentially Mendelian disorders across all ancestral populations.
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Affiliation(s)
- Yusuph Mavura
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
| | | | - Ugur Hodoglugil
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Jessica Van Ziffle
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
- Department of Pathology, University of California San Francisco, San Francisco, CA
| | - W. Patrick Devine
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
- Department of Pathology, University of California San Francisco, San Francisco, CA
| | - Sara L. Ackerman
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA
- Department of Social & Behavioral Sciences, School of Nursing, University of California San Francisco, San Francisco, CA
| | - Barbara A Koenig
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
- Program in Bioethics, University of California San Francisco, San Francisco, CA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
- Cardiovascular Research Institute and Department of Dermatology, University of California San Francisco, San Francisco, CA
| | - Mary E. Norton
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco CA
| | - Anne Slavotinek
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
- Department of Pediatrics, University of California, San Francisco, San Francisco CA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
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18
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Smallwood K, Watt KEN, Ide S, Baltrunaite K, Brunswick C, Inskeep K, Capannari C, Adam MP, Begtrup A, Bertola DR, Demmer L, Demo E, Devinsky O, Gallagher ER, Guillen Sacoto MJ, Jech R, Keren B, Kussmann J, Ladda R, Lansdon LA, Lunke S, Mardy A, McWalters K, Person R, Raiti L, Saitoh N, Saunders CJ, Schnur R, Skorvanek M, Sell SL, Slavotinek A, Sullivan BR, Stark Z, Symonds JD, Wenger T, Weber S, Whalen S, White SM, Winkelmann J, Zech M, Zeidler S, Maeshima K, Stottmann RW, Trainor PA, Weaver KN. POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies. Am J Hum Genet 2023; 110:809-825. [PMID: 37075751 PMCID: PMC10183370 DOI: 10.1016/j.ajhg.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/21/2023] [Indexed: 04/21/2023] Open
Abstract
Heterozygous pathogenic variants in POLR1A, which encodes the largest subunit of RNA Polymerase I, were previously identified as the cause of acrofacial dysostosis, Cincinnati-type. The predominant phenotypes observed in the cohort of 3 individuals were craniofacial anomalies reminiscent of Treacher Collins syndrome. We subsequently identified 17 additional individuals with 12 unique heterozygous variants in POLR1A and observed numerous additional phenotypes including neurodevelopmental abnormalities and structural cardiac defects, in combination with highly prevalent craniofacial anomalies and variable limb defects. To understand the pathogenesis of this pleiotropy, we modeled an allelic series of POLR1A variants in vitro and in vivo. In vitro assessments demonstrate variable effects of individual pathogenic variants on ribosomal RNA synthesis and nucleolar morphology, which supports the possibility of variant-specific phenotypic effects in affected individuals. To further explore variant-specific effects in vivo, we used CRISPR-Cas9 gene editing to recapitulate two human variants in mice. Additionally, spatiotemporal requirements for Polr1a in developmental lineages contributing to congenital anomalies in affected individuals were examined via conditional mutagenesis in neural crest cells (face and heart), the second heart field (cardiac outflow tract and right ventricle), and forebrain precursors in mice. Consistent with its ubiquitous role in the essential function of ribosome biogenesis, we observed that loss of Polr1a in any of these lineages causes cell-autonomous apoptosis resulting in embryonic malformations. Altogether, our work greatly expands the phenotype of human POLR1A-related disorders and demonstrates variant-specific effects that provide insights into the underlying pathogenesis of ribosomopathies.
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Affiliation(s)
- Kelly Smallwood
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Kristina Baltrunaite
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chad Brunswick
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Katherine Inskeep
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Corrine Capannari
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Margaret P Adam
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | | | - Laurie Demmer
- Atrium Health's Levine Children's Hospital, Charlotte, NC, USA
| | - Erin Demo
- Sibley Heart Center, Atlanta, GA, USA
| | - Orrin Devinsky
- Department of Neurology, Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Emily R Gallagher
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Boris Keren
- Genetic Department, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Jennifer Kussmann
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Roger Ladda
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA, USA
| | - Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy Research Institute, 2401 Gillham Road, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, USA
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Anne Mardy
- Department of Women's Health, University of Texas Austin Dell Medical Center, Austin, TX, USA
| | | | | | - Laura Raiti
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia
| | | | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy Research Institute, 2401 Gillham Road, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, USA
| | | | - Matej Skorvanek
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic; Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Susan L Sell
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Joseph D Symonds
- Paediatric Neuroscience Research Group, Royal Hospital for Children, Glasgow G667AB, UK
| | - Tara Wenger
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sacha Weber
- CCA-AHU de génétique clinique et de neurogénétique, Service de Génétique et de Neurologie, CHU de Caen, Caen, France
| | - Sandra Whalen
- Genetic Department, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - K Nicole Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Brin MF, Kirby RS, Slavotinek A, Adams AM, Parker L, Ukah A, Radulian L, Elmore MRP, Yedigarova L, Yushmanova I. Pregnancy Outcomes in Patients Exposed to OnabotulinumtoxinA Treatment: A Cumulative 29-Year Safety Update. Neurology 2023:WNL.0000000000207375. [PMID: 37137724 DOI: 10.1212/wnl.0000000000207375] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/20/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND AND OBJECTIVES A previous publication of pregnancy outcomes in onabotulinumtoxinA-exposed mothers demonstrated that the prevalence of major fetal defects (0.9%, 1/110) was comparable to background rates in the general population. There is continued interest to better understand the safety of onabotulinumtoxinA during pregnancy. This analysis evaluated pregnancy outcomes following onabotulinumtoxinA exposure to provide a cumulative 29-year update. METHODS The Allergan Global Safety Database was searched from 1/1/1990 to 12/31/2018. Data from women (<65 years or unknown) during pregnancy or ≤3 months prior to conception treated with onabotulinumtoxinA were assessed to estimate birth defect prevalence rates of live births only from prospective pregnancies. RESULTS Of 913 pregnancies, 397 (43.5%) were eligible with known outcomes. Maternal age was known in 215 pregnancies: 45.6% were ≥35 years. Indication was known in 340 pregnancies: most frequent were aesthetic (35.3%) and migraine/headache (30.3%). Timing of exposure was known in 318 pregnancies: 94.6% were prior to conception or during the first trimester. OnabotulinumtoxinA dose information was known in 242 pregnancies; the majority (83.5%) were exposed to <200 U. Of 195 prospective pregnancies with 197 fetuses, there were 152 (77.2%) live births and 45 (22.8%) fetal losses (32 spontaneous, 13 elective). Of 152 live births, 148 (97.4%) had normal outcomes, 4 had abnormal outcomes. Among the 4 abnormal outcomes, there were 1 major birth defect, 2 minor fetal defects, and 1 birth complication. The prevalence rate for overall fetal defects was 2.6% (4/152, 95% CI: 1.0-6.6%) and 0.7% (1/152, 95% CI: 0.1-3.6%) for major fetal defects (3-6% in the general population). Among cases of live births and known determinable exposure times, there was 1 birth defect with preconception exposure and 2 with first-trimester exposure. DISCUSSION Although subject to reporting bias due to the nature of the post-marketing database review, this 29-year retrospective analysis of safety data in pregnant women exposed to onabotulinumtoxinA demonstrates that the prevalence rate of major fetal defects among live births is consistent with rates reported in the general population. Even though there are limited data available for second- and third-trimester exposure, this updated and expanded safety analysis provides important real-world evidence to healthcare providers and their patients. CLASSIFICATION OF EVIDENCE This analysis provides Class III data that demonstrate that the prevalence rate of major fetal defects among live births subsequent to in utero onabotulinumtoxinA exposure is comparable to reported background rates.
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Affiliation(s)
- Mitchell F Brin
- Allergan, an AbbVie Company, Irvine, CA, USA
- University of California, Irvine, Department of Neurology, Irvine, CA, USA
| | - Russell S Kirby
- University of South Florida, College of Public Health, Tampa, FL, USA
| | - Anne Slavotinek
- University of California, San Francisco, Division of Medical Genetics, Department of Pediatrics, San Francisco, CA, USA
| | | | - Lori Parker
- Allergan, an AbbVie Company, Irvine, CA, USA
| | - Ahunna Ukah
- Allergan, an AbbVie Company, Irvine, CA, USA
| | - Lavinia Radulian
- Allergan, an AbbVie Company, Bucharest, Romania
- University of Medicine and Pharmacy, Carol Davila, Bucharest, Romania
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20
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Priestley JRC, Deshwar AR, Murthy H, D'Agostino MD, Dupuis L, Gangaram B, Gray C, Jobling R, Pannia E, Platzer K, Prescott K, Redman M, Rippert AL, Rosenfeld JA, Scott DA, Wang YW, Schmederer Z, Dalal A, Sarma AS, Skraban C, Dowling JJ, Mendoza-Londono R, Slavotinek A, Bhoj EJ. Monoallelic Loss of Function BMP2 Variants Result in BMP2-Related Skeletal Dysplasia Spectrum. Genet Med 2023:100863. [PMID: 37125634 DOI: 10.1016/j.gim.2023.100863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023] Open
Abstract
PURPOSE Bone morphogenic proteins (BMPs) regulate gene expression related to many critical developmental processes, including osteogenesis for which they are named. BMP2 is widely expressed in cells of mesenchymal origin, including bone, cartilage, skeletal and cardiac muscle, and adipose tissue. It also participates in neurodevelopment by inducing differentiation of neural stem cells. In humans, BMP2 variants result in a multiple congenital anomaly syndrome through a haploinsufficiency mechanism. We sought to expand the phenotypic spectrum and highlight phenotypes of patients harboring monoallelic missense variants in BMP2. METHODS We employed retrospective chart review to examine phenotypes from an international cohort of 18 individuals and compared these to published cases. Patient-derived missense variants were modeled in zebrafish to examine their effect on the ability of bmp2b to promote embryonic ventralization. RESULTS The presented cases recapitulated existing descriptions of BMP2-related disorder including craniofacial, cardiac, and skeletal anomalies and exhibit a wide phenotypic spectrum. We also identified patients with neural tube defects, structural brain anomalies, and endocrinopathies. Missense variants modeled in zebrafish resulted in loss of protein function. CONCLUSIONS We use this expansion of reported phenotypes to suggest multidisciplinary medical monitoring and management of patients with BMP2-related skeletal dysplasia spectrum.
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Affiliation(s)
- Jessica R C Priestley
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ashish R Deshwar
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Harsha Murthy
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria Daniela D'Agostino
- Division of Medical Genetics, Departments of Specialized Medicine and Human Genetics, McGill University Health Center, Montreal, Quebec, Canada
| | - Lucie Dupuis
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Balram Gangaram
- Division of Medical Genetics, University of California San Francisco, San Francisco, California, USA
| | - Christopher Gray
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rebekah Jobling
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada; Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Emanuela Pannia
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Katrina Prescott
- Clinical Genetics, The Leeds Teaching Hospital NHS Trust, Leeds, West Yorkshire, UK
| | - Melody Redman
- Clinical Genetics, The Leeds Teaching Hospital NHS Trust, Leeds, West Yorkshire, UK
| | - Alyssa L Rippert
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Baylor Genetics Laboratories, Houston, Texas, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Yi Wen Wang
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada; Division of Medical Genetics, Departments of Specialized Medicine and Human Genetics, McGill University Health Center, Montreal, Quebec, Canada
| | - Zelia Schmederer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany; Medizinisch Genetisches Zentrum, Munich, Germany
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Asodu Sandeep Sarma
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Cara Skraban
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James J Dowling
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Anne Slavotinek
- Division of Medical Genetics, University of California San Francisco, San Francisco, California, USA; Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Elizabeth J Bhoj
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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21
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Truty R, Rojahn S, Ouyang K, Kautzer C, Kennemer M, Pineda-Alvarez D, Johnson B, Stafford A, Basel-Salmon L, Saitta S, Slavotinek A, Chandrasekharappa SC, Suarez CJ, Burnett L, Nussbaum RL, Aradhya S. Patterns of mosaicism for sequence and copy-number variants discovered through clinical deep sequencing of disease-related genes in one million individuals. Am J Hum Genet 2023; 110:551-564. [PMID: 36933558 PMCID: PMC10119133 DOI: 10.1016/j.ajhg.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
DNA variants that arise after conception can show mosaicism, varying in presence and extent among tissues. Mosaic variants have been reported in Mendelian diseases, but further investigation is necessary to broadly understand their incidence, transmission, and clinical impact. A mosaic pathogenic variant in a disease-related gene may cause an atypical phenotype in terms of severity, clinical features, or timing of disease onset. Using high-depth sequencing, we studied results from one million unrelated individuals referred for genetic testing for almost 1,900 disease-related genes. We observed 5,939 mosaic sequence or intragenic copy number variants distributed across 509 genes in nearly 5,700 individuals, constituting approximately 2% of molecular diagnoses in the cohort. Cancer-related genes had the most mosaic variants and showed age-specific enrichment, in part reflecting clonal hematopoiesis in older individuals. We also observed many mosaic variants in genes related to early-onset conditions. Additional mosaic variants were observed in genes analyzed for reproductive carrier screening or associated with dominant disorders with low penetrance, posing challenges for interpreting their clinical significance. When we controlled for the potential involvement of clonal hematopoiesis, most mosaic variants were enriched in younger individuals and were present at higher levels than in older individuals. Furthermore, individuals with mosaicism showed later disease onset or milder phenotypes than individuals with non-mosaic variants in the same genes. Collectively, the large compendium of variants, disease correlations, and age-specific results identified in this study expand our understanding of the implications of mosaic DNA variation for diagnosis and genetic counseling.
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Affiliation(s)
- Rebecca Truty
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Karen Ouyang
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | | | | | - Britt Johnson
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | - Lina Basel-Salmon
- Rabin Medical Center-Beilinson Hospital and Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carlos Jose Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; School of Medicine, University of California - San Francisco, San Francisco, CA, USA
| | - Swaroop Aradhya
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA.
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22
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Wigby K, Hammer M, Tokita M, Patel P, Jones MC, Larson A, Bartolomei FV, Dykzeul N, Slavotinek A, Yip T, Bandres-Ciga S, Simpson BN, Suhrie K, Shankar S, Veith R, Bragg J, Powell C, Kingsmore SF, Dimmock D, Maron J, Davis J, Del Campo M. Insights into the perinatal phenotype of Kabuki syndrome in infants identified by genome-wide sequencing. Am J Med Genet A 2023; 191:930-940. [PMID: 36651673 DOI: 10.1002/ajmg.a.63097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 01/19/2023]
Abstract
Increasing use of unbiased genomic sequencing in critically ill infants can expand understanding of rare diseases such as Kabuki syndrome (KS). Infants diagnosed with KS through genome-wide sequencing performed during the initial hospitalization underwent retrospective review of medical records. Human phenotype ontology terms used in genomic analysis were aggregated and analyzed. Clinicians were surveyed regarding changes in management and other care changes. Fifteen infants met inclusion criteria. KS was not suspected prior to genomic sequencing. Variants were classified as Pathogenic (n = 10) or Likely Pathogenic (n = 5) by American College of Medical Genetics and Genomics Guidelines. Fourteen variants were de novo (KMT2D, n = 12, KDM6A, n = 2). One infant inherited a likely pathogenic variant in KMT2D from an affected father. Frequent findings involved cardiovascular (14/15) and renal (7/15) systems, with palatal defects also identified (6/15). Three infants had non-immune hydrops. No minor anomalies were universally documented; ear anomalies, micrognathia, redundant nuchal skin, and hypoplastic nails were common. Changes in management were reported in 14 infants. Early use of unbiased genome-wide sequencing enabled a molecular diagnosis prior to clinical recognition including infants with atypical or rarely reported features of KS while also expanding the phenotypic spectrum of this rare disorder.
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Affiliation(s)
- Kristen Wigby
- Department of Pediatrics, Division of Genetics, University of California, San Diego and Rady Children's Hospital-San Diego, San Diego, California, USA.,Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Monia Hammer
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Mari Tokita
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Priyanka Patel
- Department of Pediatrics, Division of Genetics, University of California, San Diego and Rady Children's Hospital-San Diego, San Diego, California, USA
| | - Marilyn C Jones
- Department of Pediatrics, Division of Genetics, University of California, San Diego and Rady Children's Hospital-San Diego, San Diego, California, USA
| | - Austin Larson
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Frances Velez Bartolomei
- Torre Medica del San Jorge Hospital, San Juan, Puerto Rico, USA.,Department of Pediatrics, Division of Genetics, Stanford University, Palo Alto, California, USA
| | - Natalie Dykzeul
- Department of Pediatrics, Division of Genetics, Stanford University, Palo Alto, California, USA
| | - Anne Slavotinek
- Department of Pediatrics, Division of Genetics, University of California San Francisco, San Francisco, California, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Tiffany Yip
- Department of Pediatrics, Division of Genetics, University of California San Francisco, San Francisco, California, USA
| | - Sara Bandres-Ciga
- Center for Alzheimer's Disease and Related Dementias (CARD), National Institute on Aging (NIA), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Brittany N Simpson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Kristen Suhrie
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Genetics, Division of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Suma Shankar
- Department of Pediatrics, Division of Genetics, University of California, Davis, Sacramento, California, USA
| | - Regan Veith
- Children's Minnesota, Minneapolis, Minnesota, USA
| | - Jennifer Bragg
- Department of Pediatrics, Division of Newborn Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Cynthia Powell
- Department of Pediatrics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | - Jill Maron
- Mother Infant Research Institute, Tufts Medical Center, Boston, Massachusetts, USA.,Department of Pediatrics, The Floating Hospital for Children at Tufts Medical Center, Boston, Massachusetts, USA.,Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Jonathan Davis
- Department of Pediatrics, The Floating Hospital for Children at Tufts Medical Center, Boston, Massachusetts, USA.,The Tufts Clinical and Translation Science Institute, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Miguel Del Campo
- Department of Pediatrics, Division of Genetics, University of California, San Diego and Rady Children's Hospital-San Diego, San Diego, California, USA
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23
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Penon-Portmann M, Hodoglugil U, Arun P W, Yip T, Slavotinek A, Tenney JL. TRAPPC9-related neurodevelopmental disorder: Report of a homozygous deletion in TRAPPC9 due to paternal uniparental isodisomy. Am J Med Genet A 2023; 191:1077-1082. [PMID: 36574751 DOI: 10.1002/ajmg.a.63100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/24/2022] [Accepted: 12/11/2022] [Indexed: 12/28/2022]
Abstract
TRAPPC9 loss-of-function biallelic variants are associated with an autosomal recessive intellectual disability syndrome (Online Mendelian Inheritance of Man no. 613192), also characterized by microcephaly, hypertelorism, obesity, growth delay, and behavioral differences. Here, we describe an 8-year-old Hispanic female with neurodevelopmental disorder, partial epilepsy, microcephaly, bilateral cleft lip and alveolus, growth delay, and dysmorphic features. She had abnormal myelination, mega cisterna magna, and colpocephaly on brain magnetic resonance imaging (MRI). Microarray showed a single ~146 Mb region of homozygosity (ROH) encompassing all of Chromosome 8, consistent with uniparental isodisomy (UPD). Exome sequencing performed in-house did not identify single nucleotide variants to explain her phenotype. Algorithms developed in-house and further evaluation of BAM files revealed a homozygous deletion overlapping Exon 2 in TRAPPC9 within the ROH. Subsequent del/dup analyses with exon-level oligo array confirmed a likely pathogenic deletion in TRAPPC9 (NM_031466.5): arr[GRCh37] 8q24.3(141460661_141461780)x0. Our case highlights the implications of downstream analyses from UPD/ROH given the increased risk for AR conditions, the strengths of combining orthologous molecular methods to establish a diagnosis and further delineates the TRAPPC9-related phenotype in an individual of Hispanic ancestry.
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Affiliation(s)
- Monica Penon-Portmann
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Ugur Hodoglugil
- Genomic Medicine Laboratory, University of California San Francisco, San Francisco, California, USA
| | - Wiita Arun P
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Tiffany Yip
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA.,Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jessica L Tenney
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
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24
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Adutwum M, Hurst A, Mirzaa G, Kushner JD, Rogers C, Khalek N, Cristancho AG, Burrill N, Seifert ME, Scarano MI, Schnur RE, Slavotinek A. Six new cases of CRB2-related syndrome and a review of clinical findings in 28 reported patients. Clin Genet 2023; 103:97-102. [PMID: 36071576 DOI: 10.1111/cge.14222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 12/14/2022]
Abstract
The Crumbs homolog-2 (CRB2)-related syndrome (CRBS-RS) is a rarely encountered condition initially described as a triad comprising ventriculomegaly, Finnish nephrosis, and elevated alpha-fetoprotein levels in maternal serum and amniotic fluid. CRB2-related syndrome is caused by biallelic, pathogenic variants in the CRB2 gene. Recent reports of CRB2-RS have highlighted renal disease with persistent proteinuria and steroid-resistant nephrotic syndrome (SRNS). We report six new and review 28 reported patients with pathogenic variants in CRB2. We compare clinical features and variant information in CRB2 in patients with CRB2-RS and in those with isolated renal disease. The kidneys were the most frequently involved body system and 11 patients had only renal manifestations with SRNS or nephrotic syndrome. Central nervous system involvement was the next most common manifestation, followed by cardiac findings that included Scimitar syndrome. There was a significant clustering of pathogenic variants for CRB2-RS in exons 8 and 10, whereas pathogenic variants in exons 12 and 13 were associated with isolated renal disease. Further information is needed to determine optimal management but monitoring for renal and ocular complications should be considered.
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Affiliation(s)
- Michelle Adutwum
- Children's Hospital Oakland Research Institute Summer Program, University of California San Francisco, San Francisco, California, USA
| | - Anna Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Jessica D Kushner
- Department of Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Caleb Rogers
- Department of Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Nahla Khalek
- Wood Center for Fetal Diagnosis and Treatment, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ana G Cristancho
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Natalie Burrill
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael E Seifert
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Maria I Scarano
- Department of Pediatrics, Cooper University Health Care, Camden, New Jersey, USA
| | - Rhonda E Schnur
- Department of Pediatrics, Cooper University Health Care, Camden, New Jersey, USA.,Cooper Medical School of Rowan University, Camden, New Jersey, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
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25
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Sparks TN, Lianoglou BR, Hodoglugil NS, Swanson K, Downum SL, Slavotinek A, Devine P, Hodoglugil U, Van Ziffle J, Norton ME. Deep phenotyping expands our knowledge of fetal manifestations of genetic disease. Am J Obstet Gynecol 2023. [DOI: 10.1016/j.ajog.2022.11.1251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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26
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Fasano G, Muto V, Radio FC, Venditti M, Mosaddeghzadeh N, Coppola S, Paradisi G, Zara E, Bazgir F, Ziegler A, Chillemi G, Bertuccini L, Tinari A, Vetro A, Pantaleoni F, Pizzi S, Conti LA, Petrini S, Bruselles A, Prandi IG, Mancini C, Chandramouli B, Barth M, Bris C, Milani D, Selicorni A, Macchiaiolo M, Gonfiantini MV, Bartuli A, Mariani R, Curry CJ, Guerrini R, Slavotinek A, Iascone M, Dallapiccola B, Ahmadian MR, Lauri A, Tartaglia M. Dominant ARF3 variants disrupt Golgi integrity and cause a neurodevelopmental disorder recapitulated in zebrafish. Nat Commun 2022; 13:6841. [PMID: 36369169 PMCID: PMC9652361 DOI: 10.1038/s41467-022-34354-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
Vesicle biogenesis, trafficking and signaling via Endoplasmic reticulum-Golgi network support essential developmental processes and their disruption lead to neurodevelopmental disorders and neurodegeneration. We report that de novo missense variants in ARF3, encoding a small GTPase regulating Golgi dynamics, cause a developmental disease in humans impairing nervous system and skeletal formation. Microcephaly-associated ARF3 variants affect residues within the guanine nucleotide binding pocket and variably perturb protein stability and GTP/GDP binding. Functional analysis demonstrates variably disruptive consequences of ARF3 variants on Golgi morphology, vesicles assembly and trafficking. Disease modeling in zebrafish validates further the dominant behavior of the mutants and their differential impact on brain and body plan formation, recapitulating the variable disease expression. In-depth in vivo analyses traces back impaired neural precursors' proliferation and planar cell polarity-dependent cell movements as the earliest detectable effects. Our findings document a key role of ARF3 in Golgi function and demonstrate its pleiotropic impact on development.
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Affiliation(s)
- Giulia Fasano
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Valentina Muto
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Clementina Radio
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Martina Venditti
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Niloufar Mosaddeghzadeh
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Simona Coppola
- grid.416651.10000 0000 9120 6856National Center for Rare Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Graziamaria Paradisi
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy ,grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Erika Zara
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy ,grid.7841.aDepartment of Biology and Biotechnology “Charles Darwin”, Università “Sapienza”, Rome, 00185 Italy
| | - Farhad Bazgir
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alban Ziegler
- grid.7252.20000 0001 2248 3363UFR Santé de l’Université d’Angers, INSERM U1083, CNRS UMR6015, MITOVASC, SFR ICAT, F-49000 Angers, France ,grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Giovanni Chillemi
- grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy ,grid.5326.20000 0001 1940 4177Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Centro Nazionale delle Ricerche, 70126 Bari, Italy
| | - Lucia Bertuccini
- grid.416651.10000 0000 9120 6856Servizio grandi strumentazioni e core facilities, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonella Tinari
- grid.416651.10000 0000 9120 6856Centro di riferimento per la medicina di genere, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Annalisa Vetro
- grid.8404.80000 0004 1757 2304Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy
| | - Francesca Pantaleoni
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Libenzio Adrian Conti
- grid.414603.4Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- grid.414603.4Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Alessandro Bruselles
- grid.416651.10000 0000 9120 6856Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Ingrid Guarnetti Prandi
- grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Cecilia Mancini
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Balasubramanian Chandramouli
- grid.431603.30000 0004 1757 1950Super Computing Applications and Innovation, CINECA, 40033 Casalecchio di Reno, Italy
| | - Magalie Barth
- grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Céline Bris
- grid.7252.20000 0001 2248 3363UFR Santé de l’Université d’Angers, INSERM U1083, CNRS UMR6015, MITOVASC, SFR ICAT, F-49000 Angers, France ,grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Donatella Milani
- grid.414818.00000 0004 1757 8749Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Angelo Selicorni
- grid.512106.1Mariani Center for Fragile Children Pediatric Unit, Azienda Socio Sanitaria Territoriale Lariana, 22100 Como, Italy
| | - Marina Macchiaiolo
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michaela V. Gonfiantini
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Bartuli
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Riccardo Mariani
- grid.414603.4Department of Laboratories Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Cynthia J. Curry
- grid.266102.10000 0001 2297 6811Genetic Medicine, Dept of Pediatrics, University of California San Francisco, Ca, Fresno, Ca, San Francisco, CA 94143 USA
| | - Renzo Guerrini
- grid.8404.80000 0004 1757 2304Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy
| | - Anne Slavotinek
- grid.266102.10000 0001 2297 6811Genetic Medicine, Dept of Pediatrics, University of California San Francisco, Ca, Fresno, Ca, San Francisco, CA 94143 USA
| | - Maria Iascone
- grid.460094.f0000 0004 1757 8431Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Bruno Dallapiccola
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Mohammad Reza Ahmadian
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Antonella Lauri
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marco Tartaglia
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
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27
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Ferket BS, Baldwin Z, Murali P, Pai A, Mittendorf KF, Russell HV, Chen F, Lynch FL, Lich KH, Hindorff LA, Savich R, Slavotinek A, Smith HS, Gelb BD, Veenstra DL. Cost-effectiveness frameworks for comparing genome and exome sequencing versus conventional diagnostic pathways: A scoping review and recommended methods. Genet Med 2022; 24:2014-2027. [PMID: 35833928 PMCID: PMC9997042 DOI: 10.1016/j.gim.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Methodological challenges have limited economic evaluations of genome sequencing (GS) and exome sequencing (ES). Our objective was to develop conceptual frameworks for model-based cost-effectiveness analyses (CEAs) of diagnostic GS/ES. METHODS We conducted a scoping review of economic analyses to develop and iterate with experts a set of conceptual CEA frameworks for GS/ES for prenatal testing, early diagnosis in pediatrics, diagnosis of delayed-onset disorders in pediatrics, genetic testing in cancer, screening of newborns, and general population screening. RESULTS Reflecting on 57 studies meeting inclusion criteria, we recommend the following considerations for each clinical scenario. For prenatal testing, performing comparative analyses of costs of ES strategies and postpartum care, as well as genetic diagnoses and pregnancy outcomes. For early diagnosis in pediatrics, modeling quality-adjusted life years (QALYs) and costs over ≥20 years for rapid turnaround GS/ES. For hereditary cancer syndrome testing, modeling cumulative costs and QALYs for the individual tested and first/second/third-degree relatives. For tumor profiling, not restricting to treatment uptake or response and including QALYs and costs of downstream outcomes. For screening, modeling lifetime costs and QALYs and considering consequences of low penetrance and GS/ES reanalysis. CONCLUSION Our frameworks can guide the design of model-based CEAs and ultimately foster robust evidence for the economic value of GS/ES.
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Affiliation(s)
- Bart S Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Zach Baldwin
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
| | - Priyanka Murali
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, University of Washington, Seattle, WA
| | - Akila Pai
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kathleen F Mittendorf
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Heidi V Russell
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX; Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Flavia Chen
- Program in Bioethics, University of California San Francisco, San Francisco, CA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | | | - Kristen Hassmiller Lich
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Renate Savich
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS; Division of Neonatology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Anne Slavotinek
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Bruce D Gelb
- Departments of Pediatrics and Genetics & Genomic Sciences, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - David L Veenstra
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
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28
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Galarreta CI, Kennedy C, Blair DR, Slavotinek A. Expanding the phenotype of PIK3C2A related syndrome: Report of two siblings with novel features and genotype. Am J Med Genet A 2022; 188:2724-2731. [PMID: 35770347 DOI: 10.1002/ajmg.a.62881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/05/2022] [Accepted: 04/15/2022] [Indexed: 01/25/2023]
Abstract
A pair of siblings was ascertained due to multiple congenital anomalies, including strikingly similar facial, skeletal, and ocular abnormalities. Exome sequencing of both the children and their mother revealed two novel PIK3C2A variants in the siblings, c.4381delC (p.Arg1461Glufs*31) and c.1555C > T (p.Arg519Ter). PIK3C2A belongs to the Class IIa family of Phosphatidylinositol-3-kinases, which create second messenger lipids that regulate a wide range of downstream signaling pathways involved in cell growth, survival and migration. Tiosano et al. (2019) identified the first monogenic disorder associated with biallelic PIK3C2A loss-of-function variants (oculoskeletodental syndrome). The novel syndrome was characterized by short stature, coarse facial features, ocular and skeletal abnormalities. This report describes two additional siblings affected by the PIK3C2A-related syndrome, confirms core clinical features, establishes intrafamilial variability and expands the phenotype to include proteinuria.
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Affiliation(s)
- Carolina I Galarreta
- Medical Genetics and Metabolism Department, Valley Children's Hospital, Madera, California, USA
| | - Colleen Kennedy
- Medical Genetics and Metabolism Department, Valley Children's Hospital, Madera, California, USA
| | - David R Blair
- Department of Pediatrics, Division of Genetics, University of California, San Francisco, California, USA
| | - Anne Slavotinek
- Department of Pediatrics, Division of Genetics, University of California, San Francisco, California, USA
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29
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Kortbawi H, Ames E, Pritchard A, Devine P, van Ziffle J, Slavotinek A. Further description of two patients with biallelic variants in NADSYN1 in association with cardiac and vertebral anomalies. Am J Med Genet A 2022; 188:2479-2484. [PMID: 35491967 DOI: 10.1002/ajmg.a.62765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 01/04/2023]
Abstract
Congenital nicotinamide adenine dinucleotide (NAD) deficiency disorders are associated with pathogenic variants in the genes NADSYN1, HAAO, and KYNU. These disorders overlap with the anomalies present in vertebral, anal, cardiac, tracheoesophageal, radial and renal, and limb anomalies (VATER/VACTERL) association and often result in premature death. Children who survive typically have developmental delays or intellectual disability. Here, we describe two patients with compound heterozygous variants in NADSYN1 who presented with cardiac and vertebral defects overlapping with the VATER/VACTERL association, although the patients did not satisfy criteria for the diagnosis of VATER/VACTERL due to their lack of limb anomalies and significant renal anomalies. One patient survived into childhood with developmental delays and may represent an expansion of the survival data for NADSYN1-associated NAD deficiency disorders. Interestingly, one patient had hypoplastic left heart syndrome (HLHS) and one had an aortic coarctation and transverse hypoplasia of the aortic arch, suggesting that NADSYN1 sequencing should be performed in children presenting with congenital anomalies related to VATER/VACTERL association and with HLHS and aortic arch abnormalities.
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Affiliation(s)
- Hannah Kortbawi
- School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Elizabeth Ames
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, C. S. Mott Children's Hospital, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Amanda Pritchard
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, C. S. Mott Children's Hospital, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Jessica van Ziffle
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
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30
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Slavotinek A, Prasad H, Yip T, Rego S, Hoban H, Kvale M. Predicting genes from phenotypes using human phenotype ontology (HPO) terms. Hum Genet 2022; 141:1749-1760. [PMID: 35357580 DOI: 10.1007/s00439-022-02449-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/16/2022] [Indexed: 11/28/2022]
Abstract
The interpretation of genomic variants following whole exome sequencing (WES) can be aided using human phenotype ontology (HPO) terms to standardize clinical features and predict causative genes. We performed WES on 453 patients diagnosed prior to 18 years of age and identified 114 pathogenic (P) or likely pathogenic (LP) variants in 112 patients. We utilized PhenoDB to extract HPO terms from provider notes and then used Phen2Gene to generate a gene score and gene ranking from each list of HPO terms. We assigned Phen2Gene gene rankings to 6 rank classes, with class 1 covering raw gene rankings of 1 to 10 and class 2 covering rankings from 11 to 50 out of a total of 17,126 possible gene rankings. Phen2Gene ranked causative genes into rank class 1 or 2 in 27.7% of cases and the genes in rank class 1 were all associated with well-characterized phenotypes. We found significant associations between the gene score and the number of years, since the gene was first published, the number of HPO terms with an hierarchical depth greater or equal to 11, and the number of Online Mendelian Inheritance in Man terms associated with the phenotype and gene. We conclude that genes associated with recognizable phenotypes and terms deep in the HPO hierarchy have the best chance of producing a high gene score and ranking in class 1 to 2 using Phen2Gene software with HPO terms. Clinicians and laboratory staff should consider these results when HPO terms are employed to prioritize candidate genes.
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Affiliation(s)
- Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
| | - Hannah Prasad
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Tiffany Yip
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Shannon Rego
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Hoban
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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31
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Chenbhanich J, Slavotinek A, Tam A. Impact of the COVID-19 pandemic on medical genetics and genomics training: Perspective from clinical trainees. Am J Med Genet A 2022; 188:1997-2004. [PMID: 35338572 PMCID: PMC9082060 DOI: 10.1002/ajmg.a.62736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/02/2022] [Accepted: 03/15/2022] [Indexed: 12/30/2022]
Abstract
We sought to understand how the coronavirus disease 2019 (COVID‐19) pandemic has affected the well‐being, clinical training, and medical education for clinical trainees in medical genetics and genomics residency and fellowship programs. All clinical genetics trainees in the Accreditation Council for Graduate Medical Education (ACGME)‐accredited training programs were invited to complete a survey. 31 out of 174 trainees completed the survey. With regards to well‐being, 18 trainees reported increased anxiety, 10 had increased depression, 3 increased financial strain, 13 worsening work‐life balance, and 13 worsening physical health. There was increased telehealth utilization in both outpatient (3% before the pandemic vs. 67% during the pandemic) and inpatient clinical encounters (0% vs. 29%). The most commonly reported challenges in telehealth use were inadequate physical examination and technical problems during visits. Twenty trainees believed that the pandemic has negatively impacted overall clinical training while none reported a positive impact. We concluded that the COVID‐19 pandemic has negatively impacted most clinical genetics trainees in ACGME‐accredited training programs. Telehealth has been increasingly used with some challenges. Further studies are needed on how to optimally integrate what we have learned into the training of medical genetics and genomics in the post‐pandemic era.
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Affiliation(s)
- Jirat Chenbhanich
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Allison Tam
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
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32
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Ferket B, Baldwin Z, Murali P, Pai A, Russell H, Lynch F, Lich KH, Hindorff L, Slavotinek A, Gelb B, Veenstra D, Smith H. eP516: Cost-effectiveness frameworks for comparing genome and exome sequencing versus conventional diagnostic pathways. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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33
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Penon-Portmann M, Carlston CM, Martin PM, Slavotinek A. Exome Sequencing Identifies a Novel <b><i>SIN3A</i></b> Variant in a Patient with Witteveen-Kolk Syndrome. Mol Syndromol 2022; 13:337-342. [PMID: 36158056 PMCID: PMC9421682 DOI: 10.1159/000520042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
Witteveen-Kolk syndrome (WITKOS; OMIM #613406) is a recently described, rare neurodevelopmental syndrome characterized by mild intellectual disability and a recognizable facial gestalt. WITKOS is caused by heterozygous loss-of-function variants in SIN3A. It shares some features with 15q24 deletion syndrome but to date has only been described in a limited number of patients mostly of Northern European ancestry. Here, we report the first patient with Hispanic ancestry to our knowledge diagnosed with WITKOS, who has a novel, truncating variant in the SIN3A gene. Clinical exome sequencing performed in-house using a custom bioinformatics pipeline identified a de novo heterozygous, nonsense variant in SIN3A, c.1015C>T (p.Gln339Ter) that has not been previously described in the literature. This 3-year-old boy with WITKOS demonstrated classic features including mild developmental delay and triangular facies with hypotelorism and deep-set, hooded eyes. This patient supports the currently described phenotype for WITKOS in more diverse populations.
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Affiliation(s)
- Monica Penon-Portmann
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Colleen M. Carlston
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
- *Anne Slavotinek,
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34
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Slavotinek A, Lefebvre M, Brehin AC, Thauvin C, Patrier S, Sparks TN, Norton M, Yu J, Huang E. Prenatal presentation of multiple anomalies associated with haploinsufficiency for ARID1A. Eur J Med Genet 2022; 65:104407. [PMID: 34942405 PMCID: PMC9162882 DOI: 10.1016/j.ejmg.2021.104407] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 11/04/2021] [Accepted: 12/14/2021] [Indexed: 02/03/2023]
Abstract
The ARID1A gene is an infrequent cause of Coffin-Siris syndrome (CSS) and has been associated with severe to profound developmental delays and hypotonia in addition to characteristic craniofacial and digital findings. We present three fetuses and a male neonate with ventriculomegaly/hydrocephalus, absence of the corpus callosum (ACC), cerebellar hypoplasia, retinal dysplasia, lung lobulation defects, renal dysplasia, imperforate or anteriorly placed anus, thymus hypoplasia and a single umbilical artery. Facial anomalies included downslanting palpebral fissures, wide-spaced eyes, low-set and posteriorly rotated ears, a small jaw, widely spaced nipples and hypoplastic nails. All fetuses had heterozygous variants predicting premature protein truncation in ARID1A (c.4886dup:p.Val1630Cysfs*18; c.4860dup:p.Pro1621Thrfs*27; and c.175G>T:p.Glu59*) and the baby's microarray demonstrated mosaicism for a deletion at chromosome 1p36.11 (arr[GRCh37] 1p36.11(26,797,508_27,052,080)×1∼2), that contained the first exon of ARID1A. Although malformations, in particular ACC, have been described with CSS caused by pathogenic variants in ARID1A, prenatal presentations associated with this gene are rare. Retinal dysplasia, lung lobulation defects and absent thymus were novel findings in association with ARID1A variants. Studies in cancer have demonstrated that pathogenic ARID1A variants hamper nuclear import of the protein and/or affect interaction with the subunits of SWI/SNF complex, resulting in dysregulation of the PI3K/AKT pathway and perturbed PTEN and PIKC3A signaling. As haploinsufficiency for PTEN and PIKC3A can be associated with ventriculomegaly/hydrocephalus, aberrant expression of these genes is a putative mechanism for the brain malformations demonstrated in patients with ARID1A variants.
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Affiliation(s)
- Anne Slavotinek
- Dept. Pediatrics, University of California San Francisco, San Francisco, CA, 94143, USA, Corresponding author. (A. Slavotinek)
| | - Mathilde Lefebvre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231, Génétique des Anomalies du Développement, Dijon, France
| | | | - Christel Thauvin
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231, Génétique des Anomalies du Développement, Dijon, France
| | - Sophie Patrier
- Department of Pathology, CHU Rouen, F-76000, Rouen, France
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mary Norton
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jingwei Yu
- Dept. Cytogenetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Huang
- Dept. Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
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35
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Minatogawa M, Unzaki A, Morisaki H, Syx D, Sonoda T, Janecke AR, Slavotinek A, Voermans NC, Lacassie Y, Mendoza-Londono R, Wierenga KJ, Jayakar P, Gahl WA, Tifft CJ, Figuera LE, Hilhorst-Hofstee Y, Maugeri A, Ishikawa K, Kobayashi T, Aoki Y, Ohura T, Kawame H, Kono M, Mochida K, Tokorodani C, Kikkawa K, Morisaki T, Kobayashi T, Nakane T, Kubo A, Ranells JD, Migita O, Sobey G, Kaur A, Ishikawa M, Yamaguchi T, Matsumoto N, Malfait F, Miyake N, Kosho T. Clinical and molecular features of 66 patients with musculocontractural Ehlers-Danlos syndrome caused by pathogenic variants in CHST14 (mcEDS- CHST14). J Med Genet 2021; 59:865-877. [PMID: 34815299 PMCID: PMC9411915 DOI: 10.1136/jmedgenet-2020-107623] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 09/25/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Musculocontractural Ehlers-Danlos syndrome is caused by biallelic loss-of-function variants in CHST14 (mcEDS-CHST14) or DSE (mcEDS-DSE). Although 48 patients in 33 families with mcEDS-CHST14 have been reported, the spectrum of pathogenic variants, accurate prevalence of various manifestations and detailed natural history have not been systematically investigated. METHODS We collected detailed and comprehensive clinical and molecular information regarding previously reported and newly identified patients with mcEDS-CHST14 through international collaborations. RESULTS Sixty-six patients in 48 families (33 males/females; 0-59 years), including 18 newly reported patients, were evaluated. Japanese was the predominant ethnicity (27 families), associated with three recurrent variants. No apparent genotype-phenotype correlation was noted. Specific craniofacial (large fontanelle with delayed closure, downslanting palpebral fissures and hypertelorism), skeletal (characteristic finger morphologies, joint hypermobility, multiple congenital contractures, progressive talipes deformities and recurrent joint dislocation), cutaneous (hyperextensibility, fine/acrogeria-like/wrinkling palmar creases and bruisability) and ocular (refractive errors) features were observed in most patients (>90%). Large subcutaneous haematomas, constipation, cryptorchidism, hypotonia and motor developmental delay were also common (>80%). Median ages at the initial episode of dislocation or large subcutaneous haematoma were both 6 years. Nine patients died; their median age was 12 years. Several features, including joint and skin characteristics (hypermobility/extensibility and fragility), were significantly more frequent in patients with mcEDS-CHST14 than in eight reported patients with mcEDS-DSE. CONCLUSION This first international collaborative study of mcEDS-CHST14 demonstrated that the subtype represents a multisystem disorder with unique set of clinical phenotypes consisting of multiple malformations and progressive fragility-related manifestations; these require lifelong, multidisciplinary healthcare approaches.
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Affiliation(s)
- Mari Minatogawa
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Ai Unzaki
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan.,Problem-Solving Oriented Training Program for Advanced Medical Personnel: NGSD (Next Generation Super Doctor) Project, Matsumoto, Japan
| | - Hiroko Morisaki
- Department of Medical Genetics, Sakakibara Heart Institute, Tokyo, Japan.,Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Delfien Syx
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tohru Sonoda
- Department of Occupational Therapy, School of Health and Science, Kyushu University of Health and Welfare, Nobeoka, Japan
| | - Andreas R Janecke
- Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Austria.,Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Yves Lacassie
- Department of Pediatrics, Louisiana State University Health Science Center, New Orleans, LA, USA.,Division of Clinical Genetics and Department of Genetics, Children's Hospital of New Orleans, New Orleans, LA, USA
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL, USA
| | - William A Gahl
- Undiagnosed Diseases Program, Office of the NIH Director, National Institutes of Health, Bethesda, MD, USA.,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- Undiagnosed Diseases Program, Office of the NIH Director, National Institutes of Health, Bethesda, MD, USA.,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Luis E Figuera
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | | | - Alessandra Maugeri
- Department of Clinical Genetics, VU University Medical Centre Amsterdam, Amsterdam, The Netherlands
| | - Ken Ishikawa
- Department of Pediatrics, Iwate Medical University, Morioka, Japan
| | - Tomoko Kobayashi
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan.,Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Senda, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Toshihiro Ohura
- Division of Clinical Laboratory, Sendai City Hospital, Sendai, Japan
| | - Hiroshi Kawame
- Division of Genomic Medicine Support and Genetic Counseling, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Miyagi Children's Hospital, Sendai, Japan.,Division of Clinical Genetics, Jikei University Hospital, Tokyo, Japan
| | - Michihiro Kono
- Department of Dermatology, Nagoya University Graduate School of Medicine Faculty of Medicine, Nagoya, Japan.,Department of Dermatology and Plastic Surgery, Akita University Graduate School of Medicine School of Medicine, Akita, Akita, Japan
| | - Kosuke Mochida
- Department of Dermatology, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
| | - Chiho Tokorodani
- Department of Pediatrics, Kochi Health Sciences Center, Kochi, Japan
| | - Kiyoshi Kikkawa
- Department of Pediatrics, Kochi Health Sciences Center, Kochi, Japan
| | - Takayuki Morisaki
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Suita, Japan.,Division of Molecular Pathology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Internal Medicine, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Takaya Nakane
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Chuo, Japan
| | - Akiharu Kubo
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Judith D Ranells
- Department of Pediatrics, University of South Florida, College of Medicine, Tampa, FL, USA
| | - Ohsuke Migita
- Department of Clinical Genetics, St. Marianna University, School of Medicine, Kawasaki, Japan
| | - Glenda Sobey
- EDS National Diagnostic Service, Sheffield Children's Hospital, Sheffield, UK
| | - Anupriya Kaur
- Department of Pediatrics (Genetics Division), Advanced Pediatric Cente, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Masumi Ishikawa
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Tomomi Yamaguchi
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan.,Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan .,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan.,Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan.,Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan
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36
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Norstad M, Outram S, Brown JEH, Zamora AN, Koenig BA, Risch N, Norton ME, Slavotinek A, Ackerman SL. The difficulties of broad data sharing in genomic medicine: Empirical evidence from diverse participants in prenatal and pediatric clinical genomics research. Genet Med 2021; 24:410-418. [PMID: 34906477 DOI: 10.1016/j.gim.2021.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/17/2021] [Accepted: 09/30/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE This study aimed to understand broad data sharing decisions among predominantly underserved families participating in genomic research. METHODS Drawing on clinic observations, semistructured interviews, and survey data from prenatal and pediatric families enrolled in a genomic medicine study focused on historically underserved and underrepresented populations, this paper expands empirical evidence regarding genomic data sharing communication and decision-making. RESULTS One-third of parents declined to share family data, and pediatric participants were significantly more likely to decline than prenatal participants. The pediatric population was significantly more socioeconomically disadvantaged and more likely to require interpreters. Opt-in was tied to altruism and participants' perception that data sharing was inherent to research participation. Opt-out was associated with privacy concerns and influenced by clinical staff's presentation of data handling procedures. The ability of participants to make informed choices during enrollment about data sharing was weakened by suboptimal circumstances, which was revealed by poor understanding of data sharing in follow-up interviews as well as discrepancies between expressed participant desires and official recorded choices. CONCLUSION These empirical data suggest that the context within which informed consent process is conducted in clinical genomics may be inadequate for respecting participants' values and preferences and does not support informed decision-making processes.
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Affiliation(s)
- Matthew Norstad
- Program in Bioethics, University of California San Francisco, San Francisco, CA; Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA.
| | - Simon Outram
- Program in Bioethics, University of California San Francisco, San Francisco, CA; Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA
| | - Julia E H Brown
- Program in Bioethics, University of California San Francisco, San Francisco, CA; Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA
| | - Astrid N Zamora
- Program in Bioethics, University of California San Francisco, San Francisco, CA; Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Barbara A Koenig
- Program in Bioethics, University of California San Francisco, San Francisco, CA; Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA; Philip R. Lee Institute for Health Policy Studies, University of California San Francisco, San Francisco, CA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA; Department of Social & Behavioral Sciences, School of Nursing, University of California San Francisco, San Francisco, CA; Department of Humanities and Social Sciences, University of California San Francisco, San Francisco, CA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA; Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
| | - Mary E Norton
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA; Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA
| | - Anne Slavotinek
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA; Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Sara L Ackerman
- Program in Bioethics, University of California San Francisco, San Francisco, CA; Department of Social & Behavioral Sciences, School of Nursing, University of California San Francisco, San Francisco, CA
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37
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Haverfield EV, Esplin ED, Aguilar SJ, Hatchell KE, Ormond KE, Hanson-Kahn A, Atwal PS, Macklin-Mantia S, Hines S, Sak CWM, Tucker S, Bleyl SB, Hulick PJ, Gordon OK, Velsher L, Gu JYJ, Weissman SM, Kruisselbrink T, Abel C, Kettles M, Slavotinek A, Mendelsohn BA, Green RC, Aradhya S, Nussbaum RL. Correction to: Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study. BMC Med 2021; 19:288. [PMID: 34732190 PMCID: PMC8567716 DOI: 10.1186/s12916-021-02141-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | | | | | | | - Kelly E Ormond
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Paldeep S Atwal
- Mayo Clinic, Jacksonville, FL, USA.,Atwal Clinic, Palm Beach, FL, USA.,PWNHealth, New York, NY, USA
| | | | | | | | | | | | | | - Ora K Gordon
- Providence Research Network, St John Cancer Institute, Los Angeles, CA, USA.,University of California, Los Angeles, CA, USA
| | | | | | - Scott M Weissman
- Genome Medical, San Francisco, CA, USA.,Chicago Genetic Consultants, Northbrook, IL, USA
| | | | | | | | - Anne Slavotinek
- University of California San Francisco, San Francisco, CA, USA
| | | | - Robert C Green
- Brigham and Women's Hospital, Boston, MA, USA.,The Broad Institute, Boston, MA, USA.,Ariadne Labs, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA, 94103, USA.,Volunteer Faculty, University of California San Francisco, San Francisco, CA, USA
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38
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Schirwani S, Albaba S, Carere DA, Guillen Sacoto MJ, Milan Zamora F, Si Y, Rabin R, Pappas J, Renaud DL, Hauser N, Reid E, Blanchet P, Foulds N, Dixit A, Fisher R, Armstrong R, Isidor B, Cogne B, Schrier Vergano S, Demirdas S, Dykzeul N, Cohen JS, Grand K, Morel D, Slavotinek A, Albassam HF, Naik S, Dean J, Ragge N, Costa C, Tedesco MG, Harrison RE, Bouman A, Palen E, Challman TD, Willemsen MH, Vogt J, Cunniff C, Bergstrom K, Walia JS, Bruel AL, Kini U, Alkuraya FS, Slegesky V, Meeks N, Girotto P, Johnson D, Newbury-Ecob R, Ockeloen CW, Prontera P, Lynch SA, Li D, Graham JM, Pierson TM, Balasubramanian M. Expanding the phenotype of ASXL3-related syndrome: A comprehensive description of 45 unpublished individuals with inherited and de novo pathogenic variants in ASXL3. Am J Med Genet A 2021; 185:3446-3458. [PMID: 34436830 DOI: 10.1002/ajmg.a.62465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/10/2021] [Accepted: 07/08/2021] [Indexed: 12/15/2022]
Abstract
The study aimed at widening the clinical and genetic spectrum of ASXL3-related syndrome, a neurodevelopmental disorder, caused by truncating variants in the ASXL3 gene. In this international collaborative study, we have undertaken a detailed clinical and molecular analysis of 45 previously unpublished individuals with ASXL3-related syndrome, as well as a review of all previously published individuals. We have reviewed the rather limited functional characterization of pathogenic variants in ASXL3 and discuss current understanding of the consequences of the different ASXL3 variants. In this comprehensive analysis of ASXL3-related syndrome, we define its natural history and clinical evolution occurring with age. We report familial ASXL3 pathogenic variants, characterize the phenotype in mildly affected individuals and discuss nonpenetrance. We also discuss the role of missense variants in ASXL3. We delineate a variable but consistent phenotype. The most characteristic features are neurodevelopmental delay with consistently limited speech, significant neuro-behavioral issues, hypotonia, and feeding difficulties. Distinctive features include downslanting palpebral fissures, hypertelorism, tubular nose with a prominent nasal bridge, and low-hanging columella. The presented data will inform clinical management of individuals with ASXL3-related syndrome and improve interpretation of new ASXL3 sequence variants.
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Affiliation(s)
- Schaida Schirwani
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
| | - Shadi Albaba
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | | | | | | | - Yue Si
- GeneDx, Inc, Gaithersburg, Maryland, USA
| | - Rachel Rabin
- Department of Pediatrics, New York University School of Medicine, New York, New York, USA
| | - John Pappas
- Department of Pediatrics, New York University School of Medicine, New York, New York, USA
| | - Deborah L Renaud
- Division of Child and Adolescent Neurology, Departments of Neurology and Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
| | - Natalie Hauser
- Department of Pediatrics, Division of Medical Genomics, Inova Health System, Falls Church, Virginia, USA
| | - Evan Reid
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Patricia Blanchet
- Département de Génétique Médicale, CHU de Montpellier, Montpellier, France
| | - Nichola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Abhijit Dixit
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Richard Fisher
- Teesside Genetics Unit, The James Cook University Hospital, Middlesbrough, UK
| | - Ruth Armstrong
- Departments of Medical Genetics and Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Benjamin Cogne
- Service de génétique médicale, CHU Nantes, Nantes, France
| | - Samantha Schrier Vergano
- Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Serwet Demirdas
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Natalie Dykzeul
- Lucile Packard Children's Hospital, Stanford Children's Health, Palo Alto, California, USA
| | - Julie S Cohen
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katheryn Grand
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dayna Morel
- University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Anne Slavotinek
- Department of Pediatrics, Division of Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Hessa F Albassam
- Department of Pediatrics, Care National Hospital, Riyadh, Saudi Arabia
| | - Swati Naik
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - John Dean
- Clinical Genetics Service, NHS Grampian, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Nicola Ragge
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Cinzia Costa
- Neurology Clinic, Department of Medicine, Santa Maria della Misericordia Hospital, University of Perugia, Perugia, Italy
| | - Maria Giovanna Tedesco
- Medical Genetics Unit, Santa Maria della Misericordia Hospital, University of Perugia, Perugia, Italy
- Genetics Unit, "Mauro Baschirotto" Institute for Rare Diseases (B.I.R.D.), Costozza di Longare, Vicenza, Italy
| | - Rachel E Harrison
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Emily Palen
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Thomas D Challman
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Christopher Cunniff
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA
| | - Katherine Bergstrom
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA
| | - Jagdeep S Walia
- Divsion of Medical Genetics, Departments of Pediatrics, Queen's University, Kingston, Ontario, Canada
| | - Ange-Line Bruel
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Dijon, France
| | - Usha Kini
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Valerie Slegesky
- University of Colorado & Children's Hospital Colorado, Denver, Colorado, USA
| | - Naomi Meeks
- University of Colorado & Children's Hospital Colorado, Denver, Colorado, USA
| | - Paula Girotto
- Division of Child Neurology, Department of Pediatrics, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Diana Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- EDS National Diagnostic Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Ruth Newbury-Ecob
- Bristol Regional Genetics Service, St Michael's Hospital, Bristol, UK
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paolo Prontera
- Medical Genetics Unit, Santa Maria della Misericordia Hospital, University of Perugia, Perugia, Italy
| | - Sally Ann Lynch
- Department of Clinical Genetics, Temple Street Children's Hospital, Dublin, Ireland
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John M Graham
- Cedars-Sinai Medical Center, Harbor-UCLA Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Tyler Mark Pierson
- Departments of Pediatrics, Neurology, Cedars-Sinai Center for the Undiagnosed Patient, and Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles CA, USA
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
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39
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Shieh JT, Penon-Portmann M, Wong KHY, Levy-Sakin M, Verghese M, Slavotinek A, Gallagher RC, Mendelsohn BA, Tenney J, Beleford D, Perry H, Chow SK, Sharo AG, Brenner SE, Qi Z, Yu J, Klein OD, Martin D, Kwok PY, Boffelli D. Application of full-genome analysis to diagnose rare monogenic disorders. NPJ Genom Med 2021; 6:77. [PMID: 34556655 PMCID: PMC8460793 DOI: 10.1038/s41525-021-00241-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/21/2020] [Indexed: 11/30/2022] Open
Abstract
Current genetic tests for rare diseases provide a diagnosis in only a modest proportion of cases. The Full-Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to detect small variants, structural variants with breakpoint resolution, and phasing. We built a variant prioritization pipeline and tested FGA’s utility for diagnosis of rare diseases in a clinical setting. FGA identified structural variants and small variants with an overall diagnostic yield of 40% (20 of 50 cases) and 35% in exome-negative cases (8 of 23 cases), 4 of these were structural variants. FGA detected and mapped structural variants that are missed by short reads, including non-coding duplication, and phased variants across long distances of more than 180 kb. With the prioritization algorithm, longer DNA technologies could replace multiple tests for monogenic disorders and expand the range of variants detected. Our study suggests that genomes produced from technologies like FGA can improve variant detection and provide higher resolution genome maps for future application.
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Affiliation(s)
- Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA. .,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA.
| | - Monica Penon-Portmann
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Karen H Y Wong
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Michelle Verghese
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Anne Slavotinek
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Renata C Gallagher
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Bryce A Mendelsohn
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tenney
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Daniah Beleford
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Hazel Perry
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Stephen K Chow
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Andrew G Sharo
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Zhongxia Qi
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jingwei Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ophir D Klein
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA.,Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
| | - David Martin
- Children's Hospital Oakland Research Institute, Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.,Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
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40
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Slavotinek A, Misceo D, Htun S, Mathisen L, Frengen E, Foreman M, Hurtig JE, Enyenihi L, Sterrett MC, Leung SW, Schneidman-Duhovny D, Estrada-Veras J, Duncan JL, Haaxma CA, Kamsteeg EJ, Xia V, Beleford D, Si Y, Douglas G, Treidene HE, van Hoof A, Fasken MB, Corbett AH. Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness. Hum Mol Genet 2021; 29:2218-2239. [PMID: 32504085 DOI: 10.1093/hmg/ddaa108] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/10/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
The RNA exosome is an essential ribonuclease complex required for processing and/or degradation of both coding and non-coding RNAs. We identified five patients with biallelic variants in EXOSC5, which encodes a structural subunit of the RNA exosome. The clinical features of these patients include failure to thrive, short stature, feeding difficulties, developmental delays that affect motor skills, hypotonia and esotropia. Brain MRI revealed cerebellar hypoplasia and ventriculomegaly. While we ascertained five patients, three patients with distinct variants of EXOSC5 were studied in detail. The first patient had a deletion involving exons 5-6 of EXOSC5 and a missense variant, p.Thr114Ile, that were inherited in trans, the second patient was homozygous for p.Leu206His and the third patient had paternal isodisomy for chromosome 19 and was homozygous for p.Met148Thr. The additional two patients ascertained are siblings who had an early frameshift mutation in EXOSC5 and the p.Thr114Ile missense variant that were inherited in trans. We employed three complementary approaches to explore the requirement for EXOSC5 in brain development and assess consequences of pathogenic EXOSC5 variants. Loss of function for exosc5 in zebrafish results in shortened and curved tails/bodies, reduced eye/head size and edema. We modeled pathogenic EXOSC5 variants in both budding yeast and mammalian cells. Some of these variants cause defects in RNA exosome function as well as altered interactions with other RNA exosome subunits. These findings expand the number of genes encoding RNA exosome subunits linked to human disease while also suggesting that disease mechanism varies depending on the specific pathogenic variant.
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Affiliation(s)
- Anne Slavotinek
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Stephanie Htun
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Linda Mathisen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Michelle Foreman
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Jennifer E Hurtig
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Liz Enyenihi
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | | | - Sara W Leung
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering and the Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Juvianee Estrada-Veras
- Department of Pediatrics-Medical Genetics and Metabolism, Uniformed Services University/Walter Reed NMMC Bethesda, MD 20889, USA
| | - Jacque L Duncan
- Department of Ophthalmology, University of California, San Francisco, CA 94143, USA
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Vivian Xia
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Daniah Beleford
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Yue Si
- GeneDx Inc., MD 20877, USA
| | | | - Hans Einar Treidene
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo 0450, Norway
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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41
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Haverfield EV, Esplin ED, Aguilar SJ, Hatchell KE, Ormond KE, Hanson-Kahn A, Atwal PS, Macklin-Mantia S, Hines S, Sak CWM, Tucker S, Bleyl SB, Hulick PJ, Gordon OK, Velsher L, Gu JYJ, Weissman SM, Kruisselbrink T, Abel C, Kettles M, Slavotinek A, Mendelsohn BA, Green RC, Aradhya S, Nussbaum RL. Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study. BMC Med 2021; 19:199. [PMID: 34404389 PMCID: PMC8371767 DOI: 10.1186/s12916-021-01999-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The use of proactive genetic screening for disease prevention and early detection is not yet widespread. Professional practice guidelines from the American College of Medical Genetics and Genomics (ACMG) have encouraged reporting pathogenic variants that confer personal risk for actionable monogenic hereditary disorders, but only as secondary findings from exome or genome sequencing. The Centers for Disease Control and Prevention (CDC) recognizes the potential public health impact of three Tier 1 actionable disorders. Here, we report results of a large multi-center cohort study to determine the yield and potential value of screening healthy individuals for variants associated with a broad range of actionable monogenic disorders, outside the context of secondary findings. METHODS Eligible adults were offered a proactive genetic screening test by health care providers in a variety of clinical settings. The screening panel based on next-generation sequencing contained up to 147 genes associated with monogenic disorders within cancer, cardiovascular, and other important clinical areas. Sequence and intragenic copy number variants classified as pathogenic, likely pathogenic, pathogenic (low penetrance), or increased risk allele were considered clinically significant and reported. Results were analyzed by clinical area and severity/burden of disease using chi-square tests without Yates' correction. RESULTS Among 10,478 unrelated adults screened, 1619 (15.5%) had results indicating personal risk for an actionable monogenic disorder. In contrast, only 3.1 to 5.2% had clinically reportable variants in genes suggested by the ACMG version 2 secondary findings list to be examined during exome or genome sequencing, and 2% had reportable variants related to CDC Tier 1 conditions. Among patients, 649 (6.2%) were positive for a genotype associated with a disease of high severity/burden, including hereditary cancer syndromes, cardiovascular disorders, or malignant hyperthermia susceptibility. CONCLUSIONS This is one of the first real-world examples of specialists and primary care providers using genetic screening with a multi-gene panel to identify health risks in their patients. Nearly one in six individuals screened for variants associated with actionable monogenic disorders had clinically significant results. These findings provide a foundation for further studies to assess the role of genetic screening as part of regular medical care.
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Affiliation(s)
| | | | | | | | - Kelly E Ormond
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Paldeep S Atwal
- Mayo Clinic, Jacksonville, FL, USA.,Atwal Clinic, Palm Beach, FL, USA.,PWNHealth, New York, NY, USA
| | | | | | | | | | | | | | - Ora K Gordon
- Providence Research Network, St John Cancer Institute, Los Angeles, CA, USA.,University of California, Los Angeles, CA, USA
| | | | | | - Scott M Weissman
- Genome Medical, San Francisco, CA, USA.,Chicago Genetic Consultants, Northbrook, IL, USA
| | | | | | | | - Anne Slavotinek
- University of California San Francisco, San Francisco, CA, USA
| | | | - Robert C Green
- Brigham and Women's Hospital, Boston, MA, USA.,The Broad Institute, Boston, MA, USA.,Ariadne Labs, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA, 94103, USA.,Volunteer Faculty, University of California San Francisco, San Francisco, CA, USA
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42
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Alankarage D, Szot JO, Pachter N, Slavotinek A, Selleri L, Shieh JT, Winlaw D, Giannoulatou E, Chapman G, Dunwoodie SL. Functional characterization of a novel PBX1 de novo missense variant identified in a patient with syndromic congenital heart disease. Hum Mol Genet 2021; 29:1068-1082. [PMID: 31625560 DOI: 10.1093/hmg/ddz231] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/13/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
Pre-B cell leukemia factor 1 (PBX1) is an essential developmental transcription factor, mutations in which have recently been associated with CAKUTHED syndrome, characterized by multiple congenital defects including congenital heart disease (CHD). During analysis of a whole-exome-sequenced cohort of heterogeneous CHD patients, we identified a de novo missense variant, PBX1:c.551G>C p.R184P, in a patient with tetralogy of Fallot with absent pulmonary valve and extra-cardiac phenotypes. Functional analysis of this variant by creating a CRISPR-Cas9 gene-edited mouse model revealed multiple congenital anomalies. Congenital heart defects (persistent truncus arteriosus and ventricular septal defect), hypoplastic lungs, hypoplastic/ectopic kidneys, aplastic adrenal glands and spleen, as well as atretic trachea and palate defects were observed in the homozygous mutant embryos at multiple stages of development. We also observed developmental anomalies in a proportion of heterozygous embryos, suggestive of a dominant mode of inheritance. Analysis of gene expression and protein levels revealed that although Pbx1 transcripts are higher in homozygotes, amounts of PBX1 protein are significantly decreased. Here, we have presented the first functional model of a missense PBX1 variant and provided strong evidence that p.R184P is disease-causal. Our findings also expand the phenotypic spectrum associated with pathogenic PBX1 variants in both humans and mice.
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Affiliation(s)
- Dimuthu Alankarage
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia
| | - Justin O Szot
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia
| | - Nick Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Western Australia, 6008 Perth, Australia.,University of Western Australia, School of Paediatrics and Child Health, Western Australia, 6009 Perth, Australia
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, 94158 CA, USA.,Institute of Human Genetics, University of California San Francisco, San Francisco, 94143 CA, USA
| | - Licia Selleri
- Institute of Human Genetics, University of California San Francisco, San Francisco, 94143 CA, USA.,Program in Craniofacial Biology, Department of Orofacial Sciences, University of California San Francisco, San Francisco, 94143 CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, 94143 CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, 94158 CA, USA.,Institute of Human Genetics, University of California San Francisco, San Francisco, 94143 CA, USA
| | - David Winlaw
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Heart Centre for Children, The Children's Hospital at Westmead, New South Wales, 2145 Sydney, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, University of Sydney, New South Wales, 2006 Sydney, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Faculty of Medicine, University of New South Wales, St Vincent's Clinical School, New South Wales, 2010 Sydney, Australia
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Faculty of Medicine, University of New South Wales, St Vincent's Clinical School, New South Wales, 2010 Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Faculty of Medicine, University of New South Wales, St Vincent's Clinical School, New South Wales, 2010 Sydney, Australia
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Chopra M, McEntagart M, Clayton-Smith J, Platzer K, Shukla A, Girisha KM, Kaur A, Kaur P, Pfundt R, Veenstra-Knol H, Mancini GM, Cappuccio G, Brunetti-Pierri N, Kortüm F, Hempel M, Denecke J, Lehman A, Kleefstra T, Stuurman KE, Wilke M, Thompson ML, Bebin EM, Bijlsma EK, Hoffer MJ, Peeters-Scholte C, Slavotinek A, Weiss WA, Yip T, Hodoglugil U, Whittle A, diMonda J, Neira J, Yang S, Kirby A, Pinz H, Lechner R, Sleutels F, Helbig I, McKeown S, Helbig K, Willaert R, Juusola J, Semotok J, Hadonou M, Short J, Yachelevich N, Lala S, Fernández-Jaen A, Pelayo JP, Klöckner C, Kamphausen SB, Abou Jamra R, Arelin M, Innes AM, Niskakoski A, Amin S, Williams M, Evans J, Smithson S, Smedley D, de Burca A, Kini U, Delatycki MB, Gallacher L, Yeung A, Pais L, Field M, Martin E, Charles P, Courtin T, Keren B, Iascone M, Cereda A, Poke G, Abadie V, Chalouhi C, Parthasarathy P, Halliday BJ, Robertson SP, Lyonnet S, Amiel J, Gordon CT, Amiel J, Gordon CT. Heterozygous ANKRD17 loss-of-function variants cause a syndrome with intellectual disability, speech delay, and dysmorphism. Am J Hum Genet 2021; 108:1138-1150. [PMID: 33909992 DOI: 10.1016/j.ajhg.2021.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/05/2021] [Indexed: 01/02/2023] Open
Abstract
ANKRD17 is an ankyrin repeat-containing protein thought to play a role in cell cycle progression, whose ortholog in Drosophila functions in the Hippo pathway as a co-factor of Yorkie. Here, we delineate a neurodevelopmental disorder caused by de novo heterozygous ANKRD17 variants. The mutational spectrum of this cohort of 34 individuals from 32 families is highly suggestive of haploinsufficiency as the underlying mechanism of disease, with 21 truncating or essential splice site variants, 9 missense variants, 1 in-frame insertion-deletion, and 1 microdeletion (1.16 Mb). Consequently, our data indicate that loss of ANKRD17 is likely the main cause of phenotypes previously associated with large multi-gene chromosomal aberrations of the 4q13.3 region. Protein modeling suggests that most of the missense variants disrupt the stability of the ankyrin repeats through alteration of core structural residues. The major phenotypic characteristic of our cohort is a variable degree of developmental delay/intellectual disability, particularly affecting speech, while additional features include growth failure, feeding difficulties, non-specific MRI abnormalities, epilepsy and/or abnormal EEG, predisposition to recurrent infections (mostly bacterial), ophthalmological abnormalities, gait/balance disturbance, and joint hypermobility. Moreover, many individuals shared similar dysmorphic facial features. Analysis of single-cell RNA-seq data from the developing human telencephalon indicated ANKRD17 expression at multiple stages of neurogenesis, adding further evidence to the assertion that damaging ANKRD17 variants cause a neurodevelopmental disorder.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jeanne Amiel
- Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris (AP-HP), and Institut Imagine, Paris 75015, France; Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Université de Paris, Paris 75015, France
| | - Christopher T Gordon
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Université de Paris, Paris 75015, France.
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44
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Mannucci I, Dang NDP, Huber H, Murry JB, Abramson J, Althoff T, Banka S, Baynam G, Bearden D, Beleza-Meireles A, Benke PJ, Berland S, Bierhals T, Bilan F, Bindoff LA, Braathen GJ, Busk ØL, Chenbhanich J, Denecke J, Escobar LF, Estes C, Fleischer J, Groepper D, Haaxma CA, Hempel M, Holler-Managan Y, Houge G, Jackson A, Kellogg L, Keren B, Kiraly-Borri C, Kraus C, Kubisch C, Le Guyader G, Ljungblad UW, Brenman LM, Martinez-Agosto JA, Might M, Miller DT, Minks KQ, Moghaddam B, Nava C, Nelson SF, Parant JM, Prescott T, Rajabi F, Randrianaivo H, Reiter SF, Schuurs-Hoeijmakers J, Shieh PB, Slavotinek A, Smithson S, Stegmann APA, Tomczak K, Tveten K, Wang J, Whitlock JH, Zweier C, McWalter K, Juusola J, Quintero-Rivera F, Fischer U, Yeo NC, Kreienkamp HJ, Lessel D. Genotype-phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders. Genome Med 2021; 13:90. [PMID: 34020708 PMCID: PMC8140440 DOI: 10.1186/s13073-021-00900-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/28/2021] [Indexed: 12/27/2022] Open
Abstract
Background We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. Results We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. Conclusions Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00900-3.
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Affiliation(s)
- Ilaria Mannucci
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Nghi D P Dang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Hannes Huber
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Jaclyn B Murry
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeff Abramson
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Thorsten Althoff
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gareth Baynam
- Faculty of Medicine and Health Sciences, University of Western Australia, Perth, WA, Australia.,Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, Australia.,Telethon Kids Institute, Perth, Australia
| | - David Bearden
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | - Ana Beleza-Meireles
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Frederic Bilan
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Laurence A Bindoff
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | - Øyvind L Busk
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jirat Chenbhanich
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246, Hamburg, Germany
| | - Luis F Escobar
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Caroline Estes
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Julie Fleischer
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Yolanda Holler-Managan
- Division of Neurology, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Boris Keren
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Gwenael Le Guyader
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Ulf W Ljungblad
- Department of Pediatrics, Vestfold Hospital, 3116, Tønsberg, Norway
| | | | - Julian A Martinez-Agosto
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Semel Institute of Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pediatrics, Division of Medical Genetics at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew Might
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kelly Q Minks
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | | | - Caroline Nava
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA.,Center for Duchenne Muscular Dystrophy, University of California Los Angeles, Los Angeles, CA, USA
| | - John M Parant
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Hanitra Randrianaivo
- UF de Génétique Médicale, GHSR, CHU de La Réunion, Saint Pierre, La Réunion, France
| | - Simone F Reiter
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | | | - Perry B Shieh
- Department of Neurology at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah Smithson
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kinga Tomczak
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Jordan H Whitlock
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.,Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | | | | | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA.
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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45
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Szot JO, Slavotinek A, Chong K, Brandau O, Nezarati M, Cueto-González AM, Patel MS, Devine WP, Rego S, Acyinena AP, Shannon P, Myles-Reid D, Blaser S, Mieghem TV, Yavuz-Kienle H, Skladny H, Miller K, Riera MDT, Martínez SA, Tizzano EF, Dupuis L, James Stavropoulos D, McNiven V, Mendoza-Londono R, Elliott AM, Phillips RS, Chapman G, Dunwoodie SL. New cases that expand the genotypic and phenotypic spectrum of Congenital NAD Deficiency Disorder. Hum Mutat 2021; 42:862-876. [PMID: 33942433 DOI: 10.1002/humu.24211] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/31/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) is an essential coenzyme involved in over 400 cellular reactions. During embryogenesis, mammals synthesize NAD de novo from dietary l -tryptophan via the kynurenine pathway. Biallelic, inactivating variants in three genes encoding enzymes of this biosynthesis pathway (KYNU, HAAO, and NADSYN1) disrupt NAD synthesis and have been identified in patients with multiple malformations of the heart, kidney, vertebrae, and limbs; these patients have Congenital NAD Deficiency Disorder HAAO and four families with biallelic variants in KYNU. These patients present similarly with multiple malformations of the heart, kidney, vertebrae, and limbs, of variable severity. We show that each variant identified in these patients results in loss-of-function, revealed by a significant reduction in NAD levels via yeast genetic complementation assays. For the first time, missense mutations are identified as a cause of malformation and shown to disrupt enzyme function. These missense and frameshift variants cause moderate to severe NAD deficiency in yeast, analogous to insufficient synthesized NAD in patients. We hereby expand the genotypic and corresponding phenotypic spectrum of Congenital NAD Deficiency Disorder.
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Affiliation(s)
- Justin O Szot
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Anne Slavotinek
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Karen Chong
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Marjan Nezarati
- Genetics Program, North York General Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Anna M Cueto-González
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Millan S Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Walter P Devine
- Department of Anatomic Pathology, University of California, San Francisco, California, USA
| | - Shannon Rego
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Alicia P Acyinena
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Patrick Shannon
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Diane Myles-Reid
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Susan Blaser
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tim V Mieghem
- Fetal Medicine Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | | | - Kristen Miller
- Genetics Program, North York General Hospital, Toronto, Ontario, Canada
| | - Miereia D T Riera
- Metabolic Unit and Pediatric Neurology Department, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Silvia A Martínez
- Fetal Medicine Unit and Obstetrics Department, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona, Barcelona, Spain
| | - Lucie Dupuis
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri James Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Vanda McNiven
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert S Phillips
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
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46
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Donohue KE, Gooch C, Katz A, Wakelee J, Slavotinek A, Korf BR. Pitfalls and challenges in genetic test interpretation: An exploration of genetic professionals experience with interpretation of results. Clin Genet 2021; 99:638-649. [PMID: 33818754 DOI: 10.1111/cge.13917] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/11/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
The interpretation of genetic testing results is subject to error. This observational study illustrates examples of pitfalls and challenges in interpretation of genetic testing results as reported by genetics professionals. We surveyed genetics professionals to describe interpretation challenges, the types of variants that were involved, and the reported clinical impact of misconception of a test result. Case studies were then collected from a select group to further explore potential causes of misunderstanding. A total of 83% of survey respondents were aware of at least one instance of genetic test misinterpretation. Both professionals with and without formal training in genetics were challenged by test reports, and variants of unknown significance were most frequently involved. Case submissions revealed that interpretation pitfalls extend beyond variant classification analyses. Inferred challenges in case submissions include lack of genetic counseling, unclear wording of reports, and suboptimal communication among providers. Respondents and case submitters noted that incorrect interpretation can trigger unnecessary follow-up tests and improperly alter clinical management. Further research is needed to validate and quantify large-scale data regarding challenges of genetic results interpretation.
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Affiliation(s)
- Katherine E Donohue
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Catherine Gooch
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Pediatrics, Division of Genetics and Genomic Medicine, Washington University at St Louis School of Medicine, St. Louis, MO, USA
| | - Alexander Katz
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Jessica Wakelee
- Center for the Study of Community Health, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California, San Francisco, California, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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47
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Sheppard SE, Campbell IM, Harr MH, Gold N, Li D, Bjornsson HT, Cohen JS, Fahrner JA, Fatemi A, Harris JR, Nowak C, Stevens CA, Grand K, Au M, Graham JM, Sanchez-Lara PA, Campo MD, Jones MC, Abdul-Rahman O, Alkuraya FS, Bassetti JA, Bergstrom K, Bhoj E, Dugan S, Kaplan JD, Derar N, Gripp KW, Hauser N, Innes AM, Keena B, Kodra N, Miller R, Nelson B, Nowaczyk MJ, Rahbeeni Z, Ben-Shachar S, Shieh JT, Slavotinek A, Sobering AK, Abbott MA, Allain DC, Amlie-Wolf L, Au PYB, Bedoukian E, Beek G, Barry J, Berg J, Bernstein JA, Cytrynbaum C, Chung BHY, Donoghue S, Dorrani N, Eaton A, Flores-Daboub JA, Dubbs H, Felix CA, Fong CT, Fung JLF, Gangaram B, Goldstein A, Greenberg R, Ha TK, Hersh J, Izumi K, Kallish S, Kravets E, Kwok PY, Jobling RK, Knight Johnson AE, Kushner J, Lee BH, Levin B, Lindstrom K, Manickam K, Mardach R, McCormick E, McLeod DR, Mentch FD, Minks K, Muraresku C, Nelson SF, Porazzi P, Pichurin PN, Powell-Hamilton NN, Powis Z, Ritter A, Rogers C, Rohena L, Ronspies C, Schroeder A, Stark Z, Starr L, Stoler J, Suwannarat P, Velinov M, Weksberg R, Wilnai Y, Zadeh N, Zand DJ, Falk MJ, Hakonarson H, Zackai EH, Quintero-Rivera F. Expanding the genotypic and phenotypic spectrum in a diverse cohort of 104 individuals with Wiedemann-Steiner syndrome. Am J Med Genet A 2021; 185:1649-1665. [PMID: 33783954 DOI: 10.1002/ajmg.a.62124] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/19/2022]
Abstract
Wiedemann-Steiner syndrome (WSS) is an autosomal dominant disorder caused by monoallelic variants in KMT2A and characterized by intellectual disability and hypertrichosis. We performed a retrospective, multicenter, observational study of 104 individuals with WSS from five continents to characterize the clinical and molecular spectrum of WSS in diverse populations, to identify physical features that may be more prevalent in White versus Black Indigenous People of Color individuals, to delineate genotype-phenotype correlations, to define developmental milestones, to describe the syndrome through adulthood, and to examine clinicians' differential diagnoses. Sixty-nine of the 82 variants (84%) observed in the study were not previously reported in the literature. Common clinical features identified in the cohort included: developmental delay or intellectual disability (97%), constipation (63.8%), failure to thrive (67.7%), feeding difficulties (66.3%), hypertrichosis cubiti (57%), short stature (57.8%), and vertebral anomalies (46.9%). The median ages at walking and first words were 20 months and 18 months, respectively. Hypotonia was associated with loss of function (LoF) variants, and seizures were associated with non-LoF variants. This study identifies genotype-phenotype correlations as well as race-facial feature associations in an ethnically diverse cohort, and accurately defines developmental trajectories, medical comorbidities, and long-term outcomes in individuals with WSS.
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Affiliation(s)
- Sarah E Sheppard
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian M Campbell
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Margaret H Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nina Gold
- Mass General Hospital for Children, Division of Medical Genetics and Metabolism and Harvard Medical School, Boston, Massachusetts, USA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Iceland
| | - Julie S Cohen
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ali Fatemi
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline R Harris
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Catherine Nowak
- Division of Genetics and Genomics, Boston Children's Hospital, The Feingold Center for Children, Boston, Massachusetts, USA
| | - Cathy A Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, Tennessee, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Miguel Del Campo
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Marilyn C Jones
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Omar Abdul-Rahman
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jennifer A Bassetti
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Katherine Bergstrom
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Elizabeth Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sarah Dugan
- Division of Medical Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Julie D Kaplan
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nada Derar
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Karen W Gripp
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Natalie Hauser
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - A Micheil Innes
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Beth Keena
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Neslida Kodra
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Rebecca Miller
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Beverly Nelson
- Department of Clinical Skills, St. George's University, True Blue, Grenada
| | | | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shay Ben-Shachar
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joseph T Shieh
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Andrew K Sobering
- Department of Biochemistry, St. George's University, True Blue, Grenada
| | - Mary-Alice Abbott
- Medical Genetics, Department of Pediatrics, University of Massachusetts Medical School - Baystate, Springfield, Massachusetts, USA
| | - Dawn C Allain
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Louise Amlie-Wolf
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Ping Yee Billie Au
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Emma Bedoukian
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Geoffrey Beek
- Children's Hospital of Minnesota, Minneapolis, Minnesota, USA
| | - James Barry
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Janet Berg
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Sarah Donoghue
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Naghmeh Dorrani
- Department of Pediatrics, University of California Los Angeles, California, Los Angeles, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA
| | - Alison Eaton
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | | | - Holly Dubbs
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Carolyn A Felix
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Chin-To Fong
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jasmine Lee Fong Fung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Balram Gangaram
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Amy Goldstein
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rotem Greenberg
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Thoa K Ha
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Joseph Hersh
- Weisskopf Child Evaluation Center, Department of Pediatrics, University of Louisville, Louisville, Kentucky, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Staci Kallish
- Division of Translational Medicine and Human Genetics Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elijah Kravets
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Pui-Yan Kwok
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Rebekah K Jobling
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | | | - Jessica Kushner
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Bo Hoon Lee
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Brooke Levin
- MD Anderson Cancer Center at Cooper, Cooper University Health Care, Camden, New Jersey, USA
| | | | - Kandamurugu Manickam
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Rebecca Mardach
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Elizabeth McCormick
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - D Ross McLeod
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - Frank D Mentch
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kelly Minks
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Colleen Muraresku
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA.,Department of Human Genetics, Center for Duchenne Muscular Dystrophy University of California Los Angeles, California, Los Angeles, USA
| | - Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Pavel N Pichurin
- Clinical Genomics Center, University of California Los Angeles, Los Angeles, California, USA
| | - Nina N Powell-Hamilton
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Zoe Powis
- Quest Diagnostics Kalamzoo, Kalamzoo, Michigan, USA
| | - Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Caleb Rogers
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Luis Rohena
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Carey Ronspies
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Audrey Schroeder
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lois Starr
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joan Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Rockville, Maryland, USA
| | - Milen Velinov
- NYS Institute for Basic Research in developmental Disabilities, Staten Island, New York, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Yael Wilnai
- Genetic Institute, Sourasky Medical Center, Te-Aviv, Tel Aviv, Israel
| | - Neda Zadeh
- Genetics Center and CHOC Children's Hospital, Orange, California, USA
| | - Dina J Zand
- Rare Disease Institute, Children's National Medical Center, Washington, District of Columbia, USA
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Fabiola Quintero-Rivera
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, California, Los Angeles, USA
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48
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Brin MF, Kirby RS, Slavotinek A, Adams A, Parker L, Ukah A, Radulian L, Yedigarova L, Yushmanova I. Pregnancy outcomes following exposure to onabotulinumtoxinA update: 29 years of safety observation. Toxicon 2021. [DOI: 10.1016/j.toxicon.2020.11.360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Klöckner C, Sticht H, Zacher P, Popp B, Babcock HE, Bakker DP, Barwick K, Bonfert MV, Bönnemann CG, Brilstra EH, Chung WK, Clarke AJ, Devine P, Donkervoort S, Fraser JL, Friedman J, Gates A, Ghoumid J, Hobson E, Horvath G, Keller-Ramey J, Keren B, Kurian MA, Lee V, Leppig KA, Lundgren J, McDonald MT, McLaughlin HM, McTague A, Mefford HC, Mignot C, Mikati MA, Nava C, Raymond FL, Sampson JR, Sanchis-Juan A, Shashi V, Shieh JTC, Shinawi M, Slavotinek A, Stödberg T, Stong N, Sullivan JA, Taylor AC, Toler TL, van den Boogaard MJ, van der Crabben SN, van Gassen KLI, van Jaarsveld RH, Van Ziffle J, Wadley AF, Wagner M, Wigby K, Wortmann SB, Zarate YA, Møller RS, Lemke JR, Platzer K. De novo variants in SNAP25 cause an early-onset developmental and epileptic encephalopathy. Genet Med 2020; 23:653-660. [PMID: 33299146 DOI: 10.1038/s41436-020-01020-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE This study aims to provide a comprehensive description of the phenotypic and genotypic spectrum of SNAP25 developmental and epileptic encephalopathy (SNAP25-DEE) by reviewing newly identified and previously reported individuals. METHODS Individuals harboring heterozygous missense or loss-of-function variants in SNAP25 were assembled through collaboration with international colleagues, matchmaking platforms, and literature review. For each individual, detailed phenotyping, classification, and structural modeling of the identified variant were performed. RESULTS The cohort comprises 23 individuals with pathogenic or likely pathogenic de novo variants in SNAP25. Intellectual disability and early-onset epilepsy were identified as the core symptoms of SNAP25-DEE, with recurrent findings of movement disorders, cerebral visual impairment, and brain atrophy. Structural modeling for all variants predicted possible functional defects concerning SNAP25 or impaired interaction with other components of the SNARE complex. CONCLUSION We provide a comprehensive description of SNAP25-DEE with intellectual disability and early-onset epilepsy mostly occurring before the age of two years. These core symptoms and additional recurrent phenotypes show an overlap to genes encoding other components or associated proteins of the SNARE complex such as STX1B, STXBP1, or VAMP2. Thus, these findings advance the concept of a group of neurodevelopmental disorders that may be termed "SNAREopathies."
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Affiliation(s)
- Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Holly E Babcock
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Dewi P Bakker
- Department of Child Neurology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Katy Barwick
- Institute of Child Health, University Collge London, London, UK
| | - Michaela V Bonfert
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU - University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Angus J Clarke
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Wales, UK
| | - Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jamie L Fraser
- Rare Disease Institute, Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California San Diego and Division of Neurology, Rady Children's Hospital, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Alyssa Gates
- Department of Genetic Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Jamal Ghoumid
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - Emma Hobson
- Yorkshire Clinical Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Gabriella Horvath
- Department of Pediatrics, Division of Biochemical Diseases, University of British Columbia, Vancouver, Canada
| | | | - Boris Keren
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Manju A Kurian
- Institute of Child Health, University Collge London, London, UK
| | - Virgina Lee
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen A Leppig
- Department of Genetic Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Johan Lundgren
- Institute of Clinical Sciences, Skane University Hospital, Lund, Sweden
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - Amy McTague
- Institute of Child Health, University Collge London, London, UK
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière et Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Caroline Nava
- Sorbonne University, Paris Brain Institute, Inserm U1127, CNRS UMR 7225, AP-HP, Pitié Salpêtrière Hospital, Department of Genetics, Paris, France
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Julian R Sampson
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Wales, UK
| | - Alba Sanchis-Juan
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Joseph T C Shieh
- Division of Medical Genetics, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Slavotinek
- Division of Medical Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Tommy Stödberg
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Ashley C Taylor
- Section of Genetics, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Tomi L Toler
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Saskia N van der Crabben
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Jessica Van Ziffle
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | | | - Matias Wagner
- Institute of Neurogenomics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Kristen Wigby
- Department of Pediatrics, Division of Genetics, University of California, San Diego and Rady Children's Hospital-San Diego, San Diego, CA, USA
| | - Saskia B Wortmann
- Amalia Children's Hospital, Radboud University Nijmegen, Nijmegen, The Netherlands.,University Childrens Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Rikke S Møller
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark.,Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
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50
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Hampshire K, Martin PM, Carlston C, Slavotinek A. Baraitser-Winter cerebrofrontofacial syndrome: Report of two adult siblings. Am J Med Genet A 2020; 182:1923-1932. [PMID: 32506774 DOI: 10.1002/ajmg.a.61637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/21/2020] [Accepted: 04/25/2020] [Indexed: 11/07/2022]
Abstract
Baraitser-Winter cerebrofrontofacial syndrome (BWCS) is a rare, autosomal dominant condition that is characterized by intellectual disability, distinctive craniofacial features, structural brain abnormalities, seizures, microcephaly, hearing loss, and ocular colobomas. The first three cases were described in 1988 by Baraitser and Winter and included two siblings and an unrelated third patient. Subsequently, causative missense variants in the ACTB and ACTG1 genes were identified, with de novo occurrence in patients with the condition. Herein, we describe two adult siblings who were born to unaffected parents and who were diagnosed with BWCS in their fourth and sixth decade of life following exome sequencing performed for intellectual disability. We review the literature reports of adult patients with BWCS to document the clinical features and phenotypic variability that can occur later in life. This is the first molecularly confirmed report of germline mosaicism in BWCS and one of only a few reports to describe two BWCS patients belonging to the same family.
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Affiliation(s)
- Karly Hampshire
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Colleen Carlston
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
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