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Hartley T, Marshall D, Acker M, Fooks K, Gillespie MK, Price EM, Graham ID, White-Brown A, MacKay L, Macdonald SK, Brady L, Hui AY, Andrews JD, Chowdhury A, Wall E, Soubry É, Ediae GU, Rojas S, Assamad D, Dyment D, Tarnopolsky M, Sawyer SL, Chisholm C, Lemire G, Amburgey K, Lazier J, Mendoza-Londono R, Dowling JJ, Balci TB, Armour CM, Bhola PT, Costain G, Dupuis L, Carter M, Badalato L, Richer J, Boswell-Patterson C, Kannu P, Cordeiro D, Warman-Chardon J, Graham G, Siu VM, Cytrynbaum C, Rusnak A, Aul RB, Yoon G, Gonorazky H, McNiven V, Mercimek-Andrews S, Guerin A, Deshwar AR, Marwaha A, Weksberg R, Karp N, Campbell M, Al-Qattan S, Shuen AY, Inbar-Feigenberg M, Cohn R, Szuto A, Inglese C, Poirier M, Chad L, Potter B, Boycott KM, Hayeems R. Evaluation of the diagnostic accuracy of exome sequencing and its impact on diagnostic thinking for patients with rare disease in a publicly funded health care system: A prospective cohort study. Genet Med 2024; 26:101012. [PMID: 37924259 DOI: 10.1016/j.gim.2023.101012] [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: 04/21/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023] Open
Abstract
PURPOSE To evaluate the diagnostic utility of publicly funded clinical exome sequencing (ES) for patients with suspected rare genetic diseases. METHODS We prospectively enrolled 297 probands who met eligibility criteria and received ES across 5 sites in Ontario, Canada, and extracted data from medical records and clinician surveys. Using the Fryback and Thornbury Efficacy Framework, we assessed diagnostic accuracy by examining laboratory interpretation of results and assessed diagnostic thinking by examining the clinical interpretation of results and whether clinical-molecular diagnoses would have been achieved via alternative hypothetical molecular tests. RESULTS Laboratories reported 105 molecular diagnoses and 165 uncertain results in known and novel genes. Of these, clinicians interpreted 102 of 105 (97%) molecular diagnoses and 6 of 165 (4%) uncertain results as clinical-molecular diagnoses. The 108 clinical-molecular diagnoses were in 104 families (35% diagnostic yield). Each eligibility criteria resulted in diagnostic yields of 30% to 40%, and higher yields were achieved when >2 eligibility criteria were met (up to 45%). Hypothetical tests would have identified 61% of clinical-molecular diagnoses. CONCLUSION We demonstrate robustness in eligibility criteria and high clinical validity of laboratory results from ES testing. The importance of ES was highlighted by the potential 40% of patients that would have gone undiagnosed without this test.
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Affiliation(s)
- Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada; University of Ottawa, Ottawa, Canada.
| | | | | | - Katharine Fooks
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Meredith K Gillespie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - E Magda Price
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Ian D Graham
- University of Ottawa, Ottawa, Canada; Ottawa Hospital Research Institute, Ottawa, Canada
| | | | - Layla MacKay
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Stella K Macdonald
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Lauren Brady
- McMaster Children's Hospital, McMaster University, Hamilton, Canada
| | - Angela Y Hui
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - Joseph D Andrews
- London Health Sciences Centre, Western University, London, Canada
| | - Ashfia Chowdhury
- London Health Sciences Centre, Western University, London, Canada
| | - Erika Wall
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Élisabeth Soubry
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Grace U Ediae
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Samantha Rojas
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | | | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada; University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Mark Tarnopolsky
- McMaster Children's Hospital, McMaster University, Hamilton, Canada
| | - Sarah L Sawyer
- University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Gabrielle Lemire
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada; University of Ottawa, Ottawa, Canada
| | - Kimberly Amburgey
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Joanna Lazier
- University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - James J Dowling
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Tugce B Balci
- London Health Sciences Centre, Western University, London, Canada
| | - Christine M Armour
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada; University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Priya T Bhola
- University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Gregory Costain
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Lucie Dupuis
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Melissa Carter
- University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Lauren Badalato
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - Julie Richer
- University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Peter Kannu
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada; The Ottawa Hospital, Ottawa, Canada
| | | | - Jodi Warman-Chardon
- University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada; Ottawa Hospital Research Institute, Ottawa, Canada; University of Alberta, Edmonton, Alberta, Canada
| | - Gail Graham
- University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Victoria Mok Siu
- London Health Sciences Centre, Western University, London, Canada
| | - Cheryl Cytrynbaum
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Alison Rusnak
- University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada; Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - Ritu B Aul
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Grace Yoon
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Hernan Gonorazky
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | | | | | - Andrea Guerin
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - Ashish R Deshwar
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Ashish Marwaha
- University of Calgary, Calgary, Canada; Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada; The Ottawa Hospital, Ottawa, Canada
| | - Rosanna Weksberg
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Natalya Karp
- London Health Sciences Centre, Western University, London, Canada
| | - Maggie Campbell
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - Sarah Al-Qattan
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Andrew Y Shuen
- University of Toronto, Toronto, Canada; McMaster Children's Hospital, McMaster University, Hamilton, Canada; London Health Sciences Centre, Western University, London, Canada
| | | | - Ronald Cohn
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Anna Szuto
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Cara Inglese
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | | | - Lauren Chad
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada
| | - Beth Potter
- University of Ottawa, Ottawa, Canada; Ottawa Hospital Research Institute, Ottawa, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada; University of Ottawa, Ottawa, Canada; Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Robin Hayeems
- Hospital for Sick Children, Toronto, Canada; University of Toronto, Toronto, Canada.
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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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3
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Sczakiel HL, Zhao M, Wollert-Wulf B, Danyel M, Ehmke N, Stoltenburg C, Damseh N, Al-Ashhab M, Balci TB, Osmond M, Andrade A, Schallner J, Porrmann J, McDonald K, Liao M, Oppermann H, Platzer K, Dierksen N, Mojarrad M, Eslahi A, Bakaeean B, Calame DG, Lupski JR, Firoozfar Z, Seyedhassani SM, Mohammadi SA, Anwaar N, Rahman F, Seelow D, Janz M, Horn D, Maroofian R, Boschann F. Broadening the phenotypic and molecular spectrum of FINCA syndrome: Biallelic NHLRC2 variants in 15 novel individuals. Eur J Hum Genet 2023; 31:905-917. [PMID: 37188825 PMCID: PMC10400545 DOI: 10.1038/s41431-023-01382-0] [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: 11/09/2022] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
FINCA syndrome [MIM: 618278] is an autosomal recessive multisystem disorder characterized by fibrosis, neurodegeneration and cerebral angiomatosis. To date, 13 patients from nine families with biallelic NHLRC2 variants have been published. In all of them, the recurrent missense variant p.(Asp148Tyr) was detected on at least one allele. Common manifestations included lung or muscle fibrosis, respiratory distress, developmental delay, neuromuscular symptoms and seizures often followed by early death due to rapid disease progression.Here, we present 15 individuals from 12 families with an overlapping phenotype associated with nine novel NHLRC2 variants identified by exome analysis. All patients described here presented with moderate to severe global developmental delay and variable disease progression. Seizures, truncal hypotonia and movement disorders were frequently observed. Notably, we also present the first eight cases in which the recurrent p.(Asp148Tyr) variant was not detected in either homozygous or compound heterozygous state.We cloned and expressed all novel and most previously published non-truncating variants in HEK293-cells. From the results of these functional studies, we propose a potential genotype-phenotype correlation, with a greater reduction in protein expression being associated with a more severe phenotype.Taken together, our findings broaden the known phenotypic and molecular spectrum and emphasize that NHLRC2-related disease should be considered in patients presenting with intellectual disability, movement disorders, neuroregression and epilepsy with or without pulmonary involvement.
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Affiliation(s)
- Henrike L Sczakiel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Ihnestr. 63-73, 14195, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Max Zhao
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Ihnestr. 63-73, 14195, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Brigitte Wollert-Wulf
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
| | - Magdalena Danyel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Nadja Ehmke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Corinna Stoltenburg
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Sozialpädiatrisches Zentrum Neuropädiatrie, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Nadirah Damseh
- Department of Pediatrics and Genetics, Al Makassed Hospital and Al-Quds University, Jerusalem, Palestine
| | - Motee Al-Ashhab
- Department of Pediatrics and Genetics, Al Makassed Hospital and Al-Quds University, Jerusalem, Palestine
| | - Tugce B Balci
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, Western University, London, ON, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Andrea Andrade
- Division of Pediatric Neurology, London Health Sciences Centre, Western University, London, ON, Canada
| | - Jens Schallner
- Department of Sozialpaediatrisches Zentrum, Klinik fuer Kinder und Jugendmedizin, Universitaetsklinikum Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Joseph Porrmann
- Institute for Clinical Genetics, Universitätsklinikum, Technischen Universität Dresden, Dresden, Germany
| | - Kimberly McDonald
- Pediatric Neurology, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | | | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atieh Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Behnaz Bakaeean
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Daniel G Calame
- Section of Pediatric Neurology and Developmental Neurosciences, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | | | - Najwa Anwaar
- Department of Developmental - Behavioral Pediatrics, University of Child Health Sciences and The Children's Hospital, Lahore, Pakistan
| | - Fatima Rahman
- Department of Developmental - Behavioral Pediatrics, University of Child Health Sciences and The Children's Hospital, Lahore, Pakistan
| | - Dominik Seelow
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Bioinformatics and Translational Genetics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Martin Janz
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
| | - Denise Horn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London, WC1N 3BG, UK
| | - Felix Boschann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany.
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4
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Wojcik MH, Srivastava S, Agrawal PB, Balci TB, Callewaert B, Calvo PL, Carli D, Caudle M, Colaiacovo S, Cross L, Demetriou K, Drazba K, Dutra-Clarke M, Edwards M, Genetti CA, Grange DK, Hickey SE, Isidor B, Küry S, Lachman HM, Lavillaureix A, Lyons MJ, Marcelis C, Marco EJ, Martinez-Agosto JA, Nowak C, Pizzol A, Planes M, Prijoles EJ, Riberi E, Rush ET, Russell BE, Sachdev R, Schmalz B, Shears D, Stevenson DA, Wilson K, Jansen S, de Vries BBA, Curry CJ. Jansen-de Vries syndrome: Expansion of the PPM1D clinical and phenotypic spectrum in 34 families. Am J Med Genet A 2023. [PMID: 37183572 DOI: 10.1002/ajmg.a.63226] [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: 01/20/2023] [Revised: 04/13/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
Jansen-de Vries syndrome (JdVS) is a neurodevelopmental condition attributed to pathogenic variants in Exons 5 and 6 of PPM1D. As the full phenotypic spectrum and natural history remain to be defined, we describe a large cohort of children and adults with JdVS. This is a retrospective cohort study of 37 individuals from 34 families with disease-causing variants in PPM1D leading to JdVS. Clinical data were provided by treating physicians and/or families. Of the 37 individuals, 27 were male and 10 female, with median age 8.75 years (range 8 months to 62 years). Four families document autosomal dominant transmission, and 32/34 probands were diagnosed via exome sequencing. The facial gestalt, including a broad forehead and broad mouth with a thin and tented upper lip, was most recognizable between 18 and 48 months of age. Common manifestations included global developmental delay (35/36, 97%), hypotonia (25/34, 74%), short stature (14/33, 42%), constipation (22/31, 71%), and cyclic vomiting (6/35, 17%). Distinctive personality traits include a hypersocial affect (21/31, 68%) and moderate-to-severe anxiety (18/28, 64%). In conclusion, JdVS is a clinically recognizable neurodevelopmental syndrome with a characteristic personality and distinctive facial features. The association of pathogenic variants in PPM1D with cyclic vomiting bears not only medical attention but also further pathogenic and mechanistic evaluation.
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Affiliation(s)
- Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics and Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Department of Pediatrics and Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pankaj B Agrawal
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Neonatology, Department of Pediatrics, Miller School of Medicine, University of Miami and Holtz Children's Hospital, Jackson Health System, Miami, Florida, USA
| | - Tugce B Balci
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - Bert Callewaert
- Center for Medical Genetics, Pediatrics Department, Ghent University Hospital, Ghent, Belgium
| | - Pier Luigi Calvo
- Pediatric Gastroenterology Unit, Regina Margherita Children's Hospital, Azienda Ospedaliera-Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Torino, Italy
| | - Michelle Caudle
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - Samantha Colaiacovo
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - Laura Cross
- Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Kalliope Demetriou
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Katy Drazba
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Marina Dutra-Clarke
- Division of Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Matthew Edwards
- Paediatrics, School of Medicine, Western Sydney University, Hunter Genetics, Newcastle, New South Wales, Australia
| | - Casie A Genetti
- Division of Genetics and Genomics, Department of Pediatrics and Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Bertrand Isidor
- Department of Medical Genetics, Nantes Hospital, Nantes, France
| | - Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du thorax, Nantes, France
| | - Herbert M Lachman
- Departments of Behavioral Science, Medicine, and Psychiatry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alinoe Lavillaureix
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN ITHACA, CHU Rennes, Hôpital Sud, Rennes, France
| | | | - Carlo Marcelis
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elysa J Marco
- Cortica Healthcare, Marin Center, San Rafael, California, USA
| | - Julian A Martinez-Agosto
- Division of Genetics, Departments of Pediatrics and Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Catherine Nowak
- Division of Genetics and Genomics, Department of Pediatrics and Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Antonio Pizzol
- Pediatric Gastroenterology Unit, Regina Margherita Children's Hospital, Azienda Ospedaliera-Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Marc Planes
- Service de Génétique Clinique, University Hospital Morvan, Brest, France
| | | | - Evelise Riberi
- Department of Public Health and Pediatrics, University of Torino, Torino, Italy
| | - Eric T Rush
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, USA
- Division of Genetics, Children's Mercy Kansas City, Kansas City, Missouri, USA
- Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, Missouri, USA
| | - Bianca E Russell
- Division of Genetics, Departments of Pediatrics and Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Betsy Schmalz
- Department of Pediatrics, The Ohio State University College of Medicine, Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Deborah Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David A Stevenson
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Kate Wilson
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sandra Jansen
- Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cynthia J Curry
- Genetic Medicine, Department of Pediatrics, University of California San Francisco/Fresno, Fresno, California, USA
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5
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Hartley T, Soubry É, Acker M, Osmond M, Couse M, Gillespie MK, Ito Y, Marshall AE, Lemire G, Huang L, Chisholm C, Eaton AJ, Price EM, Dowling JJ, Ramani AK, Mendoza-Londono R, Costain G, Axford MM, Szuto A, McNiven V, Damseh N, Jobling R, de Kock L, Mojarad BA, Young T, Shao Z, Hayeems RZ, Graham ID, Tarnopolsky M, Brady L, Armour CM, Geraghty M, Richer J, Sawyer S, Lines M, Mercimek-Andrews S, Carter MT, Graham G, Kannu P, Lazier J, Li C, Aul RB, Balci TB, Dlamini N, Badalato L, Guerin A, Walia J, Chitayat D, Cohn R, Faghfoury H, Forster-Gibson C, Gonorazky H, Grunebaum E, Inbar-Feigenberg M, Karp N, Morel C, Rusnak A, Sondheimer N, Warman-Chardon J, Bhola PT, Bourque DK, Chacon IJ, Chad L, Chakraborty P, Chong K, Doja A, Goh ESY, Saleh M, Potter BK, Marshall CR, Dyment DA, Kernohan K, Boycott KM. Bridging clinical care and research in Ontario, Canada: Maximizing diagnoses from reanalysis of clinical exome sequencing data. Clin Genet 2023; 103:288-300. [PMID: 36353900 DOI: 10.1111/cge.14262] [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: 09/25/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
We examined the utility of clinical and research processes in the reanalysis of publicly-funded clinical exome sequencing data in Ontario, Canada. In partnership with eight sites, we recruited 287 families with suspected rare genetic diseases tested between 2014 and 2020. Data from seven laboratories was reanalyzed with the referring clinicians. Reanalysis of clinically relevant genes identified diagnoses in 4% (13/287); four were missed by clinical testing. Translational research methods, including analysis of novel candidate genes, identified candidates in 21% (61/287). Of these, 24 families have additional evidence through data sharing to support likely diagnoses (8% of cohort). This study indicates few diagnoses are missed by clinical laboratories, the incremental gain from reanalysis of clinically-relevant genes is modest, and the highest yield comes from validation of novel disease-gene associations. Future implementation of translational research methods, including continued reporting of compelling genes of uncertain significance by clinical laboratories, should be considered to maximize diagnoses.
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Affiliation(s)
- Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Élisabeth Soubry
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Meryl Acker
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | | | - Meredith K Gillespie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Aren E Marshall
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Gabrielle Lemire
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Lijia Huang
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Alison J Eaton
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- University of Alberta, Edmonton, Canada
| | - E Magda Price
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - James J Dowling
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | | | | | - Gregory Costain
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Michelle M Axford
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Anna Szuto
- Hospital for Sick Children, Toronto, Canada
| | - Vanda McNiven
- Hospital for Sick Children, Toronto, Canada
- University Health Network, Toronto, Canada
| | | | | | - Leanne de Kock
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | | | - Ted Young
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Zhuo Shao
- University of Toronto, Toronto, Canada
- North York General Hospital, Toronto, Canada
| | | | - Ian D Graham
- University of Ottawa, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
| | | | | | - Christine M Armour
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Julie Richer
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Sarah Sawyer
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Matthew Lines
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Melissa T Carter
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Gail Graham
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Peter Kannu
- Hospital for Sick Children, Toronto, Canada
- University of Alberta, Edmonton, Canada
| | - Joanna Lazier
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Chumei Li
- McMaster Children's Hospital, Hamilton, Canada
| | - Ritu B Aul
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Tugce B Balci
- London Health Sciences Center, Western University, London, Canada
| | | | - Lauren Badalato
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - Andrea Guerin
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - Jagdeep Walia
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - David Chitayat
- Hospital for Sick Children, Toronto, Canada
- Mount Sinai Hospital, Toronto, Canada
| | | | | | | | | | | | | | - Natalya Karp
- London Health Sciences Center, Western University, London, Canada
| | | | - Alison Rusnak
- Children's Hospital of Eastern Ontario, Ottawa, Canada
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | | | - Jodi Warman-Chardon
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
- The Ottawa Hospital, Ottawa, Canada
| | - Priya T Bhola
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Danielle K Bourque
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Lauren Chad
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Pranesh Chakraborty
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Asif Doja
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Maha Saleh
- London Health Sciences Center, Western University, London, Canada
| | | | - Beth K Potter
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Christian R Marshall
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
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6
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Levy MA, Relator R, McConkey H, Pranckeviciene E, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Ferilli M, Fletcher RS, Cherick F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Plomp AS, Poulton C, Reilly J, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, John MS, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci TB, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Campion D, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Heron D, Husson T, Kernohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vincent M, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Hum Mutat 2022; 43:1609-1628. [PMID: 35904121 DOI: 10.1002/humu.24446] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 12/06/2021] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022]
Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Erinija Pranckeviciene
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Mariet W Elting
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Marco Ferilli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Florian Cherick
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, The Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000, Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | | | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | | | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Delphine Heron
- AP-HP, Département de Génétique Médicale, Groupe Hospitalier Pitié Salpétrière, Paris, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, UK, and Sheffield Children's Hospital NHS Foundation Trust
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Dept of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Marie Vincent
- Service de génétique Médicale, CHU Nantes, France.,Institut du thorax, INSERM, CNRS, UNIV Nantes, 44007, Nantes, France
| | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
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7
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Alves CAPF, Sherbini O, D'Arco F, Steel D, Kurian MA, Radio FC, Ferrero GB, Carli D, Tartaglia M, Balci TB, Powell-Hamilton NN, Schrier Vergano SA, Reutter H, Hoefele J, Günthner R, Roeder ER, Littlejohn RO, Lessel D, Lüttgen S, Kentros C, Anyane-Yeboa K, Catarino CB, Mercimek-Andrews S, Denecke J, Lyons MJ, Klopstock T, Bhoj EJ, Bryant L, Vanderver A. Brain Abnormalities in Patients with Germline Variants in H3F3: Novel Imaging Findings and Neurologic Symptoms Beyond Somatic Variants and Brain Tumors. AJNR Am J Neuroradiol 2022; 43:1048-1053. [PMID: 35772801 DOI: 10.3174/ajnr.a7555] [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: 02/23/2022] [Accepted: 04/18/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Pathogenic somatic variants affecting the genes Histone 3 Family 3A and 3B (H3F3) are extensively linked to the process of oncogenesis, in particular related to central nervous system tumors in children. Recently, H3F3 germline missense variants were described as the cause of a novel pediatric neurodevelopmental disorder. We aimed to investigate patterns of brain MR imaging of individuals carrying H3F3 germline variants. MATERIALS AND METHODS In this retrospective study, we included individuals with proved H3F3 causative genetic variants and available brain MR imaging scans. Clinical and demographic data were retrieved from available medical records. Molecular genetic testing results were classified using the American College of Medical Genetics criteria for variant curation. Brain MR imaging abnormalities were analyzed according to their location, signal intensity, and associated clinical symptoms. Numeric variables were described according to their distribution, with median and interquartile range. RESULTS Eighteen individuals (10 males, 56%) with H3F3 germline variants were included. Thirteen of 18 individuals (72%) presented with a small posterior fossa. Six individuals (33%) presented with reduced size and an internal rotational appearance of the heads of the caudate nuclei along with an enlarged and squared appearance of the frontal horns of the lateral ventricles. Five individuals (28%) presented with dysgenesis of the splenium of the corpus callosum. Cortical developmental abnormalities were noted in 8 individuals (44%), with dysgyria and hypoplastic temporal poles being the most frequent presentation. CONCLUSIONS Imaging phenotypes in germline H3F3-affected individuals are related to brain features, including a small posterior fossa as well as dysgenesis of the corpus callosum, cortical developmental abnormalities, and deformity of lateral ventricles.
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Affiliation(s)
| | - O Sherbini
- Department of Neurology (O.S., A.V.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - D Steel
- Neurology (D.S., M.A.K.), Great Ormond Street Hospital for Children, London, UK.,Molecular Neurosciences (D.S., M.A.K.), Zayed Centre for Research into Rare Diseases in Children, UCL GOS-Institute of Child Health, London, UK
| | - M A Kurian
- Neurology (D.S., M.A.K.), Great Ormond Street Hospital for Children, London, UK.,Molecular Neurosciences (D.S., M.A.K.), Zayed Centre for Research into Rare Diseases in Children, UCL GOS-Institute of Child Health, London, UK
| | - F C Radio
- Genetics and Rare Diseases Research Division (F.C.R., M.T.), Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - G B Ferrero
- Department of Public Health and Pediatrics (G.B.F., D.C.), University of Torino, Turin, Italy
| | - D Carli
- Department of Public Health and Pediatrics (G.B.F., D.C.), University of Torino, Turin, Italy
| | - M Tartaglia
- Genetics and Rare Diseases Research Division (F.C.R., M.T.), Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - T B Balci
- Medical Genetics Programof Southwestern Ontario (T.B.B.), London Health Sciences Centre, London, Ontario, Canada.,Department of Paediatrics (T.B.B.), Western University, London, Ontario, Canada
| | - N N Powell-Hamilton
- Division of Medical Genetics (N.N.P.-H.), Nemours Children's Hospital, Wilmington, Delaware
| | - S A Schrier Vergano
- Division of Medical Genetics and Metabolism (S.A.S.V.), Children's Hospital of The King's Daughters, Norfolk, Virginia.,Department of Pediatrics (S.A.S.V.), Eastern Virginia Medical School, Norfolk, Virginia
| | - H Reutter
- Division of Neonatology and Pediatric Intensive Care (H.R.), Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University Nürnberg-Erlangen, Erlangen, Germany
| | - J Hoefele
- Institute of Human Genetics (J.H., R.G.)
| | - R Günthner
- Institute of Human Genetics (J.H., R.G.).,Department of Nephrology (R.G.), Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - E R Roeder
- Department of Pediatrics and Molecular and Human Genetics (E.R.R., R.O.L.), Baylor College of Medicine, San Antonio, Texas
| | - R O Littlejohn
- Department of Pediatrics and Molecular and Human Genetics (E.R.R., R.O.L.), Baylor College of Medicine, San Antonio, Texas
| | - D Lessel
- Institute of Human Genetics (D.L., S.L.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - S Lüttgen
- Institute of Human Genetics (D.L., S.L.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - C Kentros
- Division of Clinical Genetics (C.K., K.A.-Y.), Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian, New York, New York
| | - K Anyane-Yeboa
- Division of Clinical Genetics (C.K., K.A.-Y.), Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian, New York, New York
| | - C B Catarino
- Friedrich-Baur-Institute (C.B.C., T.K.), Department of Neurology, University Hospital, Ludwig-Maximilian University Munich, Munich, Germany
| | - S Mercimek-Andrews
- Department of Medical Genetics (S.M.-A.), Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Genetics (S.M.-A.), The Hospital for Sick Children, Toronto, Ontario, Canada
| | - J Denecke
- Department of Pediatrics (J.D.), University Medical Center Eppendorf, Hamburg, Germany
| | - M J Lyons
- Greenwood Genetic Center (M.J.L.), Greenwood, South Carolina
| | - T Klopstock
- Friedrich-Baur-Institute (C.B.C., T.K.), Department of Neurology, University Hospital, Ludwig-Maximilian University Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (T.K.), Munich, Germany.,Munich Cluster for Systems Neurology (T.K.), Munich, Germany
| | - E J Bhoj
- Department of Radiology, Division of Human Genetics (E.J.B., L.B.)
| | - L Bryant
- Department of Radiology, Division of Human Genetics (E.J.B., L.B.)
| | - A Vanderver
- Department of Pediatrics, and Division of Neurology (A.V.), Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Neurology (O.S., A.V.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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8
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Aref-Eshghi E, Kerkhof J, Pedro VP, France GDI, Barat-Houari M, Ruiz-Pallares N, Andrau JC, Lacombe D, Van-Gils J, Fergelot P, Dubourg C, Cormier-Daire V, Rondeau S, Lecoquierre F, Saugier-Veber P, Nicolas G, Lesca G, Chatron N, Sanlaville D, Vitobello A, Faivre L, Thauvin-Robinet C, Laumonnier F, Raynaud M, Alders M, Mannens M, Henneman P, Hennekam RC, Velasco G, Francastel C, Ulveling D, Ciolfi A, Pizzi S, Tartaglia M, Heide S, Héron D, Mignot C, Keren B, Whalen S, Afenjar A, Bienvenu T, Campeau PM, Rousseau J, Levy MA, Brick L, Kozenko M, Balci TB, Siu VM, Stuart A, Kadour M, Masters J, Takano K, Kleefstra T, de Leeuw N, Field M, Shaw M, Gecz J, Ainsworth PJ, Lin H, Rodenhiser DI, Friez MJ, Tedder M, Lee JA, DuPont BR, Stevenson RE, Skinner SA, Schwartz CE, Genevieve D, Sadikovic B. Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders. Am J Hum Genet 2021; 108:1161-1163. [PMID: 34087165 DOI: 10.1016/j.ajhg.2021.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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9
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Chang CA, Perrier R, Kurek KC, Estrada-Veras J, Lehman A, Yip S, Hendson G, Diamond C, Pinchot JW, Tran JM, Arkin LM, Drolet BA, Napier MP, O'Neill SA, Balci TB, Keppler-Noreuil KM. Novel findings and expansion of phenotype in a mosaic RASopathy caused by somatic KRAS variants. Am J Med Genet A 2021; 185:2829-2845. [PMID: 34056834 DOI: 10.1002/ajmg.a.62356] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 02/16/2021] [Revised: 04/16/2021] [Accepted: 05/04/2021] [Indexed: 11/11/2022]
Abstract
Mosaic KRAS variants and other RASopathy genes cause oculoectodermal, encephalo-cranio-cutaneous lipomatosis, and Schimmelpenning-Feuerstein-Mims syndromes, and a spectrum of vascular malformations, overgrowth and other associated anomalies, the latter of which are only recently being characterized. We describe eight individuals in total (six unreported cases and two previously reported cases) with somatic KRAS variants and variably associated features. Given the findings of somatic overgrowth (in seven individuals) and vascular or lymphatic malformations (in eight individuals), we suggest mosaic RASopathies (mosaic KRAS variants) be considered in the differential diagnosis for individuals presenting with asymmetric overgrowth and lymphatic or vascular anomalies. We expand the association with embryonal tumors, including the third report of embryonal rhabdomyosarcoma, as well as novel findings of Wilms tumor and nephroblastomatosis in two individuals. Rare or novel findings in our series include the presence of epilepsy, polycystic kidneys, and T-cell deficiency in one individual, and multifocal lytic bone lesions in two individuals. Finally, we describe the first use of targeted therapy with a MEK inhibitor for an individual with a mosaic KRAS variant. The purposes of this report are to expand the phenotypic spectrum of mosaic KRAS-related disorders, and to propose possible mechanisms of pathogenesis, and surveillance of its associated findings.
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Affiliation(s)
- Caitlin A Chang
- Department of Medical Genetics, BC Women and Children's Hospital, Vancouver, British Columbia, Canada
| | - Renee Perrier
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Kyle C Kurek
- Department of Pathology, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Juvianee Estrada-Veras
- Medical Genetics Service, Walter Reed National Military Medical Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Anna Lehman
- Department of Medical Genetics, BC Women and Children's Hospital, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Glenda Hendson
- Department of Pathology, BC Women and Children's Hospital, Vancouver, British Columbia, Canada
| | - Carol Diamond
- Department of Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jason W Pinchot
- Department of Interventional Radiology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jennifer M Tran
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Lisa M Arkin
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Beth A Drolet
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Melanie P Napier
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - Sarah A O'Neill
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - Tugce B Balci
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - Kim M Keppler-Noreuil
- Division of Genetics and Metabolism, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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10
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Sadikovic B, Levy MA, Kerkhof J, Aref-Eshghi E, Schenkel L, Stuart A, McConkey H, Henneman P, Venema A, Schwartz CE, Stevenson RE, Skinner SA, DuPont BR, Fletcher RS, Balci TB, Siu VM, Granadillo JL, Masters J, Kadour M, Friez MJ, van Haelst MM, Mannens MMAM, Louie RJ, Lee JA, Tedder ML, Alders M. Correction: Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet Med 2021; 23:2228. [PMID: 33637969 PMCID: PMC9119201 DOI: 10.1038/s41436-021-01130-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Andrea Venema
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Victoria Mok Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jennefer Masters
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Mike Kadour
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | | | - Mieke M van Haelst
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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11
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Sadikovic B, Levy MA, Kerkhof J, Aref-Eshghi E, Schenkel L, Stuart A, McConkey H, Henneman P, Venema A, Schwartz CE, Stevenson RE, Skinner SA, DuPont BR, Fletcher RS, Balci TB, Siu VM, Granadillo JL, Masters J, Kadour M, Friez MJ, van Haelst MM, Mannens MMAM, Louie RJ, Lee JA, Tedder ML, Alders M. Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet Med 2021; 23:1065-1074. [PMID: 33547396 PMCID: PMC8187150 DOI: 10.1038/s41436-020-01096-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [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: 08/27/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 01/23/2023] Open
Abstract
Purpose We describe the clinical implementation of genome-wide DNA methylation analysis in rare disorders across the EpiSign diagnostic laboratory network and the assessment of results and clinical impact in the first subjects tested. Methods We outline the logistics and data flow between an integrated network of clinical diagnostics laboratories in Europe, the United States, and Canada. We describe the clinical validation of EpiSign using 211 specimens and assess the test performance and diagnostic yield in the first 207 subjects tested involving two patient subgroups: the targeted cohort (subjects with previous ambiguous/inconclusive genetic findings including genetic variants of unknown clinical significance) and the screening cohort (subjects with clinical findings consistent with hereditary neurodevelopmental syndromes and no previous conclusive genetic findings). Results Among the 207 subjects tested, 57 (27.6%) were positive for a diagnostic episignature including 48/136 (35.3%) in the targeted cohort and 8/71 (11.3%) in the screening cohort, with 4/207 (1.9%) remaining inconclusive after EpiSign analysis. Conclusion This study describes the implementation of diagnostic clinical genomic DNA methylation testing in patients with rare disorders. It provides strong evidence of clinical utility of EpiSign analysis, including the ability to provide conclusive findings in the majority of subjects tested.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Andrea Venema
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Victoria Mok Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jennefer Masters
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Mike Kadour
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | | | - Mieke M van Haelst
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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12
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Prasad M, Balci TB, Prasad C, Andrews JD, Lee R, Jurkiewicz MT, Napier MP, Colaiacovo S, Guillen Sacoto MJ, Karp N. BCL11B-related disorder in two canadian children: Expanding the clinical phenotype. Eur J Med Genet 2020; 63:104007. [PMID: 32659295 DOI: 10.1016/j.ejmg.2020.104007] [Citation(s) in RCA: 4] [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: 12/21/2019] [Revised: 05/06/2020] [Accepted: 07/07/2020] [Indexed: 12/29/2022]
Abstract
The product of the BCL11B (B-Cell Leukemia 11) gene is a bi-functional transcriptional regulator that can act as either a repressor or an activator. It plays an important role in the development of the nervous, immune, and cutaneous systems, and is also involved in dental and craniofacial development. BCL11B-Related Disorder (BCL11BRD) is a novel rare neurodevelopmental disorder associated with mutations in BCL11B. A total of 17 patients have been described in the literature thus far. The main symptoms of BCL11BRD include global developmental delay, speech impairment, dental anomalies, feeding difficulties, refractive errors, dysmorphic features, and immunological abnormalities. In this report, we describe two Canadian girls, with pathogenic de novo BCL11B variants, both diagnosed via exome sequencing. One of the patients had global developmental delay, dental anomalies, dysmorphic features, dyskinesia and hypotonia; the latter two symptoms have not been previously reported in patients with BCL11BRD. She also had dysgenesis of corpus callosum and dilatation of the frontal horns of lateral ventricles, a brain anomaly that has been previously reported in only one other patient. The second patient had developmental delay, dysmorphic features, spasticity in lower limbs and dental anomalies. Our report contributes to the knowledge of the BCL11BRD, expands the clinical phenotype, and can also aid with genetic counseling of newly identified patients.
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Affiliation(s)
- M Prasad
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - T B Balci
- Schulich School of Medicine and Dentistry, Western University, Department of Pediatrics, Division of Medical Genetics, London Health Sciences Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | - C Prasad
- Schulich School of Medicine and Dentistry, Western University, Department of Pediatrics, Division of Medical Genetics, London Health Sciences Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | - J D Andrews
- Lawson Health Research Institute, London Health Sciences Centre, London, Ontario, Canada
| | - R Lee
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Dentistry, London Health Sciences Centre, London, Ontario, Canada
| | - M T Jurkiewicz
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medical Imaging, London Health Sciences Centre, London, Ontario, Canada
| | - M P Napier
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - S Colaiacovo
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | | | - N Karp
- Schulich School of Medicine and Dentistry, Western University, Department of Pediatrics, Division of Medical Genetics, London Health Sciences Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada.
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13
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Chang WH, Mashouri P, Lozano AX, Johnstone B, Husić M, Olry A, Maiella S, Balci TB, Sawyer SL, Robinson PN, Rath A, Brudno M. Correction: Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes. Genet Med 2020; 22:1427. [PMID: 32555415 DOI: 10.1038/s41436-020-0866-6] [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] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Willie H Chang
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada.,Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Pouria Mashouri
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada
| | - Alexander X Lozano
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada.,Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Materials Science & Engineering, Stanford University, Stanford, CA, USA
| | - Brittney Johnstone
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada.,Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Mia Husić
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada
| | - Annie Olry
- Orphanet, Institut national de la santé et de la recherche médicale, Paris, France
| | - Sylvie Maiella
- Orphanet, Institut national de la santé et de la recherche médicale, Paris, France
| | - Tugce B Balci
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Sarah L Sawyer
- Department of Genetics, Children's Hospital of Eastern Ontario and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Ana Rath
- Orphanet, Institut national de la santé et de la recherche médicale, Paris, France
| | - Michael Brudno
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada. .,Department of Computer Science, University of Toronto, Toronto, ON, Canada. .,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada. .,University Health Network, Toronto, ON, Canada.
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14
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Chang WH, Mashouri P, Lozano AX, Johnstone B, Husić M, Olry A, Maiella S, Balci TB, Sawyer SL, Robinson PN, Rath A, Brudno M. Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes. Genet Med 2020; 22:1391-1400. [PMID: 32366968 DOI: 10.1038/s41436-020-0812-7] [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: 11/21/2019] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Computational documentation of genetic disorders is highly reliant on structured data for differential diagnosis, pathogenic variant identification, and patient matchmaking. However, most information on rare diseases (RDs) exists in freeform text, such as academic literature. To increase availability of structured RD data, we developed a crowdsourcing approach for collecting phenotype information using student assignments. METHODS We developed Phenotate, a web application for crowdsourcing disease phenotype annotations through assignments for undergraduate genetics students. Using student-collected data, we generated composite annotations for each disease through a machine learning approach. These annotations were compared with those from clinical practitioners and gold standard curated data. RESULTS Deploying Phenotate in five undergraduate genetics courses, we collected annotations for 22 diseases. Student-sourced annotations showed strong similarity to gold standards, with F-measures ranging from 0.584 to 0.868. Furthermore, clinicians used Phenotate annotations to identify diseases with comparable accuracy to other annotation sources and gold standards. For six disorders, no gold standards were available, allowing us to create some of the first structured annotations for them, while students demonstrated ability to research RDs. CONCLUSION Phenotate enables crowdsourcing RD phenotypic annotations through educational assignments. Presented as an intuitive web-based tool, it offers pedagogical benefits and augments the computable RD knowledgebase.
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Affiliation(s)
- Willie H Chang
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada.,Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Pouria Mashouri
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada
| | - Alexander X Lozano
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada.,Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Materials Science & Engineering, Stanford University, Stanford, CA, USA
| | - Brittney Johnstone
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada.,Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Mia Husić
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada
| | - Annie Olry
- Orphanet, Institut national de la santé et de la recherche médicale, Paris, France
| | - Sylvie Maiella
- Orphanet, Institut national de la santé et de la recherche médicale, Paris, France
| | - Tugce B Balci
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Sarah L Sawyer
- Department of Genetics, Children's Hospital of Eastern Ontario and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Ana Rath
- Orphanet, Institut national de la santé et de la recherche médicale, Paris, France
| | - Michael Brudno
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada. .,Department of Computer Science, University of Toronto, Toronto, ON, Canada. .,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada. .,University Health Network, Toronto, ON, Canada.
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15
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Aref-Eshghi E, Kerkhof J, Pedro VP, Barat-Houari M, Ruiz-Pallares N, Andrau JC, Lacombe D, Van-Gils J, Fergelot P, Dubourg C, Cormier-Daire V, Rondeau S, Lecoquierre F, Saugier-Veber P, Nicolas G, Lesca G, Chatron N, Sanlaville D, Vitobello A, Faivre L, Thauvin-Robinet C, Laumonnier F, Raynaud M, Alders M, Mannens M, Henneman P, Hennekam RC, Velasco G, Francastel C, Ulveling D, Ciolfi A, Pizzi S, Tartaglia M, Heide S, Héron D, Mignot C, Keren B, Whalen S, Afenjar A, Bienvenu T, Campeau PM, Rousseau J, Levy MA, Brick L, Kozenko M, Balci TB, Siu VM, Stuart A, Kadour M, Masters J, Takano K, Kleefstra T, de Leeuw N, Field M, Shaw M, Gecz J, Ainsworth PJ, Lin H, Rodenhiser DI, Friez MJ, Tedder M, Lee JA, DuPont BR, Stevenson RE, Skinner SA, Schwartz CE, Genevieve D, Sadikovic B, Sadikovic B. Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders. Am J Hum Genet 2020; 106:356-370. [PMID: 32109418 DOI: 10.1016/j.ajhg.2020.01.019] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [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: 11/08/2019] [Accepted: 01/27/2020] [Indexed: 01/24/2023] Open
Abstract
Genetic syndromes frequently present with overlapping clinical features and inconclusive or ambiguous genetic findings which can confound accurate diagnosis and clinical management. An expanding number of genetic syndromes have been shown to have unique genomic DNA methylation patterns (called "episignatures"). Peripheral blood episignatures can be used for diagnostic testing as well as for the interpretation of ambiguous genetic test results. We present here an approach to episignature mapping in 42 genetic syndromes, which has allowed the identification of 34 robust disease-specific episignatures. We examine emerging patterns of overlap, as well as similarities and hierarchical relationships across these episignatures, to highlight their key features as they are related to genetic heterogeneity, dosage effect, unaffected carrier status, and incomplete penetrance. We demonstrate the necessity of multiclass modeling for accurate genetic variant classification and show how disease classification using a single episignature at a time can sometimes lead to classification errors in closely related episignatures. We demonstrate the utility of this tool in resolving ambiguous clinical cases and identification of previously undiagnosed cases through mass screening of a large cohort of subjects with developmental delays and congenital anomalies. This study more than doubles the number of published syndromes with DNA methylation episignatures and, most significantly, opens new avenues for accurate diagnosis and clinical assessment in individuals affected by these disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada.
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16
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Balci TB, Strong A, Kalish JM, Zackai E, Maris JM, Reilly A, Surrey LF, Wertheim GB, Marcadier JL, Graham GE, Carter MT. Tatton-Brown-Rahman syndrome: Six individuals with novel features. Am J Med Genet A 2020; 182:673-680. [PMID: 31961069 DOI: 10.1002/ajmg.a.61475] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 10/01/2019] [Revised: 11/26/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022]
Abstract
Tatton-Brown Rahman syndrome (TBRS) is an overgrowth-intellectual disability syndrome caused by heterozygous variants in DNMT3A. Seventy-eight individuals have been reported with a consistent phenotype of somatic overgrowth, mild to moderate intellectual disability, and similar dysmorphisms. We present six individuals with TBRS, including the youngest individual thus far reported, first individual to be diagnosed with tumor testing and two individuals with variants at the Arg882 domain, bringing the total number of reported cases to 82. Patients reported herein have additional clinical features not previously reported in TBRS. One patient had congenital diaphragmatic hernia. One patient carrying the recurrent p.Arg882His DNMT3A variant, who was previously reported as having a phenotype due to a truncating variant in the CLTC gene, developed a ganglioneuroblastoma at 18 months and T-cell lymphoblastic lymphoma at 6 years of age. Four patients manifested symptoms suggestive of autonomic dysfunction, including central sleep apnea, postural orthostatic hypotension, and episodic vasomotor instability in the extremities. We discuss the molecular and clinical findings in our patients with TBRS in context of existing literature.
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Affiliation(s)
- Tugce B Balci
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Alana Strong
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jennifer M Kalish
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elaine Zackai
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - John M Maris
- Department of Pediatrics, Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Anne Reilly
- Department of Pediatrics, Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lea F Surrey
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gerald B Wertheim
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Julien L Marcadier
- Department of Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Gail E Graham
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Melissa T Carter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
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17
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Jordan VK, Fregeau B, Ge X, Giordano J, Wapner RJ, Balci TB, Carter MT, Bernat JA, Moccia AN, Srivastava A, Martin DM, Bielas SL, Pappas J, Svoboda MD, Rio M, Boddaert N, Cantagrel V, Lewis AM, Scaglia F, Kohler JN, Bernstein JA, Dries AM, Rosenfeld JA, DeFilippo C, Thorson W, Yang Y, Sherr EH, Bi W, Scott DA. Genotype-phenotype correlations in individuals with pathogenic RERE variants. Hum Mutat 2018; 39:666-675. [PMID: 29330883 PMCID: PMC5903952 DOI: 10.1002/humu.23400] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 09/12/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 12/21/2022]
Abstract
Heterozygous variants in the arginine-glutamic acid dipeptide repeats gene (RERE) have been shown to cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH). Here, we report nine individuals with NEDBEH who carry partial deletions or deleterious sequence variants in RERE. These variants were found to be de novo in all cases in which parental samples were available. An analysis of data from individuals with NEDBEH suggests that point mutations affecting the Atrophin-1 domain of RERE are associated with an increased risk of structural eye defects, congenital heart defects, renal anomalies, and sensorineural hearing loss when compared with loss-of-function variants that are likely to lead to haploinsufficiency. A high percentage of RERE pathogenic variants affect a histidine-rich region in the Atrophin-1 domain. We have also identified a recurrent two-amino-acid duplication in this region that is associated with the development of a CHARGE syndrome-like phenotype. We conclude that mutations affecting RERE result in a spectrum of clinical phenotypes. Genotype-phenotype correlations exist and can be used to guide medical decision making. Consideration should also be given to screening for RERE variants in individuals who fulfill diagnostic criteria for CHARGE syndrome but do not carry pathogenic variants in CHD7.
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Affiliation(s)
- Valerie K. Jordan
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, San Francisco, California
| | - Xiaoyan Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| | - Jessica Giordano
- Institute of Genomic Medicine and Department of OB/GYN, Columbia University Medical Center, New York, New York
| | - Ronald J. Wapner
- Institute of Genomic Medicine and Department of OB/GYN, Columbia University Medical Center, New York, New York
| | - Tugce B. Balci
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Melissa T. Carter
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - John A. Bernat
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, Iowa
| | - Amanda N. Moccia
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Donna M. Martin
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Stephanie L. Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - John Pappas
- New York University School of Medicine, New York, New York
| | - Melissa D. Svoboda
- Department of Pediatrics, Children’s Hospital of San Antonio/Baylor College of Medicine, San Antonio, Texas
| | - Marlène Rio
- Laboratory of Developmental Brain Disorders, INSERM UMR 1163, Paris, France
- Service de Génétique, Necker Enfants Malades University Hospital, APHP, Paris, France
| | - Nathalie Boddaert
- Laboratory of Developmental Brain Disorders, INSERM UMR 1163, Paris, France
- Pediatric Radiology, Necker Enfants Malades University Hospital, APHP, Paris, France
| | - Vincent Cantagrel
- Laboratory of Developmental Brain Disorders, INSERM UMR 1163, Paris, France
- Paris Descartes - Sorbonne Paris Cité UniversityImagine Institute, Paris, France
| | - Andrea M. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
| | | | | | | | - Annika M. Dries
- Stanford University School of Medicine, Stanford, California
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Colette DeFilippo
- Stanford Children’s Health/Lucile Packard Children’s Hospital Stanford, Palo Alto, California
| | - Willa Thorson
- University of MiamiMiller School of Medicine, Miami, Florida
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| | - Elliott H. Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, California
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| | - Daryl A. Scott
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
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18
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Balci TB, Davila J, Lewis D, Boafo A, Sell E, Richer J, Nikkel SM, Armour CM, Tomiak E, Lines MA, Sawyer SL. Broad spectrum of neuropsychiatric phenotypes associated with white matter disease in PTEN hamartoma tumor syndrome. Am J Med Genet B Neuropsychiatr Genet 2018; 177:101-109. [PMID: 29152901 DOI: 10.1002/ajmg.b.32610] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/30/2017] [Indexed: 11/11/2022]
Abstract
White matter lesions have been described in patients with PTEN hamartoma tumor syndrome (PHTS). How these lesions correlate with the neurocognitive features associated with PTEN mutations, such as autism spectrum disorder (ASD) or developmental delay, has not been well established. We report nine patients with PTEN mutations and white matter changes on brain magnetic resonance imaging (MRI), eight of whom were referred for reasons other than developmental delay or ASD. Their clinical presentations ranged from asymptomatic macrocephaly with normal development/intellect, to obsessive compulsive disorder, and debilitating neurological disease. To our knowledge, this report constitutes the first detailed description of PTEN-related white matter changes in adult patients and in children with normal development and intelligence. We present a detailed assessment of the neuropsychological phenotype of our patients and discuss the relationship between the wide array of neuropsychiatric features and observed white matter findings in the context of these individuals.
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Affiliation(s)
- Tugce B Balci
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Jorge Davila
- Department of Medical Imaging, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Denice Lewis
- Department of Psychiatry, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Family Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Addo Boafo
- Department of Psychiatry, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Erick Sell
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Julie Richer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Sarah M Nikkel
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Christine M Armour
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Eva Tomiak
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Matthew A Lines
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada.,Division of Metabolics and Newborn Screening, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Sarah L Sawyer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
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19
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Yuregir OO, Ayaz A, Yalcintepe S, Canbek S, Acik DY, Yilmaz BT, Balci TB. Detection of α-Thalassemia by Using Multiplex Ligation-Dependent Probe Amplification as an Additional Method for Rare Mutations in Southern Turkey. Indian J Hematol Blood Transfus 2015; 32:454-459. [PMID: 27812256 DOI: 10.1007/s12288-015-0617-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 03/16/2015] [Accepted: 11/04/2015] [Indexed: 11/30/2022] Open
Abstract
α-thalassemia is the most common single gene disorder in the Cukurova Region in Turkey. It is therefore routinely screened, including premaritally, in our region. The heterogeneous molecular basis of the disease makes α-thalassemia mutation detection difficult and complex. Besides well established methods, multiplex ligation dependent probe amplification (MLPA) is known as an effective, simple and specific method for the detection and characterization of deletions and duplications. We employed MLPA testing to 30 patients with hematological parameters suggestive of α-thalassemia carrier status but was negative for α-thalassemia with conventional reverse dot blot hybridization (RDB). We found α-globin gene deletions in 3 out of 30 (10 %) patients with MLPA. We propose that MLPA can be used as a second tier test in addition to other techniques such as RDB to identify α-thalassemia carriers in high prevalence regions such as ours, thereby allowing clinicians to provide accurate genetic counselling.
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Affiliation(s)
- Ozge Ozalp Yuregir
- Genetic Diagnosis Center, Numune Training and Research Hospital, Kurttepe Street, Cukurova, 01150 Adana, Turkey
| | - Akif Ayaz
- Genetic Diagnosis Center, Numune Training and Research Hospital, Kurttepe Street, Cukurova, 01150 Adana, Turkey
| | - Sinem Yalcintepe
- Genetic Diagnosis Center, Numune Training and Research Hospital, Kurttepe Street, Cukurova, 01150 Adana, Turkey
| | - Sezin Canbek
- Genetic Diagnosis Center, Numune Training and Research Hospital, Kurttepe Street, Cukurova, 01150 Adana, Turkey
| | - Didar Yanardag Acik
- Department of Hematology, Numune Training and Research Hospital, Adana, Turkey
| | - Basak Taburoglu Yilmaz
- Department of Pediatric Hematology, Numune Training and Research Hospital, Adana, Turkey
| | - Tugce B Balci
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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20
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Balci TB, Sawyer SL, Davila J, Humphreys P, Dyment DA. Brain malformations in a patient with deletion 2p16.1: A refinement of the phenotype to BCL11A. Eur J Med Genet 2015; 58:351-4. [PMID: 25979662 DOI: 10.1016/j.ejmg.2015.04.006] [Citation(s) in RCA: 21] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/28/2015] [Indexed: 11/25/2022]
Abstract
Microdeletions of 2p15-16.1 have been reported in 15 patients with a recognizable syndrome of dysmorphic features, intellectual disability and microcephaly. Facial features include telecanthus, short palpebral fissures, epicanthal folds, a broad nasal root, smooth and long philtrum and large ears. Brain malformations can be observed in this syndrome and include hypoplasia of the corpus callosum and a simplified cortical gyral pattern. Case reports have narrowed the critical region of the neurodevelopmental phenotype to a region that spans the B-cell CLL/lymphoma 11A (BCL11A) gene. Here we present a 3-year-old normocephalic girl with moderate development delay and dysmorphic features including a prominent forehead, telecanthus, depressed nasal bridge, thin upper vermilion and a small chin. Magnetic resonance imaging shows enlargement of the lateral, third and fourth ventricles and hypoplastic corpus callosum, cerebellar vermis and pons. Array CGH revealed a 0.875 Mb de novo deletion at 2p16.1 that includes only BCL11A. The moderate delays, hypoplastic and dysmorphic corpus callosum and hippocampi and the facial features are in keeping with the previously described 2p15-16.1 microdeletion syndrome. However, hypoplasia of the pons and cerebellum are not commonly recognized features and are reminiscent of the brain malformations observed in individuals with a mutation in CASK. CASK is known to interact with BCL11A in the normal growth of axons. This case report highlights the role of BCL11A in 2p15-16.1 microdeletion syndrome and the unique phenotype suggests a common pathway for BCL11A and other genes in neurodevelopment.
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Affiliation(s)
- Tugce B Balci
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Sarah L Sawyer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Jorge Davila
- Department of Radiology, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Peter Humphreys
- Department of Pediatrics, Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada.
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21
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Basak A, Hancarova M, Ulirsch JC, Balci TB, Trkova M, Pelisek M, Vlckova M, Muzikova K, Cermak J, Trka J, Dyment DA, Orkin SH, Daly MJ, Sedlacek Z, Sankaran VG. BCL11A deletions result in fetal hemoglobin persistence and neurodevelopmental alterations. J Clin Invest 2015; 125:2363-8. [PMID: 25938782 DOI: 10.1172/jci81163] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 04/06/2015] [Indexed: 01/18/2023] Open
Abstract
A transition from fetal hemoglobin (HbF) to adult hemoglobin (HbA) normally occurs within a few months after birth. Increased production of HbF after this period of infancy ameliorates clinical symptoms of the major disorders of adult β-hemoglobin: β-thalassemia and sickle cell disease. The transcription factor BCL11A silences HbF and has been an attractive therapeutic target for increasing HbF levels; however, it is not clear to what extent BCL11A inhibits HbF production or mediates other developmental functions in humans. Here, we identified and characterized 3 patients with rare microdeletions of 2p15-p16.1 who presented with an autism spectrum disorder and developmental delay. Moreover, these patients all exhibited substantial persistence of HbF but otherwise retained apparently normal hematologic and immunologic function. Of the genes within 2p15-p16.1, only BCL11A was commonly deleted in all of the patients. Evaluation of gene expression data sets from developing and adult human brains revealed that BCL11A expression patterns are similar to other genes associated with neurodevelopmental disorders. Additionally, common SNPs within the second intron of BCL11A are strongly associated with schizophrenia. Together, the study of these rare patients and orthogonal genetic data demonstrates that BCL11A plays a central role in silencing HbF in humans and implicates BCL11A as an important factor for neurodevelopment.
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Abstract
The many advantages of the zebrafish model provide a unique opportunity to integrate the tools of developmental embryology, transgenesis, and functional assays to elucidate the molecular pathways underlying hematopoiesis and for modeling human blood diseases. These methodologies have recently been applied to the zebrafish mast cell lineage and have resulted in a better understanding of vertebrate mast cell biology. By employing whole-mount in situ hybridization alone and in combination with co-localization approaches, fluorescence-activated cell sorting (FACS), and morpholino gene knockdown studies, new insights into early mast cell transcriptional regulation and ontogeny have been exposed in vivo. Transgenic strategies have permitted the modeling of human mast cell diseases, like systemic mastocytosis in zebrafish, which can subsequently be exploited for high-throughput chemical screens to identify potential therapies in these conditions. Mast cell functional assays have been adapted to zebrafish providing the opportunity to utilize this model for interrogating the cellular players in innate and adaptive immunity and as a live animal readout for drug responses in allergic and inflammatory reactions. These techniques are detailed in the following chapter.
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Affiliation(s)
- Sahar I Da'as
- IWK Health Centre, Dalhousie University, 9700, 5850/5980 University Avenue, Halifax, NS, Canada, B3K 6R8
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23
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Corkery D, Balci TB, Berman JN, Dellairee G. Abstract 4251: Evaluating novel targeted therapeutic agents in T-cell acute lymphoblastic leukemia using a zebrafish xenotransplantation model. Tumour Biol 2014. [DOI: 10.1158/1538-7445.am2012-4251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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24
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Balci TB, Prykhozhij SV, Teh EM, Da'as SI, McBride E, Liwski R, Chute IC, Leger D, Lewis SM, Berman JN. A transgenic zebrafish model expressing KIT-D816V recapitulates features of aggressive systemic mastocytosis. Br J Haematol 2014; 167:48-61. [PMID: 24989799 DOI: 10.1111/bjh.12999] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 03/02/2014] [Accepted: 05/20/2014] [Indexed: 12/12/2022]
Abstract
Systemic mastocytosis (SM) is a rare myeloproliferative disease without curative therapy. Despite clinical variability, the majority of patients harbour a KIT-D816V mutation, but efforts to inhibit mutant KIT with tyrosine kinase inhibitors have been unsatisfactory, indicating a need for new preclinical approaches to identify alternative targets and novel therapies in this disease. Murine models to date have been limited and do not fully recapitulate the most aggressive forms of SM. We describe the generation of a transgenic zebrafish model expressing the human KIT-D816V mutation. Adult fish demonstrate a myeloproliferative disease phenotype, including features of aggressive SM in haematopoeitic tissues and high expression levels of endopeptidases, consistent with SM patients. Transgenic embryos demonstrate a cell-cycle phenotype with corresponding expression changes in genes associated with DNA maintenance and repair, such as reduced dnmt1. In addition, epcam was consistently downregulated in both transgenic adults and embryos. Decreased embryonic epcam expression was associated with reduced neuromast numbers, providing a robust in vivo phenotypic readout for chemical screening in KIT-D816V-induced disease. This study represents the first zebrafish model of a mast cell disease with an aggressive adult phenotype and embryonic markers that could be exploited to screen for novel agents in SM.
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Affiliation(s)
- Tugce B Balci
- Department of Pediatrics, IWK Health Centre, Halifax, NS, Canada; Department of Medical Genetics, University of Ottawa, Ottawa, ON, Canada
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25
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Konantz M, Balci TB, Hartwig UF, Dellaire G, André MC, Berman JN, Lengerke C. Zebrafish xenografts as a tool for in vivo studies on human cancer. Ann N Y Acad Sci 2012; 1266:124-37. [PMID: 22901264 DOI: 10.1111/j.1749-6632.2012.06575.x] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The zebrafish has become a powerful vertebrate model for genetic studies of embryonic development and organogenesis and increasingly for studies in cancer biology. Zebrafish facilitate the performance of reverse and forward genetic approaches, including mutagenesis and small molecule screens. Moreover, several studies report the feasibility of xenotransplanting human cells into zebrafish embryos and adult fish. This model provides a unique opportunity to monitor tumor-induced angiogenesis, invasiveness, and response to a range of treatments in vivo and in real time. Despite the high conservation of gene function between fish and humans, concern remains that potential differences in zebrafish tissue niches and/or missing microenvironmental cues could limit the relevance and translational utility of data obtained from zebrafish human cancer cell xenograft models. Here, we summarize current data on xenotransplantation of human cells into zebrafish, highlighting the advantages and limitations of this model in comparison to classical murine models of xenotransplantation.
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Affiliation(s)
- Martina Konantz
- Department of Hematology and Oncology, University of Tübingen Medical Center II, Tübingen, Germany
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