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1. Genome sequencing for genetics diagnosis of patients with intellectual disability: the DEFIDIAG study

Author

Christine Binquet, Catherine Lejeune, Laurence Faivre, Marion Bouctot, Marie-Laure Asensio, Alban Simon, Jean-François Deleuze, Anne Boland, Francis Guillemin, Valérie Seror, Christelle Delmas, Hélène Espérou, Yannis Duffourd, Stanislas Lyonnet, Sylvie Odent, Delphine Heron, Damien Sanlaville, Thierry Frebourg, Bénédicte Gerard, Hélène Dollfus, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre d'Investigation Clinique 1432 (Dijon) - Epidemiologie Clinique/Essais Cliniques (CIC-EC), Université de Bourgogne (UB)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Institut National de la Santé et de la Recherche Médicale (INSERM), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire de Génétique Médicale (LGM), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut National de la Santé et de la Recherche Médicale (INSERM), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre de référence Maladies Rares CLAD-Ouest [Rennes], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de génétique [Hôpial Louis Pradel - HCL], Hôpital Louis Pradel [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), CHU Rouen, Normandie Université (NU), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Plan France Médecine Génomique 2025, Ministère Des Affaires Sociales et de La Santé, ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-18-INBS-0001,France Génomique CREFIX,Utilisation des fonds du centre de référence d'innovation et d'expertise (CREFIX) du plan de médecine génomique (PFMG 2025)(2018), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Centre de référence Déficiences Intellectuelles de Causes Rares [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), HAL UR1, Admin, Instituts Hospitalo-Universitaires - Institut Hospitalo-Universitaire Imagine - - Imagine2010 - ANR-10-IAHU-0001 - IAHU - VALID, and Utilisation des fonds du centre de référence d'innovation et d'expertise (CREFIX) du plan de médecine génomique (PFMG 2025) - - France Génomique CREFIX2018 - ANR-18-INBS-0001 - INBS - VALID

Subjects
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], minimal reference strategy, diagnostic odyssey, QH426-470, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, genome sequencing, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, intellectual disability, Genetics, [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Molecular Medicine, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], cost-effectiveness, Genetics (clinical)
Abstract

Introduction: Intellectual Disability (ID) is the most common cause of referral to pediatric genetic centers, as it affects around 1–3% of the general population and is characterized by a wide genetic heterogeneity. The Genome Sequencing (GS) approach is expected to achieve a higher diagnostic yield than exome sequencing given its wider and more homogenous coverage, and, since theoretically, it can more accurately detect variations in regions traditionally not well captured and identify structural variants, or intergenic/deep intronic putatively pathological events. The decreasing cost of sequencing, the progress in data-management and bioinformatics, prompted us to assess GS efficiency as the first line procedure to identify the molecular diagnosis in patients without obvious ID etiology. This work is being carried out in the framework of the national French initiative for genomic medicine (Plan France Médecine Génomique 2025).Methods and Analysis: This multidisciplinary, prospective diagnostic study will compare the diagnostic yield of GS trio analysis (index case, father, mother) with the French core minimal reference strategy (Fragile-X testing, chromosomal microarray analysis and Gene Panel Strategy of 44 selected ID genes). Both strategies are applied in a blinded fashion, in parallel, in the same population of 1275 ID index cases with no obvious diagnosis (50% not previously investigated). Among them, a subgroup of 196 patients are randomized to undergo GS proband analysis in addition to GS trio analysis plus the French core minimal reference strategy, in order to compare their efficiency. The study also aims to identify the most appropriate strategy according to the clinical presentation of the patients, to evaluate the impact of deployment of GS on the families’ diagnostic odyssey and the modification of their care, and to identify the advantages/difficulties for the patients and their families.Ethics Statement: The protocol was approved by the Ethics Committee Sud Méditerranée I and the French data privacy commission (CNIL, authorization 919361).Trial Registration:ClinicalTrials.gov identifier NCT04154891 (07/11/2019).

Published
2022
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2. Neurodevelopmental phenotype in 36 new patients with 8p inverted duplication-deletion: Genotype-phenotype correlation for anomalies of the corpus callosum

Author

Roseline Vibert, Cyril Mignot, Boris Keren, Sandra Chantot‐Bastaraud, Marie‐France Portnoï, Marie‐Christine Nouguès, Marie‐Laure Moutard, Anne Faudet, Sandra Whalen, Damien Haye, Catherine Garel, Nicolas Chatron, Massimiliano Rossi, Catherine Vincent‐Delorme, Odile Boute, Bruno Delobel, Joris Andrieux, Françoise Devillard, Charles Coutton, Jacques Puechberty, Céline Pebrel‐Richard, Cindy Colson, Marion Gerard, Chantal Missirian, Sabine Sigaudy, Tiffany Busa, Martine Doco‐Fenzy, Valérie Malan, Marlène Rio, Bérénice Doray, Damien Sanlaville, Jean‐Pierre Siffroi, Delphine Héron, Solveig Heide, Service de Génétique médicale [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre de référence Déficiences Intellectuelles de Causes Rares [CHU Pitié-Salpétrière], UF de Génétique chromosomique [CHU Trousseau], CHU Trousseau [APHP], Service de Neuropédiatrie [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Radiologie [CHU Trousseau], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Jeanne de Flandre [Lille], Institut Catholique de Lille (ICL), Université catholique de Lille (UCL), Hôpital Jeanne de Flandres, Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Service de génétique médicale [Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Arnaud de Villeneuve, Service de Génétique Médicale [CHU Clermont-Ferrand], CHU Estaing [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Service de Génétique Clinique [CHU Caen], Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN), Laboratoire de Génétique Moléculaire [Hôpital de la Timone - APHM], Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Reims (CHU Reims), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Génétique Médicale [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Service de Génétique [CHU La Réunion], Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Maladies génétiques d'expression pédiatrique [CHU Trousseau] (Inserm U933), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Trousseau [APHP], UF de Génétique moléculaire [CHU Trousseau], Couvet, Sandrine, and Maladies génétiques d'expression pédiatrique (U933)

Subjects
MESH: Chromosome Deletion, [SDV]Life Sciences [q-bio], AnCC, Trisomy, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, MESH: Corpus Callosum, MESH: Leukoencephalopathies, MESH: Phenotype, MESH: Intellectual Disability, Corpus Callosum, 8p inverted duplication-deletion, Leukoencephalopathies, Intellectual Disability, Genetics, anomalies of the corpus callosum, Humans, intellectual disability (ID), Genetics (clinical), Genetic Association Studies, MESH: Genetic Association Studies, MESH: Humans, MESH: Chromosome Inversion, [SDV] Life Sciences [q-bio], Phenotype, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Chromosome Inversion, MESH: Trisomy, Chromosome Deletion, candidate genes, MESH: Chromosomes, Human, Pair 8, invdupdel(8p), Chromosomes, Human, Pair 8
Abstract

International audience; Inverted duplication deletion 8p [invdupdel(8p)] is a complex and rare chromosomal rearrangement that combines a distal deletion and an inverted interstitial duplication of the short arm of chromosome 8. Carrier patients usually have developmental delay and intellectual disability (ID), associated with various cerebral and extra-cerebral malformations. Invdupdel(8p) is the most common recurrent chromosomal rearrangement in ID patients with anomalies of the corpus callosum (AnCC). Only a minority of invdupdel(8p) cases reported in the literature to date had both brain cerebral imaging and chromosomal microarray (CMA) with precise breakpoints of the rearrangements, making genotype-phenotype correlation studies for AnCC difficult. In this study, we report the clinical, radiological, and molecular data from 36 new invdupdel(8p) cases including three fetuses and five individuals from the same family, with breakpoints characterized by CMA. Among those, 97% (n = 32/33) of patients presented with mild to severe developmental delay/ID and 34% had seizures with mean age of onset of 3.9 years (2 months-9 years). Moreover, out of the 24 patients with brain MRI and 3 fetuses with neuropathology analysis, 63% (n = 17/27) had AnCC. We review additional data from 99 previously published patients with invdupdel(8p) and compare data of 17 patients from the literature with both CMA analysis and brain imaging to refine genotype-phenotype correlations for AnCC. This led us to refine a region of 5.1 Mb common to duplications of patients with AnCC and discuss potential candidate genes within this region.

Published
2021
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3. Expanding the Phenotypic Spectrum of GPI Anchoring Deficiency Due to Biallelic Variants in GPAA1

Author

Delphine Héron, Wendy Mears, Smrithi Salian, William Boyce Burns, Julia Russo, Elliot S. Stolerman, Valentina Serpieri, David A. Dyment, Philippe M. Campeau, Susanne Morlot, Kristin Herman, Thi Tuyet Mai Nguyen, Ginevra Zanni, Boris Keren, Rachel Rock, Raffaella Cusmai, Efrat Sofrin-Drucker, Hannah Wallaschek, Alison M.R. Castle, Julie R. Jones, Devon L. Johnstone, Haim Bassan, Children's Hospital of Eastern Ontario, CHU Sainte Justine [Montréal], Tel Aviv University [Tel Aviv], University of California, Bambino Gesù Children’s Hospital [Rome, Italy], Centre de référence Déficiences Intellectuelles de Causes Rares [CHU Pitié-Salpétrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Génétique médicale [CHU Pitié-Salpêtrière], Hannover Medical School [Hannover] (MHH), BC Children's Hospital Research Institute [Vancouver, BC, Canada] (BCCHR), University of British Columbia (UBC), The Greenwood Genetic Center, University of Pavia, and IRCCS Mondino Foundation

Subjects
Genetics, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, medicine.diagnostic_test, Glycosylphosphatidylinositol, Developmental disorders, Biology, Phenotype, Hypotonia, Clinical knowledge, Flow cytometry, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, chemistry, Neuroimaging, All Genetics, medicine, Alkaline phosphatase, Neurology (clinical), Functional studies, medicine.symptom, 030217 neurology & neurosurgery, Genetics (clinical), 030304 developmental biology
Abstract

Background and ObjectivesTo expand the clinical knowledge of GPAA1-related glycosylphosphatidylinositol (GPI) deficiency.MethodsAn international case series of 7 patients with biallelic GPAA1 variants were identified. Clinical, biochemical, and neuroimaging data were collected for comparison. Where possible, GPI-anchored proteins were assessed using flow cytometry.ResultsTen novel variants were identified in 7 patients. Flow cytometry samples of 3 available patients confirmed deficiency of several GPI-anchored proteins on leukocytes. Extensive phenotypic information was available for each patient. The majority experienced developmental delay, seizures, and hypotonia. Neuroimaging revealed cerebellar anomalies in the majority of the patients. Alkaline phosphatase was within the normal range in 5 individuals and low in 1 individual, as has been noted in other transamidase defects. We notably describe individuals either less affected or older than the ones published previously.DiscussionClinical features of the cases reported broaden the spectrum of the known phenotype of GPAA1-related GPI deficiency, while outlining the importance of using functional studies such as flow cytometry to aid in variant classification.

Published
2021
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4. PURA- Related Developmental and Epileptic Encephalopathy: Phenotypic and Genotypic Spectrum

Author

Dario Pruna, Theresa Grebe, Felippe Borlot, Michael J. Esser, Juan Pablo Appendino, Katherine L. Helbig, Elisa Ballardini, Casey Brew, Anne-Sophie Denommé-Pichon, Anne Ronan, Laurie A. Demmer, Usha Kini, Marta Somorai, Julie Vogt, Sébastien Moutton, Raffaella Faggioli, Julien Van-Gils, Davide Ognibene, Sara Olivotto, Sabine Grønborg, David Coman, David P. Bick, Guido Rubboli, Orrin Devinsky, Atiya S. Khan, Robyn Whitney, Christine Coubes, Caroline Nava, Karen Keough, SakkuBai R. Naidu, Lucio Giordano, Davide Colavito, Dominic Spadafore, Arnaud Isapof, Walla Al-Hertani, Antonio Vitobello, Andrea V. Andrade, Gaetano Cantalupo, Sandra Whalen, Boudewijn Gunning, Shanawaz Hussain, David Hunt, Nathan Noble, Bertrand Isidor, Beatriz Gamboni, Katrine M Johannesen, Julien Buratti, Stephanie Moortgat, Ida Cursio, Agnese Suppiej, Delphine Héron, Lía Mayorga, William Benko, Rahul Raman Singh, Cyril Mignot, Sotirios Keros, Aurore Garde, Nicola Foulds, Claudia A. L. Ruivenkamp, Elena Gardella, Barbara Scelsa, Fernanda Góes, Laurence Faivre, Richard J. Leventer, Ashley Collier, Farha Tokarz, Thomas Courtin, Klaas J. Wierenga, Xilma R. Ortiz-Gonzalez, Frédéric Tran-Mau-Them, Alejandra Mampel, Lynn Greenhalgh, Ashlea Franques, Amélie Piton, Felicia Varsalone, Marjolaine Willems, Alessandro Orsini, Diana Rodriguez, Clothilde Ormieres, Helen Stewart, Boris Keren, Austin Larson, Cathrine E. Gjerulfsen, Julie S. Cohen, Margot R.F. Reijnders, Mel Anderson, Shailesh Asakar, Rikke S. Møller, Alice Bonuccelli, Alexandra Afenjar, Claudio Graziano, Elaine Wirrell, Simona Damioli, Sangeetha Yoganathan, Devorah Segal, Ingo Helbig, Mindy H. Li, Rob P.W. Rouhl, Sarah Hicks, Allan Bayat, Holly Dubbs, Stefania Bigoni, Kelly Ratke, John Brandsema, Eva H. Brilstra, univOAK, Archive ouverte, The Danish Epilepsy Centre Filadelfia [Dianalund, Denmark], University of Southern Denmark (SDU), Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre de référence Déficiences Intellectuelles de Causes Rares [CHU Pitié-Salpétrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Mayo Clinic [Jacksonville], Département de pédiatrie [CHU Nantes], Centre hospitalier universitaire de Nantes (CHU Nantes), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Hôpital d'Enfants [CHU Dijon], Hôpital du Bocage, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Equipe GAD (LNC - U1231), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), Université Montpellier 1 (UM1)-IFR3, Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Department of Pediatrics [Univ California San Diego] (UC San Diego), School of Medicine [Univ California San Diego] (UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), and University of Colorado Anschutz [Aurora]

Subjects
Pediatrics, medicine.medical_specialty, Socio-culturale, [SDV.GEN] Life Sciences [q-bio]/Genetics, Electroencephalography, Epilepsy, Developmental and Epileptic Encephalopathy, Intellectual disability, medicine, Genetics (clinical), feeding difficulties, [SDV.GEN]Life Sciences [q-bio]/Genetics, medicine.diagnostic_test, business.industry, fungi, medicine.disease, Hypotonia, Epileptic spasms, Neonatal hypotonia, neonatal hypotonia, Epilepsy syndromes, Cohort, epilepsy, Neurology (clinical), medicine.symptom, business
Abstract

Background and ObjectivesPurine-rich element-binding protein A (PURA) gene encodes Pur-α, a conserved protein essential for normal postnatal brain development. Recently, a PURA syndrome characterized by intellectual disability, hypotonia, epilepsy, and dysmorphic features was suggested. The aim of this study was to define and expand the phenotypic spectrum of PURA syndrome by collecting data, including EEG, from a large cohort of affected patients.MethodsData on unpublished and published cases were collected through the PURA Syndrome Foundation and the literature. Data on clinical, genetic, neuroimaging, and neurophysiologic features were obtained.ResultsA cohort of 142 patients was included. Characteristics of the PURA syndrome included neonatal hypotonia, feeding difficulties, and respiratory distress. Sixty percent of the patients developed epilepsy with myoclonic, generalized tonic-clonic, focal seizures, and/or epileptic spasms. EEG showed generalized, multifocal, or focal epileptic abnormalities. Lennox-Gastaut was the most common epilepsy syndrome. Drug refractoriness was common: 33.3% achieved seizure freedom. We found 97 pathogenic variants in PURA without any clear genotype-phenotype associations.DiscussionThe PURA syndrome presents with a developmental and epileptic encephalopathy with characteristics recognizable from neonatal age, which should prompt genetic screening. Sixty percent have drug-resistant epilepsy with focal or generalized seizures. We collected more than 90 pathogenic variants without observing overt genotype-phenotype associations.

Published
2021
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5. Loss of the KH1 domain of FMR1 in humans due to a synonymous variant causes global developmental retardation

Author

Laurence Cuisset, Nathalie Carion, Laurence Pacot, Alexandra Afenjar, Thierry Bienvenu, Audrey Briand, Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre de référence Déficiences Intellectuelles de Causes Rares [CHU Pitié-Salpétrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut de psychiatrie et neurosciences de Paris (IPNP - U1266 Inserm), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), and Université de Paris (UP)

Subjects
0301 basic medicine, Adult, Male, congenital, hereditary, and neonatal diseases and abnormalities, Adolescent, [SDV]Life Sciences [q-bio], RNA Splicing, Biology, Polymorphism, Single Nucleotide, Cohort Studies, 03 medical and health sciences, Exon, Fragile X Mental Retardation Protein, 0302 clinical medicine, Protein Domains, Intellectual Disability, Genetics, medicine, Humans, Allele, Gene, Alleles, Silent Mutation, Sequence Analysis, RNA, Alternative splicing, General Medicine, Exons, medicine.disease, Phenotype, FMR1, Exon skipping, nervous system diseases, 3. Good health, Fragile X syndrome, 030104 developmental biology, 030220 oncology & carcinogenesis, Fragile X Syndrome, Mutation, Trinucleotide Repeat Expansion
Abstract

Background Fragile X syndrome (FXS) is a monogenic disorder and a common cause of intellectual disability (ID). Up to now, very few pathological variants other than the typical CGG-repeat expansion have been reported in the FMR1 gene. Methods A panel of 56 intellectual disability (ID) genes including the FMR1 gene was sequenced in a cohort of 300 patients with unexplained ID. To determine the effect of a new FMR1 variant, total RNA from peripheral blood cells was reverse transcribed, amplified by polymerase chain reaction and sequenced. Results We report a novel G to A point variant (c.801G > A) located at the last nucleotide of exon 8 in the FMR1 gene in one patient with ID. Direct sequencing of the RT-PCR products revealed that the transcript from the allele with G to A variant skips exon 8 entirely, resulting in a joining of exons 7 and 9. Skipping of exon 8 may result in an abnormal FMR1 protein (FMRP), which removes the highly conserved region that encoding the KH1 domain of FMRP. Conclusions This report describes for the first time that a synonymous variant in the FMR1 gene is associated with an error in mRNA processing, leading preferentially to the production of an aberrant transcript without exon 8. This splice variant was associated with an unspecific clinical presentation, suggesting the need for more detailed investigation of silent variants in ID patients with a large spectrum of phenotypes.

Published
2020
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6. The phenotypic spectrum of WWOX-related disorders: 20 additional cases of WOREE syndrome and review of the literature

Author

Jenny C. Taylor, Delphine Héron, Yline Capri, Lara Hawkes, Michel Koenig, Cyril Mignot, Myrthe van den Born, Usha Kini, Gabriela E. Jones, John Taylor, Renato Borgatti, Juliette Piard, Laurent Villard, Marie-Ange Nguyen-Morel, Romina Romaniello, Debbie Shears, Yoshimi Sogawa, Mélanie Fradin, Pradeep Vasudevan, Caroline Nava, Agathe Roubertie, Helen V. Firth, Christophe Philippe, Elise Brischoux-Boucher, Diana Johnson, Tiffany Busa, Mathieu Milh, Oana Tarta Arsene, Alistair T. Pagnamenta, Marie-Christine Nougues, Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC), Oxford University Hospitals NHS Trust, University of Oxford, Service de pédiatrie et neurologie pédiatrique, Université de la Méditerranée - Aix-Marseille 2-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), IRCCS Eugenio Medea, IRCCS, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hôpital Robert Debré Paris, Hôpital Robert Debré, CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Trousseau [APHP], Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Medicine and Pharmacy 'Carol Davila' Bucharest (UMPCD), Oxford NIHR Biomedical Research Centre, Children's Hospital of Pittsburgh of UPMC [Etats-Unis], Department of Clinical Genetics, Sheffield Children's NHS Foundation Trust, University Hospitals Leicester, CHU de Grenoble-Alpes, Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Neurosciences de Montpellier (INM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), Université Montpellier 1 (UM1)-IFR3, Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Plateau technique de Biologie [CHU de Dijon], Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Health Innovation Challenge Fund, University of Oxford [Oxford], Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Service de Neuropédiatrie [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut des Neurosciences de Montpellier - Déficits sensoriels et moteurs (INM), IFR3, Université Montpellier 1 (UM1)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de référence Déficiences Intellectuelles de Causes Rares [CHU Pitié-Salpétrière], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Jonchère, Laurent, Clinical Genetics, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, WWOX, Male, Adolescent, DNA Copy Number Variations, Encephalopathy, Mutation, Missense, [SDV.GEN] Life Sciences [q-bio]/Genetics, 030105 genetics & heredity, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, Compound heterozygosity, Article, 03 medical and health sciences, symbols.namesake, Genotype, medicine, Humans, Multiplex ligation-dependent probe amplification, Child, Genetics (clinical), Exome sequencing, Genetic Association Studies, Sanger sequencing, Genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, business.industry, Tumor Suppressor Proteins, Infant, Correction, Syndrome, medicine.disease, encephalopathy, 3. Good health, 030104 developmental biology, WW Domain-Containing Oxidoreductase, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Child, Preschool, Mutation, Spinocerebellar ataxia, symbols, epilepsy, Female, business, Epileptic Syndromes
Abstract

IF 9.937 (2017); International audience; PurposeGermline WWOX pathogenic variants have been associated with disorder of sex differentiation (DSD), spinocerebellar ataxia (SCA), and WWOX-related epileptic encephalopathy (WOREE syndrome). We review clinical and molecular data on WWOX-related disorders, further describing WOREE syndrome and phenotype/genotype correlations.MethodsWe report clinical and molecular findings in 20 additional patients from 18 unrelated families with WOREE syndrome and biallelic pathogenic variants in the WWOX gene. Different molecular screening approaches were used (quantitative polymerase chain reaction/multiplex ligation-dependent probe amplification [qPCR/MLPA], array comparative genomic hybridization [array-CGH], Sanger sequencing, epilepsy gene panel, exome sequencing).ResultsTwo copy-number variations (CNVs) or two single-nucleotide variations (SNVs) were found respectively in four and nine families, with compound heterozygosity for one SNV and one CNV in five families. Eight novel missense pathogenic variants have been described. By aggregating our patients with all cases reported in the literature, 37 patients from 27 families with WOREE syndrome are known. This review suggests WOREE syndrome is a very severe epileptic encephalopathy characterized by absence of language development and acquisition of walking, early-onset drug-resistant seizures, ophthalmological involvement, and a high likelihood of premature death. The most severe clinical presentation seems to be associated with null genotypes.ConclusionGermline pathogenic variants in WWOX are clearly associated with a severe early-onset epileptic encephalopathy. We report here the largest cohort of individuals with WOREE syndrome. We report here 20 additional patients with biallelic pathogenic variants in the WWOX gene associated with severe early-onset encephalopathy. After a literature review, we define the main linical features of the WWOX-related disorders and discuss genotype–phenotype correlations.

Published
2019
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7. GRIN2A-related disorders : genotype and functional consequence predict phenotype

Author

Strehlow, V., Heyne, H.O., Vlaskamp, D.R.M., Marwick, K.F.M., Rudolf, G., Bellescize, J. de, Biskup, S., Brilstra, E.H., Brouwer, O.F., Callenbach, P.M.C., Hentschel, J., Hirsch, E., Kind, P.C., Mignot, C., Platzer, K., Rump, P., Skehel, P.A., Wyllie, D.J.A., Hardingham, G.E., Ravenswaaij-Arts, C.M.A. van, Koolen, D.A., Willemsen, M.H., Lesca, G., Lemke, J.R., Clinical Cognitive Neuropsychiatry Research Program (CCNP), UCL - (MGD) Service de pédiatrie, UCL - SSS/IREC/MONT - Pôle Mont Godinne, univOAK, Archive ouverte, University Hospital Leipzig, Massachusetts General Hospital [Boston], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], University of Groningen [Groningen], University of Edinburgh, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Strasbourg, Centre Hospitalier Universitaire de Lyon (CHU Lyon), CeGaT GmbH, University Medical Center [Utrecht], Hôpital de Hautepierre [Strasbourg], Institute for Stem Cell Science and Regenerative Medicine [Bangalore, Inde] (inStem), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre de référence Déficiences Intellectuelles de Causes Rares [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Groupe de Recherche Clinique : Déficience Intellectuelle et Autisme (GRC), Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and GRIN2A study group: Alexis Arzimanoglou, Paul B Augustijn, Patrick Van Bogaert, Helene Bourry, Peter Burfeind, Yoyo Chu, Brian Chung, Diane Doummar, Patrick Edery, Aviva Fattal-Valevski, Mélanie Fradin, Marion Gerard, Christa de Geus, Boudewijn Gunning, Danielle Hasaerts, Ingo Helbig, Katherine L Helbig, Rami Jamra, Mélanie Jennesson Lyver, Jolien S Klein Wassink-Ruiter, David A Koolen, Damien Lederer, Roelineke J Lunsing, Mikaël Mathot, Hélène Maurey, Shay Menascu, Anne Michel, Ghayda Mirzaa, Diana Mitter, Hiltrud Muhle, Rikke S Møller, Caroline Nava, Margaret O'Brien, Evelyn van Pinxteren-Nagler, Anne van Riesen, Christelle Rougeot, Damien Sanlaville, Jolanda H Schieving, Steffen Syrbe, Hermine E Veenstra-Knol, Nienke Verbeek, Dorothée Ville, Yvonne J Vos, Pascal Vrielynck, Sabrina Wagner, Sarah Weckhuysen, Marjolein H Willemsen

Subjects
GLUN2A, Adult, Male, Adolescent, Genotype, [SDV.GEN] Life Sciences [q-bio]/Genetics, VARIANTS, Neurodevelopmental Disorders/genetics, Receptors, N-Methyl-D-Aspartate, Epilepsy/genetics, Cerebellar Cortex, Young Adult, channelopathy, GRIN2A MUTATIONS, Research Support, N.I.H., Extramural, Journal Article, Animals, Humans, Child, EPILEPSY, Cells, Cultured, Aged, [SDV.GEN]Life Sciences [q-bio]/Genetics, SPECTRUM, learning disability, Receptors, N-Methyl-D-Aspartate/genetics, Research Support, Non-U.S. Gov't, childhood epilepsy, Cerebellar Cortex/metabolism, Infant, ENCEPHALOPATHY, Original Articles, Middle Aged, spike-wave EEG, Rats, Editor's Choice, Phenotype, NMDA, Neurodevelopmental Disorders, Child, Preschool, molecular genetics, SUBUNIT, Mutation, Female, APHASIA, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9]
Abstract

Strehlow et al. describe the largest cohort to date of individuals with GRIN2A-related disorders. The results reveal two phenotypic subgroups associated with different classes of variants affecting distinct domains of the GluN2A protein with different functional consequences. The findings will help predict outcomes in newly diagnosed individuals., Alterations of the N-methyl-d-aspartate receptor (NMDAR) subunit GluN2A, encoded by GRIN2A, have been associated with a spectrum of neurodevelopmental disorders with prominent speech-related features, and epilepsy. We performed a comprehensive assessment of phenotypes with a standardized questionnaire in 92 previously unreported individuals with GRIN2A-related disorders. Applying the criteria of the American College of Medical Genetics and Genomics to all published variants yielded 156 additional cases with pathogenic or likely pathogenic variants in GRIN2A, resulting in a total of 248 individuals. The phenotypic spectrum ranged from normal or near-normal development with mild epilepsy and speech delay/apraxia to severe developmental and epileptic encephalopathy, often within the epilepsy-aphasia spectrum. We found that pathogenic missense variants in transmembrane and linker domains (misTMD+Linker) were associated with severe developmental phenotypes, whereas missense variants within amino terminal or ligand-binding domains (misATD+LBD) and null variants led to less severe developmental phenotypes, which we confirmed in a discovery (P = 10−6) as well as validation cohort (P = 0.0003). Other phenotypes such as MRI abnormalities and epilepsy types were also significantly different between the two groups. Notably, this was paralleled by electrophysiology data, where misTMD+Linker predominantly led to NMDAR gain-of-function, while misATD+LBD exclusively caused NMDAR loss-of-function. With respect to null variants, we show that Grin2a+/− cortical rat neurons also had reduced NMDAR function and there was no evidence of previously postulated compensatory overexpression of GluN2B. We demonstrate that null variants and misATD+LBD of GRIN2A do not only share the same clinical spectrum (i.e. milder phenotypes), but also result in similar electrophysiological consequences (loss-of-function) opposing those of misTMD+Linker (severe phenotypes; predominantly gain-of-function). This new pathomechanistic model may ultimately help in predicting phenotype severity as well as eligibility for potential precision medicine approaches in GRIN2A-related disorders.

Published
2019
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8. The complete loss of function of the SMS gene results in a severe form of Snyder-Robinson syndrome

Author

Cyril Mignot, Lise Larcher, Elodie Lejeune, Catherine Garel, Sandra Whalen, Julien Buratti, Charles E. Schwartz, Boris Keren, Joy Norris, Centre de référence Déficiences Intellectuelles de Causes Rares [CHU Pitié-Salpétrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and The Greenwood Genetic Center

Subjects
Male, [SDV]Life Sciences [q-bio], Spermine Synthase, Bioinformatics, 03 medical and health sciences, 0302 clinical medicine, Loss of Function Mutation, Intellectual disability, Genetics, medicine, Humans, Missense mutation, Gene, Kyphoscoliosis, Genetics (clinical), Loss function, 030304 developmental biology, Snyder-Robinson syndrome, 0303 health sciences, biology, business.industry, Infant, General Medicine, Prognosis, medicine.disease, Hypotonia, Spermine synthase, Mental Retardation, X-Linked, biology.protein, medicine.symptom, business, 030217 neurology & neurosurgery
Abstract

Snyder-Robinson syndrome (SRS) is an X-linked syndromic intellectual disability condition caused by variants in the spermine synthase gene (SMS). The syndrome is characterized by facial dysmorphism, thin body build, kyphoscoliosis, osteoporosis, hypotonia, developmental delay and associated neurological features (seizures, unsteady gait, abnormal speech). Until now, only missense variants with a functionally characterized partial loss of function (LoF) have been described. Here we describe the first complete LoF variant, Met303Lysfs*, in a male patient with a severe form of Snyder-Robinson syndrome. He presented with multiple malformations and severly delayed development, and died at 4 months of age. Functional in vitro assays showed a complete absence of functional SMS protein. Taken together, our findings and those of previously reported patients confirm that pathogenic variants of SMS are indeed LoF and that there might exist a genotype-phenotype correlation between the type of variant and the severity of the syndrome.

Published
2020
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