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Shepherdson JL, Hutchison K, Don DW, McGillivray G, Choi TI, Allan CA, Amor DJ, Banka S, Basel DG, Buch LD, Carere DA, Carroll R, Clayton-Smith J, Crawford A, Dunø M, Faivre L, Gilfillan CP, Gold NB, Gripp KW, Hobson E, Holtz AM, Innes AM, Isidor B, Jackson A, Katsonis P, Amel Riazat Kesh L, Küry S, Lecoquierre F, Lockhart P, Maraval J, Matsumoto N, McCarrier J, McCarthy J, Miyake N, Moey LH, Németh AH, Østergaard E, Patel R, Pope K, Posey JE, Schnur RE, Shaw M, Stolerman E, Taylor JP, Wadman E, Wakeling E, White SM, Wong LC, Lupski JR, Lichtarge O, Corbett MA, Gecz J, Nicolet CM, Farnham PJ, Kim CH, Shinawi M. Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt. Am J Hum Genet 2024; 111:487-508. [PMID: 38325380 PMCID: PMC10940019 DOI: 10.1016/j.ajhg.2024.01.007] [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: 08/06/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
Pathogenic variants in multiple genes on the X chromosome have been implicated in syndromic and non-syndromic intellectual disability disorders. ZFX on Xp22.11 encodes a transcription factor that has been linked to diverse processes including oncogenesis and development, but germline variants have not been characterized in association with disease. Here, we present clinical and molecular characterization of 18 individuals with germline ZFX variants. Exome or genome sequencing revealed 11 variants in 18 subjects (14 males and 4 females) from 16 unrelated families. Four missense variants were identified in 11 subjects, with seven truncation variants in the remaining individuals. Clinical findings included developmental delay/intellectual disability, behavioral abnormalities, hypotonia, and congenital anomalies. Overlapping and recurrent facial features were identified in all subjects, including thickening and medial broadening of eyebrows, variations in the shape of the face, external eye abnormalities, smooth and/or long philtrum, and ear abnormalities. Hyperparathyroidism was found in four families with missense variants, and enrichment of different tumor types was observed. In molecular studies, DNA-binding domain variants elicited differential expression of a small set of target genes relative to wild-type ZFX in cultured cells, suggesting a gain or loss of transcriptional activity. Additionally, a zebrafish model of ZFX loss displayed an altered behavioral phenotype, providing additional evidence for the functional significance of ZFX. Our clinical and experimental data support that variants in ZFX are associated with an X-linked intellectual disability syndrome characterized by a recurrent facial gestalt, neurocognitive and behavioral abnormalities, and an increased risk for congenital anomalies and hyperparathyroidism.
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Affiliation(s)
- James L Shepherdson
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA
| | - Katie Hutchison
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - George McGillivray
- Victorian Clinical Genetics Services, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, Daejeon 34134, Korea
| | - Carolyn A Allan
- Hudson Institute of Medical Research, Monash University, and Department of Endocrinology, Monash Health, Melbourne, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, VIC, Australia
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Donald G Basel
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | | | - Renée Carroll
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ali Crawford
- Medical Genomics Research, Illumina Inc, San Diego, CA, USA
| | - Morten Dunø
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Laurence Faivre
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, Dijon, France; INSERM UMR1231, Equipe GAD, Université de Bourgogne-Franche Comté, 21000 Dijon, France
| | - Christopher P Gilfillan
- Eastern Health Clinical School, Monash University, Melbourne, VIC, Australia; Department of Endocrinology, Eastern Health, Box Hill Hospital, Melbourne, VIC, Australia
| | - Nina B Gold
- Harvard Medical School, Boston, MA, USA; Division of Medical Genetics and Metabolism, Massachusetts General Hospital, Boston, MA, USA
| | - Karen W Gripp
- Division of Medical Genetics, Nemours Children's Hospital, Wilmington, DE, USA
| | - Emma Hobson
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Department of Clinical Genetics, Chapel Allerton Hospital, Leeds, UK
| | - Alexander M Holtz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - A Micheil Innes
- Departments of Medical Genetics and Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, 44000 Nantes, France
| | - Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Leila Amel Riazat Kesh
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Department of Clinical Genetics, Chapel Allerton Hospital, Leeds, UK
| | - Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, 44000 Nantes, France
| | - François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Paul Lockhart
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, VIC, Australia
| | - Julien Maraval
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, Dijon, France; INSERM UMR1231, Equipe GAD, Université de Bourgogne-Franche Comté, 21000 Dijon, France
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Julie McCarrier
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Josephine McCarthy
- Department of Endocrinology, Eastern Health, Box Hill Hospital, Melbourne, VIC, Australia
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Lip Hen Moey
- Department of Genetics, Penang General Hospital, George Town, Penang, Malaysia
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rushina Patel
- Medical Genetics, Kaiser Permanente Oakland Medical Center, Oakland, CA, USA
| | - Kate Pope
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Julie P Taylor
- Medical Genomics Research, Illumina Inc, San Diego, CA, USA
| | - Erin Wadman
- Division of Medical Genetics, Nemours Children's Hospital, Wilmington, DE, USA
| | - Emma Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Susan M White
- Victorian Clinical Genetics Services, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, VIC, Australia
| | - Lawrence C Wong
- Medical Genetics, Kaiser Permanente Downey Medical Center, Downey, CA, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Charles M Nicolet
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Korea.
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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Lecoquierre F, Punt AM, Ebstein F, Wallaard I, Verhagen R, Studencka-Turski M, Duffourd Y, Moutton S, Tran Mau-Them F, Philippe C, Dean J, Tennant S, Brooks AS, van Slegtenhorst MA, Jurgens JA, Barry BJ, Chan WM, England EM, Martinez Ojeda M, Engle EC, Robson CD, Morrow M, Innes AM, Lamont R, Sanderson M, Krüger E, Thauvin C, Distel B, Faivre L, Elgersma Y, Vitobello A. A recurrent missense variant in the E3 ubiquitin ligase substrate recognition subunit FEM1B causes a rare syndromic neurodevelopmental disorder. Genet Med 2024; 26:101119. [PMID: 38465576 DOI: 10.1016/j.gim.2024.101119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024] Open
Abstract
PURPOSE Fem1 homolog B (FEM1B) acts as a substrate recognition subunit for ubiquitin ligase complexes belonging to the CULLIN 2-based E3 family. Several biological functions have been proposed for FEM1B, including a structurally resolved function as a sensor for redox cell status by controlling mitochondrial activity, but its implication in human disease remains elusive. METHODS To understand the involvement of FEM1B in human disease, we made use of Matchmaker exchange platforms to identify individuals with de novo variants in FEM1B and performed their clinical evaluation. We performed functional validation using primary neuronal cultures and in utero electroporation assays, as well as experiments on patient's cells. RESULTS Five individuals with a recurrent de novo missense variant in FEM1B were identified: NM_015322.5:c.377G>A NP_056137.1:p.(Arg126Gln) (FEM1BR126Q). Affected individuals shared a severe neurodevelopmental disorder with behavioral phenotypes and a variable set of malformations, including brain anomalies, clubfeet, skeletal abnormalities, and facial dysmorphism. Overexpression of the FEM1BR126Q variant but not FEM1B wild-type protein, during mouse brain development, resulted in delayed neuronal migration of the target cells. In addition, the individuals' cells exhibited signs of oxidative stress and induction of type I interferon signaling. CONCLUSION Overall, our data indicate that p.(Arg126Gln) induces aberrant FEM1B activation, resulting in a gain-of-function mechanism associated with a severe syndromic developmental disorder in humans.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, Rouen, France; UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France.
| | - A Mattijs Punt
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Frédéric Ebstein
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany; Nantes Université, INSERM, CNRS, l'institut du thorax, Nantes Cedex 1, France
| | - Ilse Wallaard
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Rob Verhagen
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Maja Studencka-Turski
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Yannis Duffourd
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Sébastien Moutton
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Frédédic Tran Mau-Them
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Laboratoire de Génétique, CHR Metz-Thionville, Hôpital Mercy, Metz, France
| | - John Dean
- Department of Medical Genetics, NHS Grampian, Aberdeen, United Kingdom
| | - Stephen Tennant
- NHS Grampian, Genetics & Molecular Pathology Laboratory Services, Aberdeen, United Kingdom
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Julie A Jurgens
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA
| | - Brenda J Barry
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Department of Neurology, Boston Children's Hospital, Boston, MA; Howard Hughes Medical Institute, Chevy Chase, MD
| | - Wai-Man Chan
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Howard Hughes Medical Institute, Chevy Chase, MD
| | - Eleina M England
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | | | - Elizabeth C Engle
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Howard Hughes Medical Institute, Chevy Chase, MD; Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Caroline D Robson
- Division of Neuroradiology, Department of Radiology, Boston Children's Hospital, Boston, MA; Department of Radiology, Harvard Medical School, Boston, MA
| | | | - A Micheil Innes
- Alberta Children's Hospital Research Institute for Child and Maternal Health and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ryan Lamont
- Alberta Children's Hospital Research Institute for Child and Maternal Health and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Matthea Sanderson
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Elke Krüger
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Christel Thauvin
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France; Centre de référence maladies rares « Déficiences Intellectuelles de Causes Rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Ben Distel
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Laurence Faivre
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Centre de Référence maladies rares « Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Ype Elgersma
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Antonio Vitobello
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
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de Masfrand S, Cogné B, Nizon M, Deb W, Goldenberg A, Lecoquierre F, Nicolas G, Bournez M, Vitobello A, Mau-Them FT, le Guyader G, Bilan F, Bauer P, Zweier C, Piard J, Pasquier L, Bézieau S, Gerard B, Faivre L, Saugier-Veber P, Piton A, Isidor B. Penetrance, variable expressivity and monogenic neurodevelopmental disorders. Eur J Med Genet 2024:104932. [PMID: 38453051 DOI: 10.1016/j.ejmg.2024.104932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 03/09/2024]
Abstract
PURPOSE Incomplete penetrance is observed for most monogenic diseases. However, for neurodevelopmental disorders, the interpretation of single and multi-nucleotide variants (SNV/MNVs) is usually based on the paradigm of complete penetrance. METHOD From 2020 to 2022, we proposed a collaboration study with the French molecular diagnosis for intellectual disability network. The aim was to recruit families for whom the index case, diagnosed with a neurodevelopmental disorder, was carrying a pathogenic or likely pathogenic variant for an OMIM morbid gene and inherited from an asymptomatic parent. Grandparents were analyzed when available for segregation study. RESULTS We identified 12 patients affected by a monogenic neurodevelopmental disorder caused by likely pathogenic or pathogenic variant (SNV/MNV) inherited from an asymptomatic parent. These genes were usually associated with de novo variants. The patients carried different variants (1 splice-site variant, 4 nonsense and 7 frameshift) in 11 genes: CAMTA1, MBD5, KMT2C, KMT2E, ZMIZ1, MN1, NDUFB11, CUL3, MED13, ARID2 and RERE. Grandparents have been tested in 6 families, and each time the variant was confirmed de novo in the healthy carrier parent. CONCLUSION Incomplete penetrance for SNV and MNV in neurodevelopmental disorders might be more frequent than previously thought. This point is crucial to consider for interpretation of variants, family investigation, genetic counseling, and prenatal diagnosis. Molecular mechanisms underlying this incomplete penetrance still need to be identified.
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Affiliation(s)
- Servane de Masfrand
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France.
| | - Benjamin Cogné
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut Du Thorax, 44000 Nantes, France
| | - Mathilde Nizon
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut Du Thorax, 44000 Nantes, France
| | - Wallid Deb
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut Du Thorax, 44000 Nantes, France
| | - Alice Goldenberg
- CHU Rouen, Service de Génétique et Centre de Référence pour Les Troubles Du Développement, 76183, Rouen, France
| | - François Lecoquierre
- CHU Rouen, Service de Génétique et Centre de Référence pour Les Troubles Du Développement, 76183, Rouen, France
| | - Gaël Nicolas
- CHU Rouen, Service de Génétique et Centre de Référence pour Les Troubles Du Développement, 76183, Rouen, France
| | - Marie Bournez
- Centre de Référence Anomalies Du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, 21000, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France; Génétique des Anomalies Du Développement, INSERM 123, Université de Bourgogne, Dijon, France
| | - Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France; Génétique des Anomalies Du Développement, INSERM 123, Université de Bourgogne, Dijon, France
| | - Gwenaël le Guyader
- Service de Génétique Clinique, Centre de Compétence Maladies Rares Anomalies Du Développement, CHU de Poitiers, Poitiers, France
| | - Frédéric Bilan
- Service de Génétique Clinique, Centre de Compétence Maladies Rares Anomalies Du Développement, CHU de Poitiers, Poitiers, France
| | | | | | - Juliette Piard
- Centre de Génétique Humaine and Integrative and Cognitive Neuroscience Research Unit EA481, Université de Franche-Comté, Besançon, France
| | | | - Stéphane Bézieau
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut Du Thorax, 44000 Nantes, France
| | - Bénédicte Gerard
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Laurence Faivre
- Centre de Référence Anomalies Du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, 21000, Dijon, France; Génétique des Anomalies Du Développement, INSERM 123, Université de Bourgogne, Dijon, France
| | - Pascale Saugier-Veber
- CHU Rouen, Service de Génétique et Centre de Référence pour Les Troubles Du Développement, 76183, Rouen, France
| | - Amélie Piton
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, L'institut Du Thorax, 44000 Nantes, France.
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4
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Lecoquierre F, Cassinari K, Drouot N, May A, Fourneaux S, Charbonnier F, Derambure C, Coutant S, Saugier-Veber P, Hoischen A, Charbonnier C, Nicolas G. Assessment of parental mosaicism rates in neurodevelopmental disorders caused by apparent de novo pathogenic variants using deep sequencing. Sci Rep 2024; 14:5289. [PMID: 38438430 PMCID: PMC10912112 DOI: 10.1038/s41598-024-53358-9] [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: 11/28/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
While de novo variants (DNV) are overall at low risk of recurrence in subsequent pregnancies, a subset is at high risk due to parental mosaicism. Accurately identifying cases of parental mosaicism is therefore important for genetic counseling in clinical care. Some studies have investigated the rate of parental mosaics, but most were either limited by the sensitivity of the techniques (i.e. exome or genome sequencing), or focused on specific types of disease such as epileptic syndromes. This study aimed to determine the proportion of parental mosaicism among the DNV causing neurodevelopmental disorders (NDDs) in a series not enriched in epilepsy syndromes. We collected 189 patients with NDD-associated DNV. We applied a smMIP enrichment method and sequenced parental blood DNA samples to an average depth of 7000x. Power simulation indicated that mosaicism with an allelic fraction of 0.5% would have been detected for 87% of positions with 90% power. We observed seven parental mosaic variants (3.7% of families), of which four (2.1% of families) had an allelic fraction of less than 1%. In total, our study identifies a relatively low proportion of parental mosaicism in NDD-associated DNVs and raises the question of a biological mechanism behind the higher rates of parental mosaicism detected in other studies, particularly those focusing on epileptic syndromes.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France.
- Centre de Ressources Biologiques institutionnel du CHU de Rouen - Biothèque filière génétique, Rouen, France.
| | - Kévin Cassinari
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Angèle May
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Francoise Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Celine Derambure
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Camille Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
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5
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Husson T, Lecoquierre F, Nicolas G, Richard AC, Afenjar A, Audebert-Bellanger S, Badens C, Bilan F, Bizaoui V, Boland A, Bonnet-Dupeyron MN, Brischoux-Boucher E, Bonnet C, Bournez M, Boute O, Brunelle P, Caumes R, Charles P, Chassaing N, Chatron N, Cogné B, Colin E, Cormier-Daire V, Dard R, Dauriat B, Delanne J, Deleuze JF, Demurger F, Denommé-Pichon AS, Depienne C, Dieux A, Dubourg C, Edery P, El Chehadeh S, Faivre L, Fergelot P, Fradin M, Garde A, Geneviève D, Gilbert-Dussardier B, Goizet C, Goldenberg A, Gouy E, Guerrot AM, Guimier A, Harzalla I, Héron D, Isidor B, Lacombe D, Le Guillou Horn X, Keren B, Kuechler A, Lacaze E, Lavillaureix A, Lehalle D, Lesca G, Lespinasse J, Levy J, Lyonnet S, Morel G, Jean-Marçais N, Marlin S, Marsili L, Mignot C, Nambot S, Nizon M, Olaso R, Pasquier L, Perrin L, Petit F, Pingault V, Piton A, Prieur F, Putoux A, Planes M, Odent S, Quélin C, Quemener-Redon S, Rama M, Rio M, Rossi M, Schaefer E, Rondeau S, Saugier-Veber P, Smol T, Sigaudy S, Touraine R, Mau-Them FT, Trimouille A, Van Gils J, Vanlerberghe C, Vantalon V, Vera G, Vincent M, Ziegler A, Guillin O, Campion D, Charbonnier C. Episignatures in practice: independent evaluation of published episignatures for the molecular diagnostics of ten neurodevelopmental disorders. Eur J Hum Genet 2024; 32:190-199. [PMID: 37872275 PMCID: PMC10853222 DOI: 10.1038/s41431-023-01474-x] [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: 05/10/2023] [Revised: 08/29/2023] [Accepted: 09/28/2023] [Indexed: 10/25/2023] Open
Abstract
Variants of uncertain significance (VUS) are a significant issue for the molecular diagnosis of rare diseases. The publication of episignatures as effective biomarkers of certain Mendelian neurodevelopmental disorders has raised hopes to help classify VUS. However, prediction abilities of most published episignatures have not been independently investigated yet, which is a prerequisite for an informed and rigorous use in a diagnostic setting. We generated DNA methylation data from 101 carriers of (likely) pathogenic variants in ten different genes, 57 VUS carriers, and 25 healthy controls. Combining published episignature information and new validation data with a k-nearest-neighbour classifier within a leave-one-out scheme, we provide unbiased specificity and sensitivity estimates for each of the signatures. Our procedure reached 100% specificity, but the sensitivities unexpectedly spanned a very large spectrum. While ATRX, DNMT3A, KMT2D, and NSD1 signatures displayed a 100% sensitivity, CREBBP-RSTS and one of the CHD8 signatures reached <40% sensitivity on our dataset. Remaining Cornelia de Lange syndrome, KMT2A, KDM5C and CHD7 signatures reached 70-100% sensitivity at best with unstable performances, suffering from heterogeneous methylation profiles among cases and rare discordant samples. Our results call for cautiousness and demonstrate that episignatures do not perform equally well. Some signatures are ready for confident use in a diagnostic setting. Yet, it is imperative to characterise the actual validity perimeter and interpretation of each episignature with the help of larger validation sample sizes and in a broader set of episignatures.
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Affiliation(s)
- Thomas Husson
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Psychiatry, F-76000, Rouen, France
- Department of Research, Centre hospitalier du Rouvray, Sotteville-Lès-Rouen, France
| | - François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Anne-Claire Richard
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Alexandra Afenjar
- APHP. Sorbonne Université, Centre de Référence Malformations et maladies congénitales du cervelet et déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, F-75012, Paris, France
| | | | - Catherine Badens
- Aix Marseille Univ, INSERM, MMG, Marseille, France; APHM, service de génétique, Marseille, France
| | - Frédéric Bilan
- CHU de Poitiers, Service de Génétique Médicale and Université de Poitiers, INSERM U1084, LNEC, F- 86000, Poitiers, France
| | - Varoona Bizaoui
- Service de génétique et neurodéveloppement, Pôle de Santé Mentale Enfant et Adolescent, Centre Hospitalier de l'Estran, Pontorson, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | | | - Elise Brischoux-Boucher
- Centre de génétique humaine, CHU Besancon, Universite de Bourgogne Franche-Comte, Besancon, France
| | - Céline Bonnet
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
- Université de Lorraine, INSERM UMR_S1256, NGERE, F-54000, Nancy, France
| | - Marie Bournez
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Odile Boute
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Perrine Brunelle
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Institut de Génétique Médicale, F-59000, Lille, France
| | - Roseline Caumes
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Perrine Charles
- Département de génétique clinique, centre de référence des déficiences intellectuelles de causes rares, GHU Pitié Salpêtrière, Paris, France
| | | | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261 -INSERM U1315, Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Benjamin Cogné
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Estelle Colin
- Service de Génétique Médicale, CHU Angers, Angers, France
| | - Valérie Cormier-Daire
- Service de médecine génomique des maladies rares, hôpital Necker Enfants Malades, Paris, France
- Université Paris Cité, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Rodolphe Dard
- Génétique médicale, CHI Poissy-Saint-Germain-en-Laye, 78300, Poissy, France
| | - Benjamin Dauriat
- Service de cytogénétique et génétique médicale, Hôpital Mère Enfant, CHU Limoges, Limoges, France
| | - Julian Delanne
- Centre de Génétique et Centre de référence « Déficiences intellectuelles de causes rares », FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | | | - Anne-Sophie Denommé-Pichon
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon, Bourgogne, Dijon, France
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Anne Dieux
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, CHU Pontchaillou, Rennes, France
- Université de Rennes, IGDR (Institut de Génétique et Développement), CNRS UMR 6290, INSERM ERL 1305, Rennes, France
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, Genetics of Neurodevelopment (GENDEV) Team, 69500, Bron, France
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch-Graffenstaden, France
- Laboratoire de Génétique Médicale, UMRS 1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg et INSERM, Strasbourg, France
| | - Laurence Faivre
- Centre de Génétique et Centre de référence « Déficiences intellectuelles de causes rares », FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - Patricia Fergelot
- Department of Medical Genetics, University Hospital of Bordeaux and INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Rennes, Rennes, France
| | - Aurore Garde
- Centre de Génétique et Centre de référence « Déficiences intellectuelles de causes rares », FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - David Geneviève
- Université Montpellier, Inserm U1183, Montpellier, France
- Centre de référence anomalies du développement et syndromes malformatifs, Génétique Clinique, CHU Montpellier, Montpellier, France
| | | | - Cyril Goizet
- NRGEN team, Univ. Bordeaux, CNRS, INCIA, UMR 5287, EPHE, F-33000, Bordeaux, France
- Centre de Référence Maladies Rares Neurogénétique, Service de Génétique Médicale, Bordeaux University Hospital (CHU Bordeaux), Bordeaux, France
| | - Alice Goldenberg
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Evan Gouy
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Génétique et neurobiologie de C.elegans, MéLis (CNRS UMR 5284 -INSERM U1314), Institut NeuroMyogene, Université Claude Bernard Lyon 1, Lyon, France
| | - Anne-Marie Guerrot
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Anne Guimier
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Inès Harzalla
- Service de Génétique, CHU Hôpital Nord, Saint Etienne, France
| | - Delphine Héron
- APHP.Sorbonne Université, Département de Génétique, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Bertrand Isidor
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Didier Lacombe
- Department of Medical Genetics, University Hospital of Bordeaux and INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Xavier Le Guillou Horn
- CHU de Poitiers, Service de Génétique Médicale, F - 86000, Poitiers, France
- Université de Poitiers, CNRS 7348, LabCom I3M-Dactim mis / LMA, F-86000, Poitiers, France
| | - Boris Keren
- Département de génétique médicale, Hôpital Pitié-Salpêtrière, AP-HP.Sorbonne Université, 75013, Paris, France
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Elodie Lacaze
- Le Havre Hospital, Department of Medical Genetics, F 76600, Le Havre, France
| | - Alinoë Lavillaureix
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France
| | - Daphné Lehalle
- APHP.Sorbonne Université, Département de Génétique, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Gaëtan Lesca
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - James Lespinasse
- UF de génétique médicale, Centre Hospitalier Métropole Savoie, BP 31135, 73011, Chambéry, France
| | - Jonathan Levy
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Stanislas Lyonnet
- Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants malades, APHP, Paris, France
- Laboratoire embryologie et génétique des malformations, Institut Imagine, UMR-II63, INSERM, Université Paris Cité, GHU Necker- Enfants malades, Paris, France
| | - Godeliève Morel
- Service de Génétique Clinique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Rennes, Rennes, France
| | - Nolwenn Jean-Marçais
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Rennes, France
| | - Sandrine Marlin
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Luisa Marsili
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Cyril Mignot
- APHP.Sorbonne Université, Département de Génétique, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Mathilde Nizon
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Laurent Pasquier
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Rennes, France
| | - Laurine Perrin
- Médecine Physique et Réadaptation pédiatrique CHU Saint-Etienne, 42055, Saint-Etienne Cedex 2, France
| | - Florence Petit
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Institut de Génétique Médicale, F-59000, Lille, France
| | - Veronique Pingault
- Service de Médecine Génomique des maladies rares, AP-HP. Centre, Hôpital Necker-Enfants Malades, F-75015, Paris, France
- Université Paris Cité, Institut Imagine, Inserm U1163, F-75015, Paris, France
| | - Amélie Piton
- Laboratoire de diagnostic génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Fabienne Prieur
- Service de Génétique, CHU Hôpital Nord, Saint Etienne, France
| | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, Genetics of Neurodevelopment (GENDEV) Team, 69500, Bron, France
| | - Marc Planes
- Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France
| | - Chloé Quélin
- Service de Génétique Clinique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Rennes, Rennes, France
| | - Sylvia Quemener-Redon
- Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France
- Centre de Référence Déficiences Intellectuelles de causes rares, Brest, France
| | - Mélanie Rama
- CHU Lille - Institut de Génétique Médicale, F-59000, Lille, France
| | - Marlène Rio
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Massimiliano Rossi
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, Genetics of Neurodevelopment (GENDEV) Team, 69500, Bron, France
| | - Elise Schaefer
- Service de Génétique Médicale -Institut de Génétique Médicale d'Alsace - CHU Strasbourg, Strasbourg, France
| | - Sophie Rondeau
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Thomas Smol
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Institut de Génétique Médicale, F-59000, Lille, France
- CHU Lille - Institut de Génétique Médicale, F-59000, Lille, France
| | - Sabine Sigaudy
- Aix Marseille Univ, INSERM, MMG, CRMR syndromes malformatifs et anomalies du développement, département de génétique, APHM Hopital Timone, Marseille, France
| | - Renaud Touraine
- Service de Génétique, CHU Hôpital Nord, Saint Etienne, France
| | - Frederic Tran Mau-Them
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon, Bourgogne, Dijon, France
| | - Aurélien Trimouille
- Service de Pathologie, CHU Bordeaux, Bordeaux, France
- Inserm U1211 MRGM, Université de Bordeaux, Bordeaux, France
| | - Julien Van Gils
- Department of Medical Genetics, University Hospital of Bordeaux and INSERM U1211, University of Bordeaux, Bordeaux, France
| | | | - Valérie Vantalon
- Centre d'Excellence InovAND-Service de psychiatrie de l'enfant et de l'adolescent-CHU Robert Debré, Paris, France
| | - Gabriella Vera
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Marie Vincent
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Alban Ziegler
- Service de Génétique Médicale, CHU Angers, Angers, France
| | - Olivier Guillin
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Psychiatry, F-76000, Rouen, France
| | - Dominique Campion
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Psychiatry, F-76000, Rouen, France
| | - Camille Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Biostatistics, F-76000, Rouen, France.
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6
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Ruault V, Burger P, Gradels‐Hauguel J, Ruiz N, Jamra RA, Afenjar A, Alembik Y, Alessandri J, Arpin S, Barcia G, Bendová Š, Bruel A, Charles P, Chatron N, Chopra M, Conrad S, Daire VC, Cospain A, Coubes C, Coursimault J, Delahaye‐Duriez A, Doco M, Dufour W, Durand B, Engel C, Faivre L, Ferroul F, Fradin M, Frenkiel H, Fusco C, Garavelli L, Garde A, Gerard B, Germanaud D, Goujon L, Gouronc A, Ginglinger E, Goldenberg A, Hancarova M, Havlovicová M, Heron D, Isidor B, Marçais NJ, Keren B, Koch‐Hogrebe M, Kuentz P, Lamure V, Lebre A, Lecoquierre F, Lehman N, Lesca G, Lyonnet S, Martin D, Mignot C, Neuhann TM, Nicolas G, Nizon M, Petit F, Philippe C, Piton A, Pollazzon M, Prchalová D, Putoux A, Rio M, Rondeau S, Rossi M, Sabbagh Q, Saugier‐Veber P, Schmetz A, Steffann J, Thauvin‐Robinet C, Toutain A, Them FTM, Trimarchi G, Vincent M, Vlčková M, Wieczorek D, Willems M, Yauy K, Zelinová M, Ziegler A, Chaumette B, Sadikovic B, Mandel J, Geneviève D. Lessons from two series by physicians and caregivers' self-reported data in DDX3X-related disorders. Mol Genet Genomic Med 2024; 12:e2363. [PMID: 38284452 PMCID: PMC10801341 DOI: 10.1002/mgg3.2363] [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: 08/03/2023] [Revised: 12/08/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
INTRODUCTION AND METHODS We report two series of individuals with DDX3X variations, one (48 individuals) from physicians and one (44 individuals) from caregivers. RESULTS These two series include several symptoms in common, with fairly similar distribution, which suggests that caregivers' data are close to physicians' data. For example, both series identified early childhood symptoms that were not previously described: feeding difficulties, mean walking age, and age at first words. DISCUSSION Each of the two datasets provides complementary knowledge. We confirmed that symptoms are similar to those in the literature and provides more details on feeding difficulties. Caregivers considered that the symptom attention-deficit/hyperactivity disorder were most worrisome. Both series also reported sleep disturbance. Recently, anxiety has been reported in individuals with DDX3X variants. We strongly suggest that attention-deficit/hyperactivity disorder, anxiety, and sleep disorders need to be treated.
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Affiliation(s)
- Valentin Ruault
- Genetic DepartmentMontpellier University, INSERM Unit 1183MontpellierFrance
- Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics DepartmentMontpellier HospitalMontpellierFrance
| | - Pauline Burger
- Institute of Genetics and Molecular and Cellular Biology (IGBMC)Université de Strasbourg, INSERM U1258, CNRS UMR7104IllkirchFrance
| | - Johanna Gradels‐Hauguel
- Center for Rare Psychiatric Disorders – GHU Paris Psychiatrie et Neurosciences – Paris – France APHPGHU Sainte AnneParisFrance
| | - Nathalie Ruiz
- Genetic DepartmentMontpellier University, INSERM Unit 1183MontpellierFrance
- Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics DepartmentMontpellier HospitalMontpellierFrance
| | | | - Rami Abou Jamra
- Institute of Human GeneticsUniversity of Leipzig Medical CenterLeipzigGermany
| | - Alexandra Afenjar
- Département de Génétique ParisCentre de Référence Malformations et maladies congénitales du cervelet et déficiences intellectuelles de causes rares, APHP, Sorbonne UniversitéParisFrance
| | - Yves Alembik
- Service de Génétique MédicaleInstitut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de StrasbourgStrasbourgFrance
| | | | - Stéphanie Arpin
- Genetics DepartmentUniversity Hospital, UMR1253 iBrain INSERM, University of ToursToursFrance
| | - Giulia Barcia
- Service de Médecine Génomique des Maladies RaresHôpital Necker – Enfants Malades, Assistance Publique‐Hôpitaux de ParisParisFrance
| | - Šárka Bendová
- Department of Biology and Medical GeneticsCharles University Second Faculty of Medicine and University Hospital MotolPragueCzech Republic
| | - Ange‐Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies raresCHU Dijon BourgogneDijonFrance
- UFR Des Sciences de SantéINSERM‐Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement”, FHUTRANSLADDijonFrance
| | | | - Nicolas Chatron
- Department of Medical GeneticsUniversity Hospital of Lyon and Claude Bernard Lyon I UniversityLyonFrance
- Pathophysiology and Genetics of Neuron and Muscle (PNMG)UCBL, CNRS UMR5261 – INSERM U1315LyonFrance
| | - Maya Chopra
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience CenterBoston Children's HospitalBostonMassachusettsUSA
- Genetic DepartmentHarvard Medical SchoolBostonMassachusettsUSA
| | - Solène Conrad
- Genetic DepartmentCHU Nantes, Service de GénétiqueNantesFrance
| | - Valérie Cormier Daire
- Service de Médecine Génomique des Maladies RaresHôpital Necker – Enfants Malades, Assistance Publique‐Hôpitaux de ParisParisFrance
| | - Auriane Cospain
- Genetic DepartmentCHU Rennes, Service de Génétique, CLAD Ouest CRDIRennesFrance
| | - Christine Coubes
- Genetic DepartmentMontpellier University, INSERM Unit 1183MontpellierFrance
- Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics DepartmentMontpellier HospitalMontpellierFrance
| | - Juliette Coursimault
- Department of Genetics and Reference Center for Developmental DisordersUniversity of Rouen Normandie, Inserm U1245, CHU RouenRouenFrance
| | - Andrée Delahaye‐Duriez
- Medical Genomics and Clinical Genetics UnitAP‐HP, Hôpital Jean VerdierBondyFrance
- Genetic DepartmentUFR SMBH, Université Sorbonne Paris NordParisFrance
- Genetic DepartmentInserm 1141 NeuroDiderotParisFrance
| | - Martine Doco
- Genetic DepartmentCHU Nantes, Service de GénétiqueNantesFrance
- Centre Hospitalier Universitaire de ReimsPôle de Biologie Médicale et Pathologie, Service de GénétiqueReimsFrance
| | - William Dufour
- Department of Medical GeneticsUniversity Hospital of Lyon and Claude Bernard Lyon I UniversityLyonFrance
| | - Benjamin Durand
- Service de Génétique MédicaleInstitut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de StrasbourgStrasbourgFrance
| | - Camille Engel
- Oncobiologie Génétique BioinformatiquePC BIO, CHU BesançonBesançonFrance
| | - Laurence Faivre
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies raresCHU Dijon BourgogneDijonFrance
- Centre de Génétique et Centre de référence maladies rares « Anomalies du Développement et Syndromes Malformatifs », FHU TRANSLADHôpital d'Enfants, CHU DijonDijonFrance
| | - Fanny Ferroul
- CHU La Réunion, Service de génétiqueSaint DenisFrance
| | - Mélanie Fradin
- Genetic DepartmentCHU Rennes, Service de Génétique, CLAD Ouest CRDIRennesFrance
- CH Saint Brieuc, Service de GénétiqueSaint BrieuxFrance
| | | | - Carlo Fusco
- Child Neurology and Psychiatry UnitAzienda USL‐IRCCS di Reggio EmiliaReggio EmiliaItaly
| | - Livia Garavelli
- Medical Genetics UnitAzienda USL‐IRCCS di Reggio EmiliaReggio EmiliaItaly
| | - Aurore Garde
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies raresCHU Dijon BourgogneDijonFrance
- Centre de Génétique et Centre de référence maladies rares « Anomalies du Développement et Syndromes Malformatifs », FHU TRANSLADHôpital d'Enfants, CHU DijonDijonFrance
| | - Bénédicte Gerard
- Service de Génétique MédicaleInstitut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de StrasbourgStrasbourgFrance
| | - David Germanaud
- Genetic DepartmentCEA Paris‐Saclay, NeuroSpinGif‐sur‐YvetteFrance
- Département de GénétiqueCentre de référence Déficiences intellectuelles de causes rares, Assistance publique‐Hopitaux de Paris (AP‐HP), Hopital Robert‐DebréParisFrance
| | - Louise Goujon
- Genetic DepartmentCEA Paris‐Saclay, NeuroSpinGif‐sur‐YvetteFrance
- Département de GénétiqueCentre de référence Déficiences intellectuelles de causes rares, Assistance publique‐Hopitaux de Paris (AP‐HP), Hopital Robert‐DebréParisFrance
| | - Aurélie Gouronc
- Service de Génétique MédicaleInstitut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de StrasbourgStrasbourgFrance
| | | | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental DisordersUniversity of Rouen Normandie, Inserm U1245, CHU RouenRouenFrance
| | - Miroslava Hancarova
- Department of Biology and Medical GeneticsCharles University Second Faculty of Medicine and University Hospital MotolPragueCzech Republic
| | - Markéta Havlovicová
- Department of Biology and Medical GeneticsCharles University Second Faculty of Medicine and University Hospital MotolPragueCzech Republic
| | | | - Bertrand Isidor
- Genetic DepartmentCHU Nantes, Service de GénétiqueNantesFrance
| | | | - Boris Keren
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes RaresAPHP Sorbonne UniversitéParisFrance
| | - Margarete Koch‐Hogrebe
- Institute of Human Genetics, Medical FacultyUniversity Hospital Düsseldorf, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Paul Kuentz
- UFR Des Sciences de SantéINSERM‐Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement”, FHUTRANSLADDijonFrance
- Oncobiologie Génétique BioinformatiquePC BIO, CHU BesançonBesançonFrance
| | - Victoria Lamure
- Genetic DepartmentUFR SMBH, Université Sorbonne Paris NordParisFrance
| | - Anne‐Sophie Lebre
- Centre Hospitalier Universitaire de ReimsPôle de Biologie Médicale et Pathologie, Service de GénétiqueReimsFrance
- Institute of Psychiatry and Neuroscience of Paris (IPNP)INSERM U1266, Université Paris CitéParisFrance
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental DisordersUniversity of Rouen Normandie, Inserm U1245, CHU RouenRouenFrance
| | - Natacha Lehman
- Genetic DepartmentMontpellier University, INSERM Unit 1183MontpellierFrance
- Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics DepartmentMontpellier HospitalMontpellierFrance
| | - Gaetan Lesca
- Department of Medical GeneticsUniversity Hospital of Lyon and Claude Bernard Lyon I UniversityLyonFrance
- Pathophysiology and Genetics of Neuron and Muscle (PNMG)UCBL, CNRS UMR5261 – INSERM U1315LyonFrance
| | - Stanislas Lyonnet
- Service de Médecine Génomique des Maladies RaresHôpital Necker – Enfants Malades, Assistance Publique‐Hôpitaux de ParisParisFrance
- Laboratoire Embryologie et Génétique des MalformationsUniversité Paris Cité, INSERM, IHU Imagine – Institut des maladies génétiquesParisFrance
| | | | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes RaresAPHP Sorbonne UniversitéParisFrance
| | | | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental DisordersUniversity of Rouen Normandie, Inserm U1245, CHU RouenRouenFrance
| | - Mathilde Nizon
- Genetic DepartmentCHU Nantes, Service de GénétiqueNantesFrance
| | - Florence Petit
- Genetic DepartmentCHU Lille, Clinique de Génétique Guy FontaineLilleFrance
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies raresCHU Dijon BourgogneDijonFrance
- UFR Des Sciences de SantéINSERM‐Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement”, FHUTRANSLADDijonFrance
| | - Amélie Piton
- Service de Génétique MédicaleInstitut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de StrasbourgStrasbourgFrance
| | - Marzia Pollazzon
- Medical Genetics UnitAzienda USL‐IRCCS di Reggio EmiliaReggio EmiliaItaly
| | - Darina Prchalová
- Department of Biology and Medical GeneticsCharles University Second Faculty of Medicine and University Hospital MotolPragueCzech Republic
| | - Audrey Putoux
- Department of Medical GeneticsUniversity Hospital of Lyon and Claude Bernard Lyon I UniversityLyonFrance
- INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV TeamUniversité Claude Bernard Lyon 1BronFrance
| | - Marlène Rio
- Service de Médecine Génomique des Maladies RaresHôpital Necker – Enfants Malades, Assistance Publique‐Hôpitaux de ParisParisFrance
| | - Sophie Rondeau
- Service de Médecine Génomique des Maladies RaresHôpital Necker – Enfants Malades, Assistance Publique‐Hôpitaux de ParisParisFrance
| | - Massimiliano Rossi
- Department of Medical GeneticsUniversity Hospital of Lyon and Claude Bernard Lyon I UniversityLyonFrance
- INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV TeamUniversité Claude Bernard Lyon 1BronFrance
| | - Quentin Sabbagh
- Genetic DepartmentMontpellier University, INSERM Unit 1183MontpellierFrance
- Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics DepartmentMontpellier HospitalMontpellierFrance
| | - Pascale Saugier‐Veber
- Department of Genetics and Reference Center for Developmental DisordersUniversity of Rouen Normandie, Inserm U1245, CHU RouenRouenFrance
| | - Ariane Schmetz
- Institute of Human Genetics, Medical FacultyUniversity Hospital Düsseldorf, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Julie Steffann
- Service de Médecine Génomique des Maladies RaresHôpital Necker – Enfants Malades, Assistance Publique‐Hôpitaux de ParisParisFrance
| | - Christel Thauvin‐Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies raresCHU Dijon BourgogneDijonFrance
- UFR Des Sciences de SantéINSERM‐Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement”, FHUTRANSLADDijonFrance
- Centre de Génétique et Centre de référence maladies rares « Anomalies du Développement et Syndromes Malformatifs », FHU TRANSLADHôpital d'Enfants, CHU DijonDijonFrance
| | - Annick Toutain
- Genetics DepartmentUniversity Hospital, UMR1253 iBrain INSERM, University of ToursToursFrance
| | - Frederic Tran Mau Them
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies raresCHU Dijon BourgogneDijonFrance
- UFR Des Sciences de SantéINSERM‐Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement”, FHUTRANSLADDijonFrance
| | - Gabriele Trimarchi
- Medical Genetics UnitAzienda USL‐IRCCS di Reggio EmiliaReggio EmiliaItaly
| | - Marie Vincent
- Genetic DepartmentCHU Nantes, Service de GénétiqueNantesFrance
| | - Markéta Vlčková
- Department of Biology and Medical GeneticsCharles University Second Faculty of Medicine and University Hospital MotolPragueCzech Republic
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical FacultyUniversity Hospital Düsseldorf, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Marjolaine Willems
- Genetic DepartmentMontpellier University, INSERM Unit 1183MontpellierFrance
- Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics DepartmentMontpellier HospitalMontpellierFrance
| | - Kevin Yauy
- Genetic DepartmentMontpellier University, INSERM Unit 1183MontpellierFrance
- Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics DepartmentMontpellier HospitalMontpellierFrance
| | - Michaela Zelinová
- Department of Biology and Medical GeneticsCharles University Second Faculty of Medicine and University Hospital MotolPragueCzech Republic
| | - Alban Ziegler
- Genetic DepartmentService de Génétique, CHU d'AngersAngers Cedex 9France
| | - GENIDA Project
- Institute of Genetics and Molecular and Cellular Biology (IGBMC)Université de Strasbourg, INSERM U1258, CNRS UMR7104IllkirchFrance
| | - Boris Chaumette
- Center for Rare Psychiatric Disorders – GHU Paris Psychiatrie et Neurosciences – Paris – France APHPGHU Sainte AnneParisFrance
- Institute of Psychiatry and Neuroscience of ParisUniversité Paris Cité, INSERM U1266ParisFrance
- Department of PsychiatryMcGill UniversityMontrealQuebecCanada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory MedicineWestern UniversityLondonOntarioCanada
- Verspeeten Clinical Genome CentreLondon Health Sciences CentreLondonOntarioCanada
| | - Jean‐Louis Mandel
- Institute of Genetics and Molecular and Cellular Biology (IGBMC)Université de Strasbourg, INSERM U1258, CNRS UMR7104IllkirchFrance
- Genetic DepartmentUniversity of Strasbourg Institute for Advanced Studies (USIAS)StrasbourgFrance
| | - David Geneviève
- Genetic DepartmentMontpellier University, INSERM Unit 1183MontpellierFrance
- Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics DepartmentMontpellier HospitalMontpellierFrance
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7
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Blackburn PR, Ebstein F, Hsieh TC, Motta M, Radio FC, Herkert JC, Rinne T, Thiffault I, Rapp M, Alders M, Maas S, Gerard B, Smol T, Vincent-Delorme C, Cogné B, Isidor B, Vincent M, Bachmann-Gagescu R, Rauch A, Joset P, Ferrero GB, Ciolfi A, Husson T, Guerrot AM, Bacino C, Macmurdo C, Thompson SS, Rosenfeld JA, Faivre L, Mau-Them FT, Deb W, Vignard V, Agrawal PB, Madden JA, Goldenberg A, Lecoquierre F, Zech M, Prokisch H, Necpál J, Jech R, Winkelmann J, Koprušáková MT, Konstantopoulou V, Younce JR, Shinawi M, Mighton C, Fung C, Morel C, Ellis JL, DiTroia S, Barth M, Bonneau D, Krapels I, Stegmann S, van der Schoot V, Brunet T, Bußmann C, Mignot C, Courtin T, Ravelli C, Keren B, Ziegler A, Hasadsri L, Pichurin PN, Klee EW, Grand K, Sanchez-Lara PA, Krüger E, Bézieau S, Klinkhammer H, Krawitz PM, Eichler EE, Tartaglia M, Küry S, Wang T. Loss-of-function variants in CUL3 cause a syndromic neurodevelopmental disorder. medRxiv 2023:2023.06.13.23290941. [PMID: 37398376 PMCID: PMC10312857 DOI: 10.1101/2023.06.13.23290941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Purpose De novo variants in CUL3 (Cullin-3 ubiquitin ligase) have been strongly associated with neurodevelopmental disorders (NDDs), but no large case series have been reported so far. Here we aimed to collect sporadic cases carrying rare variants in CUL3, describe the genotype-phenotype correlation, and investigate the underlying pathogenic mechanism. Methods Genetic data and detailed clinical records were collected via multi-center collaboration. Dysmorphic facial features were analyzed using GestaltMatcher. Variant effects on CUL3 protein stability were assessed using patient-derived T-cells. Results We assembled a cohort of 35 individuals with heterozygous CUL3 variants presenting a syndromic NDD characterized by intellectual disability with or without autistic features. Of these, 33 have loss-of-function (LoF) and two have missense variants. CUL3 LoF variants in patients may affect protein stability leading to perturbations in protein homeostasis, as evidenced by decreased ubiquitin-protein conjugates in vitro . Specifically, we show that cyclin E1 (CCNE1) and 4E-BP1 (EIF4EBP1), two prominent substrates of CUL3, fail to be targeted for proteasomal degradation in patient-derived cells. Conclusion Our study further refines the clinical and mutational spectrum of CUL3 -associated NDDs, expands the spectrum of cullin RING E3 ligase-associated neuropsychiatric disorders, and suggests haploinsufficiency via LoF variants is the predominant pathogenic mechanism.
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Moisan A, Soares A, De Oliveira F, Alessandri-Gradt E, Lecoquierre F, Fourneaux S, Plantier JC, Gueudin M. Evaluation of Analytical and Clinical Performance and Usefulness in a Real-Life Hospital Setting of Two in-House Real-Time RT-PCR Assays to Track SARS-CoV-2 Variants of Concern. Viruses 2023; 15:v15051115. [PMID: 37243201 DOI: 10.3390/v15051115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023] Open
Abstract
Since the end of 2020, multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have emerged and spread worldwide. Tracking their evolution has been a challenge due to the huge number of positive samples and limited capacities of whole-genome sequencing. Two in-house variant-screening RT-PCR assays were successively designed in our laboratory in order to detect specific known mutations in the spike region and to rapidly detect successively emerging VOCs. The first one (RT-PCR#1) targeted the 69-70 deletion and the N501Y substitution simultaneously, whereas the second one (RT-PCR#2) targeted the E484K, E484Q, and L452R substitutions simultaneously. To evaluate the analytical performance of these two RT-PCRs, 90 negative and 30 positive thawed nasopharyngeal swabs were retrospectively analyzed, and no discordant results were observed. Concerning the sensitivity, for RT-PCR#1, serial dilutions of the WHO international standard SARS-CoV-2 RNA, corresponding to the genome of an Alpha variant, were all detected up to 500 IU/mL. For RT-PCR#2, dilutions of a sample harboring the E484K substitution and of a sample harboring the L452R and E484Q substitutions were all detected up to 1000 IU/mL and 2000 IU/mL, respectively. To evaluate the performance in a real-life hospital setting, 1308 and 915 profiles of mutations, obtained with RT-PCR#1 and RT-PCR#2, respectively, were prospectively compared to next-generation sequencing (NGS) data. The two RT-PCR assays showed an excellent concordance with the NGS data, with 99.8% for RT-PCR#1 and 99.2% for RT-PCR#2. Finally, for each mutation targeted, the clinical sensitivity, the clinical specificity and the positive and negative predictive values showed excellent clinical performance. Since the beginning of the SARS-CoV-2 pandemic, the emergence of variants-impacting the disease's severity and the efficacy of vaccines and therapies-has forced medical analysis laboratories to constantly adapt to the strong demand for screening them. Our data showed that in-house RT-PCRs are useful and adaptable tools for monitoring such rapid evolution and spread of SARS-CoV-2 VOCs.
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Affiliation(s)
- Alice Moisan
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - Anaïs Soares
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - Fabienne De Oliveira
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - Elodie Alessandri-Gradt
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France
| | - Steeve Fourneaux
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France
| | - Jean-Christophe Plantier
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - Marie Gueudin
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
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Lecoquierre F, Quenez O, Fourneaux S, Coutant S, Vezain M, Rolain M, Drouot N, Boland A, Olaso R, Meyer V, Deleuze JF, Dabbagh D, Gilles I, Gayet C, Saugier-Veber P, Goldenberg A, Guerrot AM, Nicolas G. High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders. Hum Genet 2023; 142:773-783. [PMID: 37076692 DOI: 10.1007/s00439-023-02553-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/05/2023] [Indexed: 04/21/2023]
Abstract
Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
| | - Olivier Quenez
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Myriam Vezain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Marion Rolain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Dana Dabbagh
- Department of Pediatrics, Elbeuf Hospital, Elbeuf, France
| | | | - Claire Gayet
- Department of Pediatrics, CHU Rouen, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne-Marie Guerrot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
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10
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Luppe J, Sticht H, Lecoquierre F, Goldenberg A, Gorman KM, Molloy B, Agolini E, Novelli A, Briuglia S, Kuismin O, Marcelis C, Vitobello A, Denommé-Pichon AS, Julia S, Lemke JR, Abou Jamra R, Platzer K. Heterozygous and homozygous variants in STX1A cause a neurodevelopmental disorder with or without epilepsy. Eur J Hum Genet 2023; 31:345-352. [PMID: 36564538 PMCID: PMC9995539 DOI: 10.1038/s41431-022-01269-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
The neuronal SNARE complex drives synaptic vesicle exocytosis. Therefore, one of its core proteins syntaxin 1A (STX1A) has long been suspected to play a role in neurodevelopmental disorders. We assembled eight individuals harboring ultra rare variants in STX1A who present with a spectrum of intellectual disability, autism and epilepsy. Causative variants comprise a homozygous splice variant, three de novo missense variants and two inframe deletions of a single amino acid. We observed a phenotype mainly driven by epilepsy in the individuals with missense variants in contrast to intellectual disability and autistic behavior in individuals with single amino acid deletions and the splicing variant. In silico modeling of missense variants and single amino acid deletions show different impaired protein-protein interactions. We hypothesize the two phenotypic courses of affected individuals to be dependent on two different pathogenic mechanisms: (1) a weakened inhibitory STX1A-STXBP1 interaction due to missense variants results in an STX1A-related developmental epileptic encephalopathy and (2) a hampered SNARE complex formation due to inframe deletions causes an STX1A-related intellectual disability and autism phenotype. Our description of a STX1A-related neurodevelopmental disorder with or without epilepsy thus expands the group of rare diseases called SNAREopathies.
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Affiliation(s)
- Johannes Luppe
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Kathleen M Gorman
- Department of Neurology and Clinical Neurophysiology, Children's Health Ireland at Temple Street, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | | | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Silvana Briuglia
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Messina, Italy
| | - Outi Kuismin
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Carlo Marcelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Antonio Vitobello
- Inserm UMR1231 GAD, University of Burgundy-Franche Comté, Dijon, France
| | | | - Sophie Julia
- Federative Institute of Biology, CHU de Toulouse, Toulouse, France
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
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11
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Vezain M, Thauvin-Robinet C, Vial Y, Coutant S, Drunat S, Urtizberea JA, Rolland A, Jacquin-Piques A, Fehrenbach S, Nicolas G, Lecoquierre F, Saugier-Veber P. Retrotransposon insertion as a novel mutational cause of spinal muscular atrophy. Hum Genet 2023; 142:125-138. [PMID: 36138164 DOI: 10.1007/s00439-022-02473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/15/2022] [Indexed: 01/18/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder resulting from biallelic alterations of the SMN1 gene: deletion, gene conversion or, in rare cases, intragenic variants. The disease severity is mainly influenced by the copy number of SMN2, a nearly identical gene, which produces only low amounts of full-length (FL) mRNA. Here we describe the first example of retrotransposon insertion as a pathogenic SMN1 mutational event. The 50-year-old patient is clinically affected by SMA type III with a diagnostic odyssey spanning nearly 30 years. Despite a mild disease course, he carries a single SMN2 copy. Using Exome Sequencing and Sanger sequencing, we characterized a SINE-VNTR-Alu (SVA) type F retrotransposon inserted in SMN1 intron 7. Using RT-PCR and RNASeq experiments on lymphoblastoid cell lines, we documented the dramatic decrease of FL transcript production in the patient compared to subjects with the same SMN1 and SMN2 copy number, thus validating the pathogenicity of this SVA insertion. We described the mutant FL-SMN1-SVA transcript characterized by exon extension and showed that it is subject to degradation by nonsense-mediated mRNA decay. The stability of the SMN-SVA protein may explain the mild course of the disease. This observation exemplifies the role of retrotransposons in human genetic disorders.
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Affiliation(s)
- Myriam Vezain
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Christel Thauvin-Robinet
- INSERM UMR1231 GAD-Génétique des Anomalies du Développement, Bourgogne Franche-Comté University, F-21000 , Dijon, France.,Genetics Center, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Yoann Vial
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, 48 boulevard Sérurier, 75019 , Paris, France
| | - Sophie Coutant
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Séverine Drunat
- INSERM UMR 1141, PROTECT, Paris University, F-75019, Paris, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, F-75019, Paris, France
| | - Jon Andoni Urtizberea
- Myology Institute, AP-HP Pitié-Salpêtrière University Hospital, F-75013, Paris, France
| | - Anne Rolland
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Pediatrics Department, Valence Hospital, 179 boulevard du Maréchal Juin, 26000, Valence, France
| | - Agnès Jacquin-Piques
- Department of Neurology, Clinical Neurophysiology, Competence Center of Neuromuscular Diseases, Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Séverine Fehrenbach
- Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Gaël Nicolas
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - François Lecoquierre
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France. .,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France. .,Laboratoire de Génétique Moléculaire, UFR-Santé, 22 boulevard Gambetta, 76183, Rouen, France.
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12
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Cali E, Suri M, Scala M, Ferla MP, Alavi S, Faqeih EA, Bijlsma EK, Wigby KM, Baralle D, Mehrjardi MYV, Schwab J, Platzer K, Steindl K, Hashem M, Jones M, Niyazov DM, Jacober J, Littlejohn RO, Weis D, Zadeh N, Rodan L, Goldenberg A, Lecoquierre F, Dutra-Clarke M, Horvath G, Young D, Orenstein N, Bawazeer S, Vulto-van Silfhout AT, Herenger Y, Dehghani M, Seyedhassani SM, Bahreini A, Nasab ME, Ercan-Sencicek AG, Firoozfar Z, Movahedinia M, Efthymiou S, Striano P, Karimiani EG, Salpietro V, Taylor JC, Redman M, Stegmann APA, Laner A, Abdel-Salam G, Li M, Bengala M, Müller AJ, Digilio MC, Rauch A, Gunel M, Titheradge H, Schweitzer DN, Kraus A, Valenzuela I, McLean SD, Phornphutkul C, Salih M, Begtrup A, Schnur RE, Torti E, Haack TB, Prada CE, Alkuraya FS, Houlden H, Maroofian R. Biallelic PRMT7 pathogenic variants are associated with a recognizable syndromic neurodevelopmental disorder with short stature, obesity, and craniofacial and digital abnormalities. Genet Med 2023; 25:135-142. [PMID: 36399134 PMCID: PMC10620944 DOI: 10.1016/j.gim.2022.09.016] [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: 04/10/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Protein arginine methyltransferase 7 (PRMT7) is a member of a family of enzymes that catalyzes the methylation of arginine residues on several protein substrates. Biallelic pathogenic PRMT7 variants have previously been associated with a syndromic neurodevelopmental disorder characterized by short stature, brachydactyly, intellectual developmental disability, and seizures. To our knowledge, no comprehensive study describes the detailed clinical characteristics of this syndrome. Thus, we aim to delineate the phenotypic spectrum of PRMT7-related disorder. METHODS We assembled a cohort of 51 affected individuals from 39 different families, gathering clinical information from 36 newly described affected individuals and reviewing data of 15 individuals from the literature. RESULTS The main clinical characteristics of the PRMT7-related syndrome are short stature, mild to severe developmental delay/intellectual disability, hypotonia, brachydactyly, and distinct facial morphology, including bifrontal narrowing, prominent supraorbital ridges, sparse eyebrows, short nose with full/broad nasal tip, thin upper lip, full and everted lower lip, and a prominent or squared-off jaw. Additional variable findings include seizures, obesity, nonspecific magnetic resonance imaging abnormalities, eye abnormalities (i.e., strabismus or nystagmus), and hearing loss. CONCLUSION This study further delineates and expands the molecular, phenotypic spectrum and natural history of PRMT7-related syndrome characterized by a neurodevelopmental disorder with skeletal, growth, and endocrine abnormalities.
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Affiliation(s)
- Elisa Cali
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, United Kingdom
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Matteo P Ferla
- Genomic Medicine theme, Oxford Biomedical Research Centre, NIHR, Oxford, Oxfordshire, United Kingdom; Wellcome Centre for Human Genetics, Oxford University, Oxford, Oxfordshire, United Kingdom
| | - Shahryar Alavi
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran; Palindrome, Isfahan, Iran
| | - Eissa Ali Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical, City, Riyadh, Saudi Arabia
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kristen M Wigby
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, CA
| | - Diana Baralle
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom; Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Mohammad Y V Mehrjardi
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Science, Yazd, Iran
| | - Jennifer Schwab
- Division of Human Genetics, Warren Alpert Medical School of Brown University, Hasbro Children's Hospital/Rhode Island Hospital, Providence, RI
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Marilyn Jones
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, CA
| | - Dmitriy M Niyazov
- Section of Medical Genetics, Department of Pediatrics, Ochsner Health System and University of Queensland, New Orleans, LA
| | - Jennifer Jacober
- Section of Medical Genetics, Department of Pediatrics, Ochsner Health System and University of Queensland, New Orleans, LA
| | | | - Denisa Weis
- Department of Medical Genetics, Kepler University Hospital Med Campus IV, Johannes Kepler University, Linz, Austria
| | - Neda Zadeh
- Children's Hospital of Orange County, Orange, CA; Genetics Center, Orange, California
| | - Lance Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, Normandie University, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, Rouen, France
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandie University, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, Rouen, France
| | - Marina Dutra-Clarke
- Division of Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA
| | - Gabriella Horvath
- BC Children's Hospital Research Institute, BC Children's Hospital, Vancouver, British Columbia, Canada; Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - Dana Young
- Adult Metabolic Diseases Clinic, Vancouver General Hospital, Vancouver, Canada
| | - Naama Orenstein
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shahad Bawazeer
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical, City, Riyadh, Saudi Arabia
| | | | | | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Science, Yazd, Iran
| | | | - Amir Bahreini
- Palindrome, Isfahan, Iran; KaryoGen, Isfahan, Iran; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA
| | | | - A Gulhan Ercan-Sencicek
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT; Masonic Medical Research Institute, Utica, NY
| | - Zahra Firoozfar
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran; Palindrome, Isfahan, Iran
| | - Mojtaba Movahedinia
- Children Growth Disorder Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Ehsan Ghayoor Karimiani
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran; Molecular and Clinical Sciences Institute, St. George's, University of London, London, United Kingdom; Innovative Medical Research Center, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Jenny C Taylor
- Genomic Medicine theme, Oxford Biomedical Research Centre, NIHR, Oxford, Oxfordshire, United Kingdom; Wellcome Centre for Human Genetics, Oxford University, Oxford, Oxfordshire, United Kingdom
| | - Melody Redman
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, United Kingdom
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Ghada Abdel-Salam
- Human Genetics and Genome Research Division, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | | | - Mario Bengala
- Laboratory of Medical Genetics, Tor Vergata Hospital, Rome, Italy
| | - Amelie Johanna Müller
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Maria C Digilio
- Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Murat Gunel
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT
| | - Hannah Titheradge
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham, United Kingdom; Women's and Children's NHS Trust, Birmingham, United Kingdom
| | - Daniela N Schweitzer
- Division of Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, United Kingdom; Castle Hill Hospital, Cottingham, Hull, United Kingdom
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, University Hospital Vall d'Hebron, Barcelona, Spain; Medicine Genetics Group, Valle Hebron Research Institute, Barcelona, Spain
| | - Scott D McLean
- Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, TX
| | - Chanika Phornphutkul
- Section of Medical Genetics, Department of Pediatrics, Ochsner Health System and University of Queensland, New Orleans, LA
| | - Mustafa Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediatrics, College of Medicine, AlMughtaribeen University, Khartoum, Sudan
| | | | | | | | - Tobias B Haack
- Institute of Human Genetics and Applied Genomics University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Carlos E Prada
- Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, OH; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL; Department of Pediatrics, Feinberg School of Medicine of Northwestern University, Chicago, IL
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
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13
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Coursimault J, Cassinari K, Lecoquierre F, Quenez O, Coutant S, Derambure C, Vezain M, Drouot N, Vera G, Schaefer E, Philippe A, Doray B, Lambert L, Ghoumid J, Smol T, Rama M, Legendre M, Lacombe D, Fergelot P, Olaso R, Boland A, Deleuze JF, Goldenberg A, Saugier-Veber P, Nicolas G. Deep intronic NIPBL de novo mutations and differential diagnoses revealed by whole genome and RNA sequencing in Cornelia de Lange syndrome patients. Hum Mutat 2022; 43:1882-1897. [PMID: 35842780 DOI: 10.1002/humu.24438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/23/2022] [Accepted: 07/09/2022] [Indexed: 01/25/2023]
Abstract
Cornelia de Lange syndrome (CdLS; MIM# 122470) is a rare developmental disorder. Pathogenic variants in 5 genes explain approximately 50% cases, leaving the other 50% unsolved. We performed whole genome sequencing (WGS) ± RNA sequencing (RNA-seq) in 5 unsolved trios fulfilling the following criteria: (i) clinical diagnosis of classic CdLS, (ii) negative gene panel sequencing from blood and saliva-isolated DNA, (iii) unaffected parents' DNA samples available and (iv) proband's blood-isolated RNA available. A pathogenic de novo mutation (DNM) was observed in a CdLS differential diagnosis gene in 3/5 patients, namely POU3F3, SPEN, and TAF1. In the other two, we identified two distinct deep intronic DNM in NIPBL predicted to create a novel splice site. RT-PCRs and RNA-Seq showed aberrant transcripts leading to the creation of a novel frameshift exon. Our findings suggest the relevance of WGS in unsolved suspected CdLS cases and that deep intronic variants may account for a proportion of them.
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Affiliation(s)
- Juliette Coursimault
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Kévin Cassinari
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Olivier Quenez
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Céline Derambure
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Myriam Vezain
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Nathalie Drouot
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Gabriella Vera
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Elise Schaefer
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Anaïs Philippe
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Bérénice Doray
- Service de Génétique Médicale, Centre Hospitalier Universitaire Félix Guyon, Bellepierre Saint Denis, France
| | - Laëtitia Lambert
- Service de Génétique Clinique, CHRU NANCY, F-54000 France, UMR INSERM U 1256 N-GERE, F-54000, Nancy, France
| | - Jamal Ghoumid
- Université de Lille, ULR7364 RADEME, CHU Lille, Clinique de Génétique « Guy Fontaine », and FHU-G4 Génomique, F-59000, Lille, France
| | - Thomas Smol
- Université de Lille, ULR7364 RADEME, CHU Lille, Institut de Génétique Médicale, and FHU-G4 Génomique, F-59000, Lille, France
| | - Mélanie Rama
- Institut de Génétique Médicale, CHU de Lille, France
| | - Marine Legendre
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Didier Lacombe
- INSERM U1211, Université de Bordeaux; Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Patricia Fergelot
- INSERM U1211, Université de Bordeaux; Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
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14
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Schalk A, Cousin MA, Dsouza NR, Challman TD, Wain KE, Powis Z, Minks K, Trimouille A, Lasseaux E, Lacombe D, Angelini C, Michaud V, Van-Gils J, Spataro N, Ruiz A, Gabau E, Stolerman E, Washington C, Louie RJ, Lanpher BC, Kemppainen JL, Innes AM, Kooy RF, Meuwissen M, Goldenberg A, Lecoquierre F, Vera G, Diderich KEM, Sheidley BR, Achkar CME, Park M, Hamdan FF, Michaud JL, Lewis AJ, Zweier C, Reis A, Wagner M, Weigand H, Journel H, Keren B, Passemard S, Mignot C, van Gassen KL, Brilstra EH, Itzikowitz G, O’Heir E, Allen J, Donald KA, Korf BR, Skelton T, Thompson ML, Robin NH, Rudy N, Dobyns WB, Foss K, Zarate YA, Bosanko KA, Alembik Y, Durand B, Mau-Them FT, Ranza E, Blanc X, Antonarakis SE, McWalter K, Torti E, Millan F, Dameron A, Tokita MJ, Zimmermann MT, Klee EW, Piton A, Gerard B. De novo coding variants in the AGO1 gene cause a neurodevelopmental disorder with intellectual disability. J Med Genet 2022; 59:965-975. [PMID: 34930816 PMCID: PMC9241146 DOI: 10.1136/jmedgenet-2021-107751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 01/28/2021] [Accepted: 11/09/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND High-impact pathogenic variants in more than a thousand genes are involved in Mendelian forms of neurodevelopmental disorders (NDD). METHODS This study describes the molecular and clinical characterisation of 28 probands with NDD harbouring heterozygous AGO1 coding variants, occurring de novo for all those whose transmission could have been verified (26/28). RESULTS A total of 15 unique variants leading to amino acid changes or deletions were identified: 12 missense variants, two in-frame deletions of one codon, and one canonical splice variant leading to a deletion of two amino acid residues. Recurrently identified variants were present in several unrelated individuals: p.(Phe180del), p.(Leu190Pro), p.(Leu190Arg), p.(Gly199Ser), p.(Val254Ile) and p.(Glu376del). AGO1 encodes the Argonaute 1 protein, which functions in gene-silencing pathways mediated by small non-coding RNAs. Three-dimensional protein structure predictions suggest that these variants might alter the flexibility of the AGO1 linker domains, which likely would impair its function in mRNA processing. Affected individuals present with intellectual disability of varying severity, as well as speech and motor delay, autistic behaviour and additional behavioural manifestations. CONCLUSION Our study establishes that de novo coding variants in AGO1 are involved in a novel monogenic form of NDD, highly similar to the recently reported AGO2-related NDD.
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Affiliation(s)
- Audrey Schalk
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Margot A. Cousin
- Department of Health Sciences Research, Mayo Clinic,
Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
| | - Nikita R. Dsouza
- Bioinformatics Research and Development Laboratory,
Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
| | - Thomas D. Challman
- Autism & Developmental Medicine Institute, Geisinger,
Lewisburg, Pennsylvania, PA 17837, United States
| | - Karen E. Wain
- Autism & Developmental Medicine Institute, Geisinger,
Lewisburg, Pennsylvania, PA 17837, United States
| | - Zöe Powis
- Department of Clinical Genomics, Ambry Genetics, Aliso
Viejo, California, CA 92656, United States
| | - Kelly Minks
- Department of Clinical Genomics, Ambry Genetics, Aliso
Viejo, California, CA 92656, United States
| | - Aurélien Trimouille
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Eulalie Lasseaux
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
| | - Didier Lacombe
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Chloé Angelini
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Vincent Michaud
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Julien Van-Gils
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
| | - Nino Spataro
- Genetics Laboratory, UDIAT-Centre Diagnòstic. Parc
Taulí Hospital Universitari. Institut d’Investigació i
Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona.
Sabadell, Spain
| | - Anna Ruiz
- Genetics Laboratory, UDIAT-Centre Diagnòstic. Parc
Taulí Hospital Universitari. Institut d’Investigació i
Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona.
Sabadell, Spain
| | - Elizabeth Gabau
- Paediatric Unit. ParcTaulí Hospital Universitari.
Institut d’Investigació i Innovació Parc Taulí I3PT.
Universitat Autònoma de Barcelona. Sabadell, Spain
| | - Elliot Stolerman
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Camerun Washington
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Raymond J. Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester,
Minnesota, MN 55905, United States
| | - Jennifer L. Kemppainen
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester,
Minnesota, MN 55905, United States
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta
Children’s Hospital Research Institute, Cumming School of Medicine,
University of Calgary, Calgary, AB, Canada
| | - R. Frank Kooy
- Department of Medical Genetics, University and University
Hospital Antwerp, Antwerp, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University and University
Hospital Antwerp, Antwerp, Belgium
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - Gabriella Vera
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center,
Rotterdam, The Netherlands
| | - Beth Rosen Sheidley
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Christelle Moufawad El Achkar
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Meredith Park
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Fadi F. Hamdan
- Division of Medical Genetics, Department of Pediatrics,
CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Jacques L. Michaud
- Division of Medical Genetics, Department of Pediatrics,
CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Ann J. Lewis
- Pediatric Neurology, Kaiser Permanente Santa Clara
Homestead, Santa Clara, United States
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern
University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics,
Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - André Reis
- Department of Human Genetics, Inselspital, Bern
University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics,
Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich,
Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum
München, Neuherberg, Germany
| | - Heike Weigand
- Department of Pediatric Neurology, Developmental Medicine
and Social Pediatrics, Dr. von Hauner’s Children’s Hospital,
University of Munich, Munich, Germany
| | - Hubert Journel
- Service de Génétique Médicale,
Hôpital Chubert, Vannes, France
| | - Boris Keren
- Département de Génétique et de
Cytogénétique, Centre de Reference Déficience Intellectuelle de
Causes Rares, GRC UPMC « Déficience Intellectuelle et Autisme
», Hôpital Pitié-Salpêtrière, AP-HP, Paris,
France
- INSERM U 1127, CNRS UMR 7225, Sorbonne
Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la
Moelle épinière, ICM, Paris, France
| | | | - Cyril Mignot
- Département de Génétique et de
Cytogénétique, Centre de Reference Déficience Intellectuelle de
Causes Rares, GRC UPMC « Déficience Intellectuelle et Autisme
», Hôpital Pitié-Salpêtrière, AP-HP, Paris,
France
- INSERM U 1127, CNRS UMR 7225, Sorbonne
Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la
Moelle épinière, ICM, Paris, France
| | | | - Eva H. Brilstra
- Department of Genetics, Center for Molecular Medicine,
University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gina Itzikowitz
- Department of Paediatrics and Child Health, Red Cross War
Memorial Children’s Hospital, University of Cape Town, SA
| | - Emily O’Heir
- Center for Mendelian Genomics and Program in Medical and
Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston
Children’s Hospital, Boston, MA, USA
| | - Jake Allen
- Stanley Center for Psychiatric Research, Broad Institute
of MIT and Harvard, Cambridge, MA, USA
| | - Kirsten A. Donald
- Department of Paediatrics and Child Health, Red Cross War
Memorial Children’s Hospital, University of Cape Town, SA
- Neuroscience Institute, University of Cape Town, SA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at
Birmingham, Birmingham, AL 35294, USA
| | - Tammi Skelton
- Department of Genetics, University of Alabama at
Birmingham, Birmingham, AL 35294, USA
| | - Michelle L Thompson
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
- HudsonAlpha Institute for Biotechnology, Huntsville,
Alabama, USA
| | - Nathaniel H. Robin
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Natasha Rudy
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - William B. Dobyns
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Kimberly Foss
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of
Arkansas for Medical Sciences, Little Rock, USA
| | - Katherine A. Bosanko
- Section of Genetics and Metabolism, University of
Arkansas for Medical Sciences, Little Rock, USA
| | - Yves Alembik
- Service de Génétique Médicale,
Institut de génétique médicale d’Alsace (IGMA),
Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Benjamin Durand
- Service de Génétique Médicale,
Institut de génétique médicale d’Alsace (IGMA),
Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Frédéric Tran Mau-Them
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, 1207
Geneva, Switzerland
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, 1207
Geneva, Switzerland
| | | | | | | | | | | | | | - Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory,
Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
- Clinical and Translational Sciences Institute, Medical
College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
| | - Eric W. Klee
- Department of Health Sciences Research, Mayo Clinic,
Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Amélie Piton
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
- Institut de Genetique et de Biologie Moleculaire et
Cellulaire, Illkirch 67400, France
| | - Bénédicte Gerard
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
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15
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O'Grady L, Schrier Vergano SA, Hoffman TL, Sarco D, Cherny S, Bryant E, Schultz-Rogers L, Chung WK, Sacharow S, Immken LL, Holder S, Blackwell RR, Buchanan C, Yusupov R, Lecoquierre F, Guerrot AM, Rodan L, de Vries BBA, Kamsteeg EJ, Santos Simarro F, Palomares-Bralo M, Brown N, Pais L, Ferrer A, Klee EW, Babovic-Vuksanovic D, Rhodes L, Person R, Begtrup A, Keller-Ramey J, Santiago-Sim T, Schnur RE, Sweetser DA, Gold NB. Heterozygous variants in PRPF8 are associated with neurodevelopmental disorders. Am J Med Genet A 2022; 188:2750-2759. [PMID: 35543142 DOI: 10.1002/ajmg.a.62772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/22/2022] [Accepted: 04/05/2022] [Indexed: 01/25/2023]
Abstract
The pre-mRNA-processing factor 8, encoded by PRPF8, is a scaffolding component of a spliceosome complex involved in the removal of introns from mRNA precursors. Previously, heterozygous pathogenic variants in PRPF8 have been associated with autosomal dominant retinitis pigmentosa. More recently, PRPF8 was suggested as a candidate gene for autism spectrum disorder due to the enrichment of sequence variants in this gene in individuals with neurodevelopmental disorders. We report 14 individuals with various forms of neurodevelopmental conditions, found to have heterozygous, predominantly de novo, missense, and loss-of-function variants in PRPF8. These individuals have clinical features that may represent a new neurodevelopmental syndrome.
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Affiliation(s)
- Lauren O'Grady
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts, USA.,MGH Institute of Health Professions, Charlestown, Massachusetts, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughter, Norfolk, Virginia, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Trevor L Hoffman
- Department of Genetics, Southern California Kaiser Permanente Medical Group, Anaheim, California, USA
| | - Dean Sarco
- Department of Neurology, Kaiser Permanente-Los Angeles Medical Center, Los Angeles, California, USA
| | - Sara Cherny
- Division of Cardiology, Ann & Robert H. Lurie Children's Hospital, Chicago, Illinois, USA
| | - Emily Bryant
- Division of Neurology, Ann & Robert H. Lurie Children's Hospital, Chicago, Illinois, USA
| | - Laura Schultz-Rogers
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Stephanie Sacharow
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Ladonna L Immken
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Susan Holder
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Rebecca R Blackwell
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Catherine Buchanan
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Roman Yusupov
- Division of Pediatric Genetics, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, Rouen, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, Rouen, France
| | - Lance Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - Erik Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - Fernando Santos Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Maria Palomares-Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Natasha Brown
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | | | | | | | - David A Sweetser
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Nina B Gold
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
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16
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Coursimault J, Goldenberg A, Nicolas G, Saugier-Veber P, Coutant S, Vincent A, Pouliquen D, Feltin C, Aref-Eshghi E, Sadikovic B, Lecoquierre F. Contribution of DNA methylation profiling to the reclassification of a variant of uncertain significance in the KDM5C gene. Eur J Med Genet 2022; 65:104556. [PMID: 35781022 DOI: 10.1016/j.ejmg.2022.104556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/21/2022] [Accepted: 06/27/2022] [Indexed: 11/03/2022]
Abstract
KDM5C encodes a demethylase of the histone H3 lysine 4 residue, involved in chromatin regulation and gene expression. Hemizygous KDM5C pathogenic variants cause X-linked intellectual disability of Claes-Jensen type. Because of its mode of inheritance and the low specificity of the clinical phenotype, interpretation of variants can be difficult, hence the need for functional studies and biomarkers specific to this disorder. We present the case of a male patient with intellectual disability, behavioral abnormalities and subtle dysmorphic features, in which genetic investigation identified a hemizygous novel missense KDM5C variant of uncertain significance (VUS), inherited from his asymptomatic mother and present in his paucisymptomatic sister. We assessed the global genomic DNA methylation status from a whole blood sample of the proband. Global DNA methylation profiling specifically identified the recently discovered epi-signature of Claes-Jensen syndrome. This result served as a biomarker which independently highlighted KDM5C as the cause of the disorder in this patient. Because of the X-linked mode of inheritance, variant reclassification had a high impact on genetic counseling in this family. This example highlights the value of global methylome profiling in situations of variants of uncertain significance in genes with a known specific epi-signature.
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Affiliation(s)
- Juliette Coursimault
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Anne Vincent
- Reference Centre for Learning Disorders, Rouen University Hospital, F-76031 Rouen Cedex, France; Department of Neonatology and Paediatric Intensive Care, Rouen University Hospital, F-76031 Cedex, France
| | | | - Cécile Feltin
- Institut de Psychiatrie - Centre Hospitalier du Rouvray, Sotteville-lès-Rouen, France
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Canada and Verspeeten Clinical Genome Centre, London Health Sciences, London, Ontario, Canada
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France.
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17
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Yauy K, Lecoquierre F, Baert-Desurmont S, Trost D, Boughalem A, Luscan A, Costa JM, Geromel V, Raymond L, Richard P, Coutant S, Broutin M, Lanos R, Fort Q, Cackowski S, Testard Q, Diallo A, Soirat N, Holder JM, Duforet-Frebourg N, Bouge AL, Beaumeunier S, Bertrand D, Audoux J, Genevieve D, Mesnard L, Nicolas G, Thevenon J, Philippe N. Genome Alert!: A standardized procedure for genomic variant reinterpretation and automated gene-phenotype reassessment in clinical routine. Genet Med 2022; 24:1316-1327. [PMID: 35311657 DOI: 10.1016/j.gim.2022.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Retrospective interpretation of sequenced data in light of the current literature is a major concern of the field. Such reinterpretation is manual and both human resources and variable operating procedures are the main bottlenecks. METHODS Genome Alert! method automatically reports changes with potential clinical significance in variant classification between releases of the ClinVar database. Using ClinVar submissions across time, this method assigns validity category to gene-disease associations. RESULTS Between July 2017 and December 2019, the retrospective analysis of ClinVar submissions revealed a monthly median of 1247 changes in variant classification with potential clinical significance and 23 new gene-disease associations. Re-examination of 4929 targeted sequencing files highlighted 45 changes in variant classification, and of these classifications, 89% were expert validated, leading to 4 additional diagnoses. Genome Alert! gene-disease association catalog provided 75 high-confidence associations not available in the OMIM morbid list; of which, 20% became available in OMIM morbid list For more than 356 negative exome sequencing data that were reannotated for variants in these 75 genes, this elective approach led to a new diagnosis. CONCLUSION Genome Alert! (https://genomealert.univ-grenoble-alpes.fr/) enables systematic and reproducible reinterpretation of acquired sequencing data in a clinical routine with limited human resource effect.
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Affiliation(s)
- Kevin Yauy
- Institute for Advanced Biosciences, Centre de recherche UGA / Inserm U 1209 / CNRS UMR 5309, Grenoble, France; SeqOne Genomics, Montpellier, France.
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | - Stéphanie Baert-Desurmont
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | | | | | | | | | | | | | - Pascale Richard
- Unité Fonctionnelle de Cardiogénétique et Myogénétique, Centre de Génétique, Hôpitaux Universitaire Pitié Salpêtrière-Charles Foix, Paris, France
| | - Sophie Coutant
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | | | | | | | - Stenzel Cackowski
- Grenoble Institut Neurosciences, GIN, Inserm U1216, Université de Grenoble Alpes, Grenoble, France
| | - Quentin Testard
- Institute for Advanced Biosciences, Centre de recherche UGA / Inserm U 1209 / CNRS UMR 5309, Grenoble, France; Laboratoire Eurofins Biomnis, Lyon, France
| | | | | | | | | | | | | | | | | | - David Genevieve
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France
| | - Laurent Mesnard
- Soins Intensifs Néphrologiques et Rein Aigu, Hôpital Tenon, Assistance Publique des Hôpitaux de Paris, Paris, France; UMR_S1155, INSERM, Sorbonne Université, Paris, France
| | - Gael Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | - Julien Thevenon
- Institute for Advanced Biosciences, Centre de recherche UGA / Inserm U 1209 / CNRS UMR 5309, Grenoble, France
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18
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Coursimault J, Rovelet-Lecrux A, Cassinari K, Brischoux-Boucher E, Saugier-Veber P, Goldenberg A, Lecoquierre F, Drouot N, Richard AC, Vera G, Coutant S, Quenez O, Rolain M, Bonnet C, Bronner M, Lecourtois M, Nicolas G. uORF-introducing variants in the 5'UTR of the NIPBL gene as a cause of Cornelia de Lange syndrome. Hum Mutat 2022; 43:1239-1248. [PMID: 35446447 DOI: 10.1002/humu.24384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/02/2021] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 11/08/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a clinically-recognizable rare developmental disorder. About 70% of patients carry a missense or loss-of-function pathogenic variant in the NIPBL gene. We hypothesized that some variants in the 5' Untranslated Region (UTR) of NIPBL may create an upstream open reading frame (uORF), putatively leading to a loss of function. We searched for NIPBL 5'UTR variants potentially introducing uORF by (i) reannotating NGS data of 102 unsolved CdLS patients and (ii) literature and variant databases search. We set up a GFP reporter assay and studied NIPBL expression in a lymphoblastoid cell line (LCL). We identified two variants introducing a novel ATG codon sequence in the 5'UTR of NIPBL, both predicted to introduce uORF: a novel c.-457_-456delinsAT de novo mutation in a 15-year-old male with classic CdLS, and a c.-94C>T variant in a published family. Our reporter assay showed a significant decrease of GFP levels in both mutant contexts, with similar levels of mRNA as compared to wt constructs. Assessment of LCL of one patient showed consistent results with decreased NIPBL protein and unchanged mRNA levels. 5'UTR uORF-introducing NIPBL variants may represent a rare source of pathogenic variants in unsolved CdLS patients. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Juliette Coursimault
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Anne Rovelet-Lecrux
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Kévin Cassinari
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | | | - Pascale Saugier-Veber
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Nathalie Drouot
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Anne-Claire Richard
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Gabriella Vera
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Olivier Quenez
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Marion Rolain
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Céline Bonnet
- Department of Genetics, Nancy University Hospital, Nancy, France
| | - Myriam Bronner
- Department of Genetics, Nancy University Hospital, Nancy, France
| | - Magalie Lecourtois
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000, Rouen, France
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19
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Nicolas G, Sévigny M, Lecoquierre F, Marguet F, Deschênes A, del Pelaez MC, Feuillette S, Audebrand A, Lecourtois M, Rousseau S, Richard AC, Cassinari K, Deramecourt V, Duyckaerts C, Boland A, Deleuze JF, Meyer V, Clarimon Echavarria J, Gelpi E, Akiyama H, Hasegawa M, Kawakami I, Wong TH, Van Rooij JGJ, Van Swieten JC, Campion D, Dutchak PA, Wallon D, Lavoie-Cardinal F, Laquerrière A, Rovelet-Lecrux A, Sephton CF. A postzygotic de novo NCDN mutation identified in a sporadic FTLD patient results in neurochondrin haploinsufficiency and altered FUS granule dynamics. Acta Neuropathol Commun 2022; 10:20. [PMID: 35151370 PMCID: PMC8841087 DOI: 10.1186/s40478-022-01314-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/18/2022] [Indexed: 12/19/2022] Open
Abstract
Frontotemporal dementia (FTD) is a heterogeneous clinical disorder characterized by progressive abnormalities in behavior, executive functions, personality, language and/or motricity. A neuropathological subtype of FTD, frontotemporal lobar degeneration (FTLD)-FET, is characterized by protein aggregates consisting of the RNA-binding protein fused in sarcoma (FUS). The cause of FTLD-FET is not well understood and there is a lack of genetic evidence to aid in the investigation of mechanisms of the disease. The goal of this study was to identify genetic variants contributing to FTLD-FET and to investigate their effects on FUS pathology. We performed whole-exome sequencing on a 50-year-old FTLD patient with ubiquitin and FUS-positive neuronal inclusions and unaffected parents, and identified a de novo postzygotic nonsense variant in the NCDN gene encoding Neurochondrin (NCDN), NM_014284.3:c.1206G > A, p.(Trp402*). The variant was associated with a ~ 31% reduction in full-length protein levels in the patient’s brain, suggesting that this mutation leads to NCDN haploinsufficiency. We examined the effects of NCDN haploinsufficiency on FUS and found that depleting primary cortical neurons of NCDN causes a reduction in the total number of FUS-positive cytoplasmic granules. Moreover, we found that these granules were significantly larger and more highly enriched with FUS. We then examined the effects of a loss of FUS function on NCDN in neurons and found that depleting cells of FUS leads to a decrease in NCDN protein and mRNA levels. Our study identifies the NCDN protein as a likely contributor of FTLD-FET pathophysiology. Moreover, we provide evidence for a negative feedback loop of toxicity between NCDN and FUS, where loss of NCDN alters FUS cytoplasmic dynamics, which in turn has an impact on NCDN expression.
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20
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Coursimault J, Guerrot AM, Morrow MM, Schramm C, Zamora FM, Shanmugham A, Liu S, Zou F, Bilan F, Le Guyader G, Bruel AL, Denommé-Pichon AS, Faivre L, Tran Mau-Them F, Tessarech M, Colin E, El Chehadeh S, Gérard B, Schaefer E, Cogne B, Isidor B, Nizon M, Doummar D, Valence S, Héron D, Keren B, Mignot C, Coutton C, Devillard F, Alaix AS, Amiel J, Colleaux L, Munnich A, Poirier K, Rio M, Rondeau S, Barcia G, Callewaert B, Dheedene A, Kumps C, Vergult S, Menten B, Chung WK, Hernan R, Larson A, Nori K, Stewart S, Wheless J, Kresge C, Pletcher BA, Caumes R, Smol T, Sigaudy S, Coubes C, Helm M, Smith R, Morrison J, Wheeler PG, Kritzer A, Jouret G, Afenjar A, Deleuze JF, Olaso R, Boland A, Poitou C, Frebourg T, Houdayer C, Saugier-Veber P, Nicolas G, Lecoquierre F. MYT1L-associated neurodevelopmental disorder: description of 40 new cases and literature review of clinical and molecular aspects. Hum Genet 2021; 141:65-80. [PMID: 34748075 DOI: 10.1007/s00439-021-02383-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/30/2021] [Indexed: 12/20/2022]
Abstract
Pathogenic variants of the myelin transcription factor-1 like (MYT1L) gene include heterozygous missense, truncating variants and 2p25.3 microdeletions and cause a syndromic neurodevelopmental disorder (OMIM#616,521). Despite enrichment in de novo mutations in several developmental disorders and autism studies, the data on clinical characteristics and genotype-phenotype correlations are scarce, with only 22 patients with single nucleotide pathogenic variants reported. We aimed to further characterize this disorder at both the clinical and molecular levels by gathering a large series of patients with MYT1L-associated neurodevelopmental disorder. We collected genetic information on 40 unreported patients with likely pathogenic/pathogenic MYT1L variants and performed a comprehensive review of published data (total = 62 patients). We confirm that the main phenotypic features of the MYT1L-related disorder are developmental delay with language delay (95%), intellectual disability (ID, 70%), overweight or obesity (58%), behavioral disorders (98%) and epilepsy (23%). We highlight novel clinical characteristics, such as learning disabilities without ID (30%) and feeding difficulties during infancy (18%). We further describe the varied dysmorphic features (67%) and present the changes in weight over time of 27 patients. We show that patients harboring highly clustered missense variants in the 2-3-ZNF domains are not clinically distinguishable from patients with truncating variants. We provide an updated overview of clinical and genetic data of the MYT1L-associated neurodevelopmental disorder, hence improving diagnosis and clinical management of these patients.
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Affiliation(s)
- Juliette Coursimault
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | | | - Catherine Schramm
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | | | | | | | | | - Frédéric Bilan
- Service de Génétique, Centre Hospitalier Universitaire de Poitiers, BP577, 86021, Poitiers, France
| | - Gwenaël Le Guyader
- Service de Génétique, Centre Hospitalier Universitaire de Poitiers, BP577, 86021, Poitiers, France
| | - Ange-Line Bruel
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Inter-Région est, FHU TRANSLAD, CHU Dijon-Bourgogne, Dijon, France
| | - Frédéric Tran Mau-Them
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | - Estelle Colin
- Service de Génétique Médicale, CHU d'Angers, Angers, France.,Univ Angers, [CHU Angers], INSERM, CNRS, MITOVASC, ICAT, 49000, Angers, SFR, France
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Bénédicte Gérard
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Elise Schaefer
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Diane Doummar
- Hôpital Trousseau, APHP.Sorbonne Université, Service de Neuropédiatrie, Paris, France
| | - Stéphanie Valence
- Hôpital Trousseau, APHP.Sorbonne Université, Service de Neuropédiatrie, Paris, France
| | - Delphine Héron
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP.Sorbonne Université, Paris, France
| | - Boris Keren
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP.Sorbonne Université, Paris, France
| | - Cyril Mignot
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP.Sorbonne Université, Paris, France
| | - Charles Coutton
- Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, UMR 5309, CNRS, Université Grenoble Alpes, Inserm U1209, Grenoble, France
| | | | - Anne-Sophie Alaix
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Jeanne Amiel
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Laurence Colleaux
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Arnold Munnich
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Karine Poirier
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Marlène Rio
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Sophie Rondeau
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Giulia Barcia
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Bert Callewaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Candy Kumps
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Wendy K Chung
- Columbia University Irving Medical Center, New York, NY, USA
| | - Rebecca Hernan
- Columbia University Irving Medical Center, New York, NY, USA
| | - Austin Larson
- School of Medicine and Children's Hospital, University of Colorado, Aurora, CO, USA
| | - Kelly Nori
- School of Medicine and Children's Hospital, University of Colorado, Aurora, CO, USA
| | - Sarah Stewart
- School of Medicine and Children's Hospital, University of Colorado, Aurora, CO, USA
| | - James Wheless
- Division of Pediatric Neurology, University of Tennessee, Health Science Center, Memphis, USA
| | - Christina Kresge
- Division of Clinical Genetics, Rutgers New Jersey Medical School, Newark, USA
| | - Beth A Pletcher
- Division of Clinical Genetics, Rutgers New Jersey Medical School, Newark, USA
| | - Roseline Caumes
- Université de Lille, CHU de Lille, Clinique de Génétique « Guy Fontaine », EA7364 RADEMEF-59000, Lille, France
| | - Thomas Smol
- Université de Lille, CHU de Lille, Institut de Génétique Médicale, EA7364 RADEMEF-59000, Lille, France
| | - Sabine Sigaudy
- Département de Génétique Médicale, Hôpital Timone Enfant, Marseille, France
| | - Christine Coubes
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier, France
| | - Margaret Helm
- Department of Pediatrics, Division of Genetics. Portland, Maine Medical Center, Maine, USA
| | - Rosemarie Smith
- Department of Pediatrics, Division of Genetics. Portland, Maine Medical Center, Maine, USA
| | | | | | - Amy Kritzer
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Guillaume Jouret
- National Center of Genetics (NCG), Laboratoire National de Santé (LNS), L-3555, Dudelange, Luxembourg
| | - Alexandra Afenjar
- Centre de Référence Malformations et Maladies Congénitales du Cervelet et Déficiences Intellectuelles de Causes Rares, Département de Génétique et Embryologie Médicale, APHP. Sorbonne Université, Hôpital Trousseau, 75012, Paris, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, 91057, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, 91057, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, 91057, Evry, France
| | - Christine Poitou
- Service de Nutrition, Hôpital de la Pitié Salpêtrière - AP-HP, Paris, France
| | - Thierry Frebourg
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Claude Houdayer
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France.
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21
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Hadouiri N, Thomas Q, Darmency V, Dulieu V, De Rougemont MGM, Bruel AL, Duffourd Y, Lecoquierre F, Colomb B, Perez-Martin S, Ornetti P, Blanchard O, Sorlin A, Philippe C, Faivre L, Vitobello A, Thauvin-Robinet C. Homozygous TRAPPC11 truncating variant revealing segmental uniparental disomy of chromosome 4 as a cause of a recessive limb-girdle muscular dystrophy-18. Clin Genet 2021; 100:643-644. [PMID: 34435357 DOI: 10.1111/cge.14045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 12/01/2022]
Affiliation(s)
- Nawale Hadouiri
- INSERM-Université Bourgogne, Dijon, France.,Pôle Rééducation-Réadaptation, Dijon, France
| | - Quentin Thomas
- INSERM-Université Bourgogne, Dijon, France.,Service de Neurologie, Dijon, France
| | | | | | | | - Ange-Line Bruel
- INSERM-Université Bourgogne, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France
| | - Yannis Duffourd
- INSERM-Université Bourgogne, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France
| | - François Lecoquierre
- INSERM-Université Bourgogne, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France
| | | | | | - Paul Ornetti
- INSERM, Plateforme d'Investigation Technologique, Dijon, France.,Service de Rhumatologie, Dijon, France
| | | | - Arthur Sorlin
- INSERM-Université Bourgogne, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Dijon, France
| | - Christophe Philippe
- INSERM-Université Bourgogne, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France
| | - Laurence Faivre
- INSERM-Université Bourgogne, Dijon, France.,Centre de Référence Maladies Rares, Anomalies du Développement et Syndromes Malformatifs, Dijon, France
| | - Antonio Vitobello
- INSERM-Université Bourgogne, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France
| | - Christel Thauvin-Robinet
- INSERM-Université Bourgogne, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France.,Centre de Référence Maladies Rares, Déficiences Intellectuelles de Causes Rares, Dijon, France
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22
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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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23
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Dabaj I, Sudrié-Arnaud B, Lecoquierre F, Raymond K, Ducatez F, Guerrot AM, Snanoudj S, Coutant S, Saugier-Veber P, Marret S, Nicolas G, Tebani A, Bekri S. NGLY1 Deficiency: A Rare Newly Described Condition with a Typical Presentation. Life (Basel) 2021; 11:life11030187. [PMID: 33673403 PMCID: PMC7996810 DOI: 10.3390/life11030187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
NGLY1 deficiency is the first recognized autosomal recessive disorder of N-linked deglycosylation (NGLY1-CDDG). This severe multisystemic disease is still poorly known and, to date, most cases have been diagnosed through whole exome or genome sequencing. The aim of this study is to provide the clinical, biochemical and molecular description of the first NGLY1-CDDG patient from France along with a literature review. The index case presented with developmental delay, acquired microcephaly, hypotonia, alacrimia, feeding difficulty, and dysmorphic features. Given the complex clinical picture and the multisystemic involvement, a trio-based exome sequencing was conducted and urine oligosaccharides were assessed using mass spectrometry. The exome sequencing revealed a novel variant in the NGLY1 gene in a homozygous state. NGLY1 deficiency was confirmed by the identification of the Neu5Ac1Hex1GlcNAc1-Asn oligosaccharide in the urine of the patient. Literature review revealed the association of some key clinical and biological features such as global developmental delay-hypertransaminasemia, movement disorders, feeding difficulties and alacrima/hypolacrima.
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Affiliation(s)
- Ivana Dabaj
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (I.D.); (F.D.); (S.M.)
| | - Bénédicte Sudrié-Arnaud
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Kimiyo Raymond
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA;
| | - Franklin Ducatez
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (I.D.); (F.D.); (S.M.)
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Sarah Snanoudj
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
| | - Sophie Coutant
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Stéphane Marret
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (I.D.); (F.D.); (S.M.)
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Abdellah Tebani
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
| | - Soumeya Bekri
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
- Correspondence:
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24
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Coursimault J, Lecoquierre F, Saugier-Veber P, Drouin-Garraud V, Lechevallier J, Boland A, Deleuze JF, Frebourg T, Nicolas G, Brehin AC. Hypersociability associated with developmental delay, macrocephaly and facial dysmorphism points to CHD3 mutations. Eur J Med Genet 2021; 64:104166. [PMID: 33571694 DOI: 10.1016/j.ejmg.2021.104166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/03/2020] [Revised: 01/22/2021] [Accepted: 02/04/2021] [Indexed: 02/02/2023]
Abstract
CHD3-related syndrome, also known as Snijders Blok-Campeau syndrome, is a rare developmental disorder described in 2018, caused by de novo pathogenic variants in the CHD3 gene. This syndrome is characterized by global developmental delay, speech delay, intellectual disability, hypotonia and behavioral disorders including autism spectrum disorder (ASD). Typical dysmorphic features include macrocephaly, hypertelorism, enophthalmia, sparse eyebrows, bulging forehead, midface hypoplasia, prominent nose and pointed chin. To our knowledge, there have been no other clinical descriptions of patients since the initial publication. We report the clinical description of a 21-year-old patient harboring a pathogenic de novo variant in CHD3. We reviewed the clinical features of the 35 previously reported patients. Main features were severe intellectual disability, dysmorphic facies, macrocephaly, cryptorchidism, pectus carinatum, severe ophthalmologic abnormalities and behavioral disorders including ASD, and a frank happy demeanor. Hypersociability, which was a noticeable clinical feature in our case, despite ASD, is an uncommon behavioral feature in syndromic intellectual disabilities. Our report supports hypersociability as a suggestive feature of CHD3-related syndrome along with developmental delay, macrocephaly and a dysmorphic facies.
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Affiliation(s)
- Juliette Coursimault
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000 Rouen, France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000 Rouen, France
| | - Pascale Saugier-Veber
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000 Rouen, France
| | | | - Joël Lechevallier
- Department of Pediatric Surgery, Rouen University Hospital, F-76000, Rouen, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000 Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000 Rouen, France
| | - Anne-Claire Brehin
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU G4 Génomique, F-76000 Rouen, France.
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25
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Cassinari K, Rovelet-Lecrux A, Tury S, Quenez O, Richard AC, Charbonnier C, Olaso R, Boland A, Deleuze JF, Besancenot JF, Delpont B, Pouliquen D, Lecoquierre F, Chambon P, Thauvin-Robinet C, Campion D, Frebourg T, Battini JL, Nicolas G. Haploinsufficiency of the Primary Familial Brain Calcification Gene SLC20A2 Mediated by Disruption of a Regulatory Element. Mov Disord 2020; 35:1336-1345. [PMID: 32506582 DOI: 10.1002/mds.28090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 12/10/2019] [Revised: 01/17/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Primary familial brain calcification (PFBC) is a rare cerebral microvascular calcifying disorder with diverse neuropsychiatric expression. Five genes were reported as PFBC causative when carrying pathogenic variants. Haploinsufficiency of SLC20A2, which encodes an inorganic phosphate importer, is a major cause of autosomal-dominant PFBC. However, PFBC remains genetically unexplained in a proportion of patients, suggesting the existence of additional genes or cryptic mutations. We analyzed exome sequencing data of 71 unrelated, genetically unexplained PFBC patients with the aim to detect copy number variations that may disrupt the expression of core PFBC-causing genes. METHODS After the identification of a deletion upstream of SLC20A2, we assessed its consequences on gene function by reverse transcriptase droplet digital polymerase chain reaction (RT-ddPCR), an ex vivo inorganic phosphate uptake assay, and introduced the deletion of a putative SLC20A2 enhancer mapping to this region in human embryonic kidney 293 (HEK293) cells by clustered regularly interspaced short palindromic repeats (CRISPR) - CRISPR-associated protein 9 (Cas9). RESULTS The 8p11.21 deletion, segregating with PFBC in a family, mapped 35 kb upstream of SLC20A2. The deletion carriers/normal controls ratio of relative SLC20A2 mRNA levels was 60.2% (P < 0.001). This was comparable with that of patients carrying an SLC20A2 premature stop codon (63.4%; P < 0.001). The proband exhibited a 39.3% decrease of inorganic phosphate uptake in blood (P = 0.015). In HEK293 cells, we observed a 39.8% decrease in relative SLC20A2 mRNA levels after normalization on DNA copy number (P < 0.001). DISCUSSION We identified a deletion of an enhancer of SLC20A2 expression, with carriers showing haploinsufficiency in similar ranges to loss-of-function alleles, and we observed reduced mRNA levels after deleting this element in a cellular model. We propose a 3-step strategy to identify and easily assess the effect of such events. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Kévin Cassinari
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Anne Rovelet-Lecrux
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Sandrine Tury
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, Montpellier, France
| | - Olivier Quenez
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Anne-Claire Richard
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Camille Charbonnier
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | | | - Benoit Delpont
- Department of Internal Medicine and Systemic Diseases, Dijon University Hospital, Dijon, France
| | - Dorothée Pouliquen
- Department of Neurology and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - François Lecoquierre
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Pascal Chambon
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Genetics of Developmental Disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- CHU Dijon Bourgogne, Unité Fonctionnelle "Innovation diagnostique dans les maladies rares," laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, Dijon, France
- Centre de Référence Maladies Rares "Déficiences Intellectuelles de causes rares," FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Dominique Campion
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
- Department of Research, Rouvray Psychiatric Hospital, Sotteville-les-Rouen, France
| | - Thierry Frebourg
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Jean-Luc Battini
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, Montpellier, France
| | - Gaël Nicolas
- Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
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26
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Chevarin M, Duffourd Y, A Barnard R, Moutton S, Lecoquierre F, Daoud F, Kuentz P, Cabret C, Thevenon J, Gautier E, Callier P, St-Onge J, Jouan T, Lacombe D, Delrue MA, Goizet C, Morice-Picard F, Van-Gils J, Munnich A, Lyonnet S, Cormier-Daire V, Baujat G, Holder M, Petit F, Leheup B, Odent S, Jouk PS, Lopez G, Geneviève D, Collignon P, Martin-Coignard D, Jacquette A, Perrin L, Putoux A, Sarrazin E, Amarof K, Missotte I, Coubes C, Jagadeesh S, Lapi E, Demurger F, Goldenberg A, Doco-Fenzy M, Mignot C, Héron D, Jean-Marçais N, Masurel A, El Chehadeh S, Marle N, Huet F, Binquet C, Collod-Beroud G, Arnaud P, Hanna N, Boileau C, Jondeau G, Olaso R, Lechner D, Poe C, Assoum M, Carmignac V, Duplomb L, Tran Mau-Them F, Philippe C, Vitobello A, Bruel AL, Boland A, Deleuze JF, Thauvin-Robinet C, Rivière JB, O'Roak BJ, Faivre L. Excess of de novo variants in genes involved in chromatin remodelling in patients with marfanoid habitus and intellectual disability. J Med Genet 2020; 57:466-474. [PMID: 32277047 DOI: 10.1136/jmedgenet-2019-106425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/16/2019] [Revised: 11/22/2019] [Accepted: 12/21/2019] [Indexed: 01/10/2023]
Abstract
PURPOSE Marfanoid habitus (MH) combined with intellectual disability (ID) (MHID) is a clinically and genetically heterogeneous presentation. The combination of array CGH and targeted sequencing of genes responsible for Marfan or Lujan-Fryns syndrome explain no more than 20% of subjects. METHODS To further decipher the genetic basis of MHID, we performed exome sequencing on a combination of trio-based (33 subjects) or single probands (31 subjects), of which 61 were sporadic. RESULTS We identified eight genes with de novo variants (DNVs) in at least two unrelated individuals (ARID1B, ATP1A1, DLG4, EHMT1, NFIX, NSD1, NUP205 and ZEB2). Using simulation models, we showed that five genes (DLG4, NFIX, EHMT1, ZEB2 and ATP1A1) met conservative Bonferroni genomewide significance for an excess of the observed de novo point variants. Overall, at least one pathogenic or likely pathogenic variant was identified in 54.7% of subjects (35/64). These variants fell within 27 genes previously associated with Mendelian disorders, including NSD1 and NFIX, which are known to be mutated in overgrowth syndromes. CONCLUSION We demonstrated that DNVs were enriched in chromatin remodelling (p=2×10-4) and genes regulated by the fragile X mental retardation protein (p=3×10-8), highlighting overlapping genetic mechanisms between MHID and related neurodevelopmental disorders.
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Affiliation(s)
- Martin Chevarin
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Yannis Duffourd
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France.,FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Rebecca A Barnard
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA
| | - Sébastien Moutton
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France.,Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Ouest, Centre Hospitalier Universitaire Bordeaux, Bordeaux, France
| | - François Lecoquierre
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Fatma Daoud
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Paul Kuentz
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France.,FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Caroline Cabret
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Julien Thevenon
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | | | - Patrick Callier
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France.,FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Judith St-Onge
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Thibaud Jouan
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Didier Lacombe
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Ouest, Centre Hospitalier Universitaire Bordeaux, Bordeaux, France
| | - Marie Ange Delrue
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Ouest, Centre Hospitalier Universitaire Bordeaux, Bordeaux, France
| | - Cyril Goizet
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Ouest, Centre Hospitalier Universitaire Bordeaux, Bordeaux, France
| | - Fanny Morice-Picard
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Ouest, Centre Hospitalier Universitaire Bordeaux, Bordeaux, France
| | - Julien Van-Gils
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Ouest, Centre Hospitalier Universitaire Bordeaux, Bordeaux, France
| | - Arnold Munnich
- IHU Imagine, Département de Génétique, APHP, Hôpital Necker Enfants Malades, Paris, France
| | - Stanislas Lyonnet
- IHU Imagine, Département de Génétique, APHP, Hôpital Necker Enfants Malades, Paris, France
| | - Valérie Cormier-Daire
- IHU Imagine, Département de Génétique, APHP, Hôpital Necker Enfants Malades, Paris, France
| | - Geneviève Baujat
- IHU Imagine, Département de Génétique, APHP, Hôpital Necker Enfants Malades, Paris, France
| | - Muriel Holder
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Nord, Centre Hospitalier Universitaire Lille, Lille, France
| | - Florence Petit
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Nord, Centre Hospitalier Universitaire Lille, Lille, France
| | - Bruno Leheup
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Ouest, Centre Hospitalier Universitaire Nancy, Nancy, France
| | - Sylvie Odent
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est, Centre Hospitalier Universitaire Rennes, Rennes, France
| | - Pierre-Simon Jouk
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Centre Est, Centre Hospitalier Universitaire Grenoble, Grenoble, France
| | - Gipsy Lopez
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Centre Est, Centre Hospitalier Universitaire Grenoble, Grenoble, France
| | - David Geneviève
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | - Patrick Collignon
- Centre de Compétence Anomalies du Développement et Syndromes Malformatifs Sud-Est, CHI de Toulon - La Seyne-sur-Mer, France
| | - Dominique Martin-Coignard
- Centre de compétence Anomalies du Développement et Syndromes Malformatifs, CH Le Mans, Le Mans, France
| | - Aurélia Jacquette
- Département de Génétique et Centre de Référence Déficiences intellectuelles de causes rares, APHP, La Pitié Salpêtrière, Paris, France
| | - Laurence Perrin
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Ile de France, APHP, Hôpital Robert Debré, Paris, France
| | - Audrey Putoux
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Centre Est, Hospices Civils de Lyon, Lyon, France
| | - Elisabeth Sarrazin
- Centre de Référence Caribéen des Maladies Rares Neurologiques et Neuromusculaires, CHU de Fort de France, Hôpital Pierre Zobda-Quitman, La Martinique, France
| | - Khadija Amarof
- Centre de Référence Caribéen des Maladies Rares Neurologiques et Neuromusculaires, CHU de Fort de France, Hôpital Pierre Zobda-Quitman, La Martinique, France
| | - Isabelle Missotte
- Service de Pédiatrie, Centre Hospitalier Territorial, Nouvelle Calédonie, France
| | - Christine Coubes
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | | | - Elisabetta Lapi
- Genetica Medica, Azienda Ospedaliera Universitaria Anna Meyer, Firenze, Italia
| | | | - Alice Goldenberg
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Rouen, Rouen, France
| | - Martine Doco-Fenzy
- EA3801, Centre de Référence Anomalies du Développement et Syndromes Malformatifs et service de génétique, CHU Reims et UFR de médecine de Reims, Reims, France
| | - Cyril Mignot
- Département de Génétique et Centre de Référence Déficiences intellectuelles de causes rares, APHP, La Pitié Salpêtrière, Paris, France
| | - Delphine Héron
- Département de Génétique et Centre de Référence Déficiences intellectuelles de causes rares, APHP, La Pitié Salpêtrière, Paris, France
| | | | - Alice Masurel
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Salima El Chehadeh
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Nathalie Marle
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France.,FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Frédéric Huet
- FHU TRANSLAD, CHU Dijon, Dijon, France.,Service de Pédiatrie 1, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Christine Binquet
- Centre d'Investigation Clinique - Epidémiologie Clinique, Centre Hospitalier Universitaire Dijon, Dijon, France
| | | | - Pauline Arnaud
- Centre de référence syndromes de Marfan et syndromes apparentés, APHP, Hôpital Bichat, Paris, France
| | - Nadine Hanna
- Centre de référence syndromes de Marfan et syndromes apparentés, APHP, Hôpital Bichat, Paris, France
| | - Catherine Boileau
- Centre de référence syndromes de Marfan et syndromes apparentés, APHP, Hôpital Bichat, Paris, France
| | - Guillaume Jondeau
- Centre de référence syndromes de Marfan et syndromes apparentés, APHP, Hôpital Bichat, Paris, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Doris Lechner
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Charlotte Poe
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Mirna Assoum
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Virginie Carmignac
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Laurence Duplomb
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Frédéric Tran Mau-Them
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Christophe Philippe
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Antonio Vitobello
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Ange-Line Bruel
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Christel Thauvin-Robinet
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France.,FHU TRANSLAD, CHU Dijon, Dijon, France.,Centre de Référence Déficience intellectuelle, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Jean-Baptiste Rivière
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France.,FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Brian J O'Roak
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA
| | - Laurence Faivre
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France .,FHU TRANSLAD, CHU Dijon, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France.,Centre de Référence Déficience intellectuelle, Centre Hospitalier Universitaire Dijon, Dijon, France
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27
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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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28
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Lecoquierre F, Brehin A, Coutant S, Coursimault J, Bazin A, Finck W, Benoist G, Begorre M, Beneteau C, Cailliez D, Chenal P, De Jong M, Degré S, Devisme L, Francannet C, Gérard B, Jeanne C, Joubert M, Journel H, Laurichesse Delmas H, Layet V, Liquier A, Mangione R, Patrier S, Pelluard F, Petit F, Tillouche N, Ravenswaaij‐Arts C, Frebourg T, Saugier‐Veber P, Gruchy N, Nicolas G, Gerard M. Exome sequencing identifies the first genetic determinants of sirenomelia in humans. Hum Mutat 2020; 41:926-933. [DOI: 10.1002/humu.23998] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/19/2020] [Accepted: 02/09/2020] [Indexed: 12/25/2022]
Affiliation(s)
- François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie UnivUNIROUENInserm U1245 and Rouen University Hospital Rouen France
| | - Anne‐Claire Brehin
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie UnivUNIROUENInserm U1245 and Rouen University Hospital Rouen France
- Department of FoetopathologyCHU Rouen Rouen France
| | - Sophie Coutant
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie UnivUNIROUENInserm U1245 and Rouen University Hospital Rouen France
| | - Juliette Coursimault
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie UnivUNIROUENInserm U1245 and Rouen University Hospital Rouen France
| | - Anne Bazin
- Département de Génétique et de Biologie SpécialiséeLaboratoire Cerba Saint Ouen l'Aumone France
| | - Wilfrid Finck
- Unité de Foetopathologie, Laboratoire d'anatomie et cytologie pathologiqueCHU Clermont Ferrand Clermont‐Ferrand France
| | - Guillaume Benoist
- Service de gynécologie‐obstétrique et médecine de la reproductionCentre Hospitalier Universitaire de Caen, Universite de Caen Normandie Caen Basse‐Normandie France
| | | | - Claire Beneteau
- Department of Clinical geneticsCHU Hôpital mère et enfant Nantes France
| | | | - Pierre Chenal
- Department of FoetopathologyHopital Monod Le Havre France
| | - Mirjam De Jong
- Department of GeneticsUniversity Medical Centre Groningen, University of Groningen Groningen The Netherlands
| | | | | | - Christine Francannet
- Centre de référence des anomalies malformatives, Service de génétique médicaleCHU Clermont‐Ferrand Clermont‐Ferrand France
- Centre d'Etude des Malformations Congénitales, CEMC‐AuvergneCHU Clermont‐Ferrand Clermont‐Ferrand France
| | - Bénédicte Gérard
- Department of GeneticsCHU de Strasbourg, Hôpital CivilStrasbourg France
| | - Corinne Jeanne
- Department of Foetopathology, Centre François BaclesseCHU Côte de NacreCaen France
| | | | | | - Hélène Laurichesse Delmas
- Centre d'Etude des Malformations Congénitales, CEMC‐AuvergneCHU Clermont‐Ferrand Clermont‐Ferrand France
- Unité de Médecine Fœtale, Service de gynécologie‐obstétriqueCHU Clermont‐FerrandClermont‐Ferrand France
| | - Valérie Layet
- Department of Clinical GeneticsHopital MonodLe Havre France
| | | | - Raphaele Mangione
- Departement of RadiologyPolyclinique Bordeaux Nord‐AquitaineBordeaux France
| | | | - Fanny Pelluard
- Service d'Anatomie‐Cytologie PathologiqueCentre Hospitalier Universitaire de BordeauxBordeaux France
- INSERM UMR1053, Bordeaux Research in Translational Oncology, BaRITOnUniversité de Bordeaux Bordeaux France
| | - Florence Petit
- Clinique de Génétique “Guy Fontaine”—Centre de référence CLAD, Hôpital Jeanne de FlandreCHU LilleLille France
| | - Nadia Tillouche
- Pôle Femme‐Mère‐Nouveau‐néCentre Hospitalier de ValenciennesValenciennes France
| | - Conny Ravenswaaij‐Arts
- Department of GeneticsUniversity Medical Centre Groningen, University of Groningen Groningen The Netherlands
| | - Thierry Frebourg
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie UnivUNIROUENInserm U1245 and Rouen University Hospital Rouen France
| | - Pascale Saugier‐Veber
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie UnivUNIROUENInserm U1245 and Rouen University Hospital Rouen France
| | - Nicolas Gruchy
- Department of Genetics, Normandy Center for Genomic and Personalized MedicineCaen University HospitalCaen France
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie UnivUNIROUENInserm U1245 and Rouen University Hospital Rouen France
| | - Marion Gerard
- Department of Genetics, Normandy Center for Genomic and Personalized MedicineCaen University HospitalCaen France
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29
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Lecoquierre F, Cassinari K, Chambon P, Nicolas G, Malsa S, Marlin R, Assouline Y, Fléjou JF, Frebourg T, Houdayer C, Bera O, Baert-Desurmont S. Patients with 10q22.3q23.1 recurrent deletion syndrome are at risk for juvenile polyposis. Eur J Med Genet 2019; 63:103773. [PMID: 31561016 DOI: 10.1016/j.ejmg.2019.103773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/16/2019] [Accepted: 09/22/2019] [Indexed: 01/10/2023]
Abstract
Juvenile polyposis syndrome (JPS) is a rare autosomal dominant predisposition to hamartomatous polyps within the gastrointestinal tract, at high risk for malignant transformation. BMPR1A and SMAD4 loss-of-function variants account for 50% of the cases. More specifically, point mutations and structural abnormalities in BMPR1A lead to a highly penetrant yet variable phenotype of JPS. Intriguingly, in the developmental disorder caused by a recurrent 10q22.3q23.1 7 Mb deletion which includes BMPR1A, juvenile polyps have never been reported. We present the case of a young adult harboring this recurrent deletion, in a context of intellectual disability, ventricular septal defect and severe juvenile polyposis syndrome diagnosed at the age of 25 years, requiring a surgical preventive colectomy. She developed a gastric adenocarcinoma from which she died at the age of 32. We hypothesize that with the current available pangenomic CNV arrays, the diagnosis of 10q22.3q23.1 deletion is often made several years before the onset of the digestive phenotype, which could explain the absence of reports for juvenile polyps. This observation highlights the importance of an active digestive surveillance of patients with 10q22.3q23.1 deletion.
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Affiliation(s)
- François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France.
| | - Kévin Cassinari
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Pascal Chambon
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Sarah Malsa
- Department of Cancer Genetics, Martinique University Hospital, Fort-de-France, Martinique, France
| | - Régine Marlin
- Department of Cancer Genetics, Martinique University Hospital, Fort-de-France, Martinique, France
| | - Yvon Assouline
- Departement of Gastro-Enterology, Clinique Saint Paul, Fort-de-France, Martinique, France
| | - Jean-François Fléjou
- Pathology Department, AP-HP, Hôpital Saint-Antoine, Faculté de Médecine Sorbonne Université, Paris, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Claude Houdayer
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
| | - Odile Bera
- Department of Cancer Genetics, Martinique University Hospital, Fort-de-France, Martinique, France
| | - Stéphanie Baert-Desurmont
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, F76000, Rouen, France
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30
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Lecoquierre F, Bonnevalle A, Chadie A, Gayet C, Dumant‐Forest C, Renaux‐Petel M, Leca J, Hazelzet T, Brasseur‐Daudruy M, Louillet F, Muraine M, Coutant S, Quenez O, Boland A, Deleuze J, Frebourg T, Goldenberg A, Saugier‐Veber P, Guerrot A, Nicolas G. Confirmation and further delineation of the SMG9‐deficiency syndrome, a rare and severe developmental disorder. Am J Med Genet A 2019; 179:2257-2262. [DOI: 10.1002/ajmg.a.61317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/22/2019] [Indexed: 11/06/2022]
Affiliation(s)
- François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Antoine Bonnevalle
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Alexandra Chadie
- Department of Neonatal Pediatrics and Intensive Care—NeuropediatricsRouen University Hospital Rouen France
| | - Claire Gayet
- Department of PediatricsRouen University Hospital Rouen France
| | | | | | | | | | | | | | - Marc Muraine
- Department of OphthalmologyRouen University Hospital Rouen France
| | - Sophie Coutant
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Olivier Quenez
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH)Institut de Biologie François Jacob, CEA, Université Paris‐Saclay Evry France
| | - Jean‐François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH)Institut de Biologie François Jacob, CEA, Université Paris‐Saclay Evry France
| | - Thierry Frebourg
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Pascale Saugier‐Veber
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Anne‐Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
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31
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Chatron N, Cassinari K, Quenez O, Baert-Desurmont S, Bardel C, Buisine MP, Calpena E, Capri Y, Corominas Galbany J, Diguet F, Edery P, Isidor B, Labalme A, Le Caignec C, Lévy J, Lecoquierre F, Lindenbaum P, Pichon O, Rollat-Farnier PA, Simonet T, Saugier-Veber P, Tabet AC, Toutain A, Wilkie AOM, Lesca G, Sanlaville D, Nicolas G, Schluth-Bolard C. Identification of mobile retrocopies during genetic testing: Consequences for routine diagnosis. Hum Mutat 2019; 40:1993-2000. [PMID: 31230393 DOI: 10.1002/humu.23845] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 02/13/2019] [Revised: 05/29/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022]
Abstract
Human retrocopies, that is messenger RNA transcripts benefitting from the long interspersed element 1 machinery for retrotransposition, may have specific consequences for genomic testing. Next genetration sequencing (NGS) techniques allow the detection of such mobile elements but they may be misinterpreted as genomic duplications or be totally overlooked. We report eight observations of retrocopies detected during diagnostic NGS analyses of targeted gene panels, exome, or genome sequencing. For seven cases, while an exons-only copy number gain was called, read alignment inspection revealed a depth of coverage shift at every exon-intron junction where indels were also systematically called. Moreover, aberrant chimeric read pairs spanned entire introns or were paired with another locus for terminal exons. The 8th retrocopy was present in the reference genome and thus showed a normal NGS profile. We emphasize the existence of retrocopies and strategies to accurately detect them at a glance during genetic testing and discuss pitfalls for genetic testing.
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Affiliation(s)
- Nicolas Chatron
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | - Kevin Cassinari
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Olivier Quenez
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Stéphanie Baert-Desurmont
- Department of Genetics, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Claire Bardel
- Bioinformatics group of the Lyon University Hospital NGS facility, Groupement Hospitalier Est, Lyon, France.,Biostatistics and Bioinformatics Department, HCL, Lyon, France
| | - Marie-Pierre Buisine
- Department of Biochemistry and Molecular Biology, JPA Research Center, Inserm UMR-S 1172, Lille University, Lille University Hospital, Lille, France
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Yline Capri
- Genetics Department, Clinical Genetics Unit, Hôpital Universitaire Robert Debré, Paris, France
| | | | - Flavie Diguet
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | - Patrick Edery
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | | | - Audrey Labalme
- Genetics Department, Hospices Civils de Lyon, Lyon, France
| | - Cedric Le Caignec
- Genetics Department, CHU Nantes, Nantes, France.,INSERM UMR_S915, Institut du thorax, Nantes University, Nantes, France
| | - Jonathan Lévy
- Genetics Department, Cytogenetics Unit, Hôpital Universitaire Robert Debré, Paris, France
| | - François Lecoquierre
- Department of Genetics, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Pierre Lindenbaum
- INSERM, UMR_S1087, Institut du thorax, Nantes, France.,CNRS, UMR 6291, Nantes, France
| | | | - Pierre-Antoine Rollat-Farnier
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,Bioinformatics group of the Lyon University Hospital NGS facility, Groupement Hospitalier Est, Lyon, France
| | - Thomas Simonet
- Cellular Biotechnology Center, Hospices Civils de Lyon, Lyon, France.,Nerve-Muscle Interactions Team, Institut NeuroMyoGène CNRS UMR 5310-INSERM U1217-Université Claude Bernard Lyon 1, Lyon, France
| | - Pascale Saugier-Veber
- Department of Genetics, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Anne-Claude Tabet
- Genetics Department, Cytogenetics Unit, Hôpital Universitaire Robert Debré, Paris, France.,Neuroscience Department, Human Genetics and Cognitive Function Unit, Institut Pasteur, Paris, France
| | - Annick Toutain
- Genetics Department, Hôpital Bretonneau, CHU, Tours, France.,UMR 1253, iBrain, Tours University, Inserm, Tours, France
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gaetan Lesca
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | - Damien Sanlaville
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | - Gaël Nicolas
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Caroline Schluth-Bolard
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
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32
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Lecoquierre F, Duffourd Y, Vitobello A, Bruel AL, Urteaga B, Coubes C, Garret P, Nambot S, Chevarin M, Jouan T, Moutton S, Tran-Mau-Them F, Philippe C, Sorlin A, Faivre L, Thauvin-Robinet C. Variant recurrence in neurodevelopmental disorders: the use of publicly available genomic data identifies clinically relevant pathogenic missense variants. Genet Med 2019; 21:2504-2511. [DOI: 10.1038/s41436-019-0518-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/12/2019] [Indexed: 12/19/2022] Open
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Collet G, Parodi N, Cassinari K, Neviere Z, Cohen F, Gasnier C, Brahimi A, Lecoquierre F, Thery JC, Tennevet I, Lacaze E, Berthet P, Frebourg T. Cost-effectiveness evaluation of pre-counseling telephone interviews before face-to-face genetic counseling in cancer genetics. Fam Cancer 2019; 17:451-457. [PMID: 29080081 DOI: 10.1007/s10689-017-0049-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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] [Indexed: 11/26/2022]
Abstract
One of the main challenges in cancer genetics is responding to the exponential demand for genetic counseling, especially in patients with breast and/or ovarian cancer. To address this demand, we have set up a new procedure, based on pre-genetic counseling telephone interviews (PTI) followed by routing of patients: D1, a PTI is scheduled within 14 days; D7-D14, genetic counselors perform a 20 min PTI in order to establish a pre-genetic counseling file, by collecting personal and family medical history via a structured questionnaire and; D10-17, routing: pre-genetic counseling appointment files are analyzed by a cancer geneticist with 3 possible conclusions: (a) priority face-to-face genetic counseling (FTFGC) appointment with a cancer geneticist, if the genetic test results have an immediate therapeutic impact; (b) non-priority FTFGC with a genetic counselor, or (c) no FTFGC required or substitution by a more appropriate index case. In the context of breast and/or ovarian cancer, 1012 patients received PTIs, 39.1% of which did not lead to FTFGC. The mean delay for non-priority FTFGC was maintained at 18 weeks and priority FTFGC appointments were guaranteed within 8 weeks. The required resources for 1012 patients was estimated at 0.12 FTE secretaries, 0.62 FTE genetic counselors and 0.08 FTE cancer geneticists and the procedure was shown to be cost-effective. This new procedure allows the suppression of up to 1/3 of appointments, guarantees priority for appointments with therapeutic impact and optimizes the interaction and breakdown of tasks between genetic counselors and cancer geneticists.
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Affiliation(s)
- Gaëlle Collet
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
| | - Nathalie Parodi
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
| | - Kevin Cassinari
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
| | - Zoe Neviere
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
- Department of Genetics, Comprehensive Cancer Centre François Baclesse, Normandy Centre for Genomic and Personalized Medicine, 14000, Caen, France
| | - Fanny Cohen
- Department of Genetics, Comprehensive Cancer Centre François Baclesse, Normandy Centre for Genomic and Personalized Medicine, 14000, Caen, France
| | - Céline Gasnier
- Department of Genetics, Comprehensive Cancer Centre François Baclesse, Normandy Centre for Genomic and Personalized Medicine, 14000, Caen, France
| | - Afane Brahimi
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
| | - François Lecoquierre
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
| | - Jean-Christophe Thery
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
- Department of Oncology, Comprehensive Cancer Centre Henri Becquerel, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
| | - Isabelle Tennevet
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
- Department of Oncology, Comprehensive Cancer Centre Henri Becquerel, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France
| | - Elodie Lacaze
- Department of Genetics, Le Havre General Hospital, Normandy Centre for Genomic and Personalized Medicine, 76600, Le Havre, France
| | - Pascaline Berthet
- Department of Genetics, Comprehensive Cancer Centre François Baclesse, Normandy Centre for Genomic and Personalized Medicine, 14000, Caen, France
| | - Thierry Frebourg
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, 76000, Rouen, France.
- Department of Genetics, Rouen University Hospital, 22 boulevard Gambetta, 76183, Rouen Cedex 1, France.
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Saugier-Veber P, Marguet F, Lecoquierre F, Adle-Biassette H, Guimiot F, Cipriani S, Patrier S, Brasseur-Daudruy M, Goldenberg A, Layet V, Capri Y, Gérard M, Frébourg T, Laquerrière A. Hydrocephalus due to multiple ependymal malformations is caused by mutations in the MPDZ gene. Acta Neuropathol Commun 2017; 5:36. [PMID: 28460636 PMCID: PMC5412059 DOI: 10.1186/s40478-017-0438-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 04/14/2017] [Indexed: 11/20/2022] Open
Abstract
Congenital hydrocephalus is considered as either acquired due to haemorrhage, infection or neoplasia or as of developmental nature and is divided into two subgroups, communicating and obstructive. Congenital hydrocephalus is either syndromic or non-syndromic, and in the latter no cause is found in more than half of the patients. In patients with isolated hydrocephalus, L1CAM mutations represent the most common aetiology. More recently, a founder mutation has also been reported in the MPDZ gene in foetuses presenting massive hydrocephalus, but the neuropathology remains unknown. We describe here three novel homozygous null mutations in the MPDZ gene in foetuses whose post-mortem examination has revealed a homogeneous phenotype characterized by multiple ependymal malformations along the aqueduct of Sylvius, the third and fourth ventricles as well as the central canal of the medulla, consisting in multifocal rosettes with immature cell accumulation in the vicinity of ependymal lining early detached from the ventricular zone. MPDZ also named MUPP1 is an essential component of tight junctions which are expressed from early brain development in the choroid plexuses and ependyma. Alterations in the formation of tight junctions within the ependyma very likely account for the lesions observed and highlight for the first time that primary multifocal ependymal malformations of the ventricular system is genetically determined in humans. Therefore, MPDZ sequencing should be performed when neuropathological examination reveals multifocal ependymal rosette formation within the aqueduct of Sylvius, of the third and fourth ventricles and of the central canal of the medulla.
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