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4. Systematic analysis and prediction of genes associated with monogenic disorders on human chromosome X

Author

Elsa Leitão, Christopher Schröder, Ilaria Parenti, Carine Dalle, Agnès Rastetter, Theresa Kühnel, Alma Kuechler, Sabine Kaya, Bénédicte Gérard, Elise Schaefer, Caroline Nava, Nathalie Drouot, Camille Engel, Juliette Piard, Bénédicte Duban-Bedu, Laurent Villard, Alexander P. A. Stegmann, Els K. Vanhoutte, Job A. J. Verdonschot, Frank J. Kaiser, Frédéric Tran Mau-Them, Marcello Scala, Pasquale Striano, Suzanna G. M. Frints, Emanuela Argilli, Elliott H. Sherr, Fikret Elder, Julien Buratti, Boris Keren, Cyril Mignot, Delphine Héron, Jean-Louis Mandel, Jozef Gecz, Vera M. Kalscheuer, Bernhard Horsthemke, Amélie Piton, and Christel Depienne

Subjects
Science
Abstract

Discovering disease genes on the X chromosome can be particularly challenging. Here, the authors use features of known disease genes and machine learning to predict genes that remain to be associated with disorders on this chromosome.

Published
2022
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5. The impact of lockdown on young people with genetic neurodevelopmental disabilities: a study with the international participatory database GenIDA

Author

Romain Coutelle, Morgane Boedec, Karlijn Vermeulen, Joost Kummeling, David A. Koolen, Tjitske Kleefstra, Camille Fournier, Florent Colin, Axelle Strehle, David Geneviève, Pauline Burger, and Jean-Louis Mandel

Subjects
Intellectual disability, Autism spectrum disorder, Behavioural problems, Genetic disorders, COVID-19, Self-report, Psychiatry, RC435-571
Abstract

Abstract Background Previous publications suggested that lockdown is likely to impact daily living issues of individuals with intellectual disabilities. The authors notably suspected an intensification of behavioural, eating and sleep problems. Methods To test these hypotheses, we conducted an international online survey about the impact of COVID-19-associated first lockdown on people with genetic neurodevelopmental disorders. This survey was carried out using GenIDA, an international participatory database collecting medical information on genetic neurodevelopmental disorders. Patients’ relatives took part in this online survey from 30/04/2020 to 09/06/2020. This survey adapted from GenIDA standard questionnaire requested information on diagnosis, lifestyle and was based on yes/no answers to questions regarding behaviour, diet, and sleep, in the 6-months period before lockdown and during lockdown. We also asked relatives to evaluate the intensity of these problems by severity level. Finally, relatives could freely comment in open fields on the medical and/or quality of life problems they had encountered during lockdown. Results In total 199 participants—144 children and 45 adults—with neurodevelopmental disorders (intellectual disability (79.4%) and/or autism spectrum disorder (21.6%)) of various genetic origins, with near-equal male/female (96/103) contribution and originating mainly from Europe and Northern America, were included. The average lockdown duration at time of the survey was 57 days. We did not find differences in the frequency of behavioural, eating and sleep problems before and during lockdown. Moreover, there was no apparent difference in the intensity of eating and sleep disorders between both periods. However, for persons with behavioural problems at both periods, relatives reported an increase in aggressivity, self-aggressivity, depressiveness, stereotypies, and restricted interests during lockdown, all of which might be interpreted as consequences of a lack of stimulation or a reaction to unexpected changes in daily habits. Conclusions Our results support previous studies that suggest that the negative impact of lockdown does not depend on the intellectual disability per se but on the associated comorbidities such as behavioural disorders. This study addresses the need for prevention of behavioural disturbance in the vulnerable population with genetic neurodevelopmental disabilities.

Published
2022
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6. AAV‐delivered diacylglycerol kinase DGKk achieves long‐term rescue of fragile X syndrome mouse model

Author

Karima Habbas, Oktay Cakil, Boglárka Zámbó, Ricardos Tabet, Fabrice Riet, Doulaye Dembele, Jean‐Louis Mandel, Michaël Hocquemiller, Ralph Laufer, Françoise Piguet, and Hervé Moine

Subjects
AAV, diacylglycerol kinase, Fmr1‐KO, FMRP, Fragile X syndrome, Medicine (General), R5-920, Genetics, QH426-470
Abstract

Abstract Fragile X syndrome (FXS) is the most frequent form of familial intellectual disability. FXS results from the lack of the RNA‐binding protein FMRP and is associated with the deregulation of signaling pathways downstream of mGluRI receptors and upstream of mRNA translation. We previously found that diacylglycerol kinase kappa (DGKk), a main mRNA target of FMRP in cortical neurons and a master regulator of lipid signaling, is downregulated in the absence of FMRP in the brain of Fmr1‐KO mouse model. Here we show that adeno‐associated viral vector delivery of a modified and FMRP‐independent form of DGKk corrects abnormal cerebral diacylglycerol/phosphatidic acid homeostasis and FXS‐relevant behavioral phenotypes in the Fmr1‐KO mouse. Our data suggest that DGKk is an important factor in FXS pathogenesis and provide preclinical proof of concept that its replacement could be a viable therapeutic strategy in FXS.

Published
2022
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9. O46: GenIDA, an international participatory database to better characterize comorbidities of genetic forms of intellectual disability: insights on Koolen-de Vries syndrome

Author

Pauline Burger, Florent Colin, Axelle Strehle, Timothée Mazzucotelli, Nicole Collot, Ariane Bouman, Daphna Landau Prat, David Geneviève, Valentin Ruault, Roseline Caumes, Thomas Smol, Jamal Ghoumid, Joost Kummeling, Charlotte Ockeloen, Tjitske Kleefstra, Pierre Parrend, Amélie Piton, David Koolen, and Jean-Louis Mandel

Subjects
Genetics, QH426-470, Medicine
Published
2023
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10. GenIDA, a participatory patient registry for genetic forms of intellectual disability provides detailed caregiver-reported information on 237 individuals with Koolen-de Vries syndrome

Author

Florent Colin, Pauline Burger, Timothée Mazzucotelli, Axelle Strehle, Joost Kummeling, Nicole Collot, Elyette Broly, Angela T. Morgan, Kenneth A. Myers, Agnès Bloch-Zupan, Charlotte W. Ockeloen, Bert B.A. de Vries, Tjitske Kleefstra, Pierre Parrend, David A. Koolen, and Jean-Louis Mandel

Subjects
GenIDA, Intellectual disability, Koolen-de Vries syndrome, Neurodevelopmental disorders, Patient registry, Genetics, QH426-470, Medicine
Abstract

Purpose: GenIDA is an international patient registry for individuals diagnosed with intellectual disability, autism spectrum disorder, and/or epilepsy, which is based on an online questionnaire that is completed by parent caregivers. In this study, the GenIDA data on Koolen-de Vries syndrome (KdVS) was analyzed illustrating the value of GenIDA and patient/caregiver participation in rare genetic neurodevelopmental disorders (NDDs). Methods: Recruitment was done on the GenIDA website from November 2016 to February 2022. Clinical information on individuals with KdVS was extracted for in-depth analysis and for comparison with the GenIDA data of individuals diagnosed with other NDDs. Results: A total of 1417 patients/caregivers across 35 genetic conditions answered to the GenIDA questionnaire, including caregivers of 237 individuals with KdVS. GenIDA findings on KdVS were consistent with the existing literature, and there were no significant differences between individuals with a 17q21.31 microdeletion and those with a pathogenic variant in the KANSL1 gene. GenIDA provided detailed clinical information including features that are over-represented in KdVS compared with other NDDs (eg, laryngomalacia). Modeling of the natural history showed a positive development of speech and language over time and relatively good reading ability in KdVS. Valproate and oxcarbazepine were reported as effective antiepileptic drugs, and responses to open-ended questions indicated that childhood recurrent pneumonia and asthma are clinically relevant comorbidities that were not described in KdVS before. Conclusion: GenIDA is a powerful registry to collect and harness valuable data on rare NDDs. The study shows that caregiver-driven data collection is effective in terms of global recruitment and centralization of clinical data.

Published
2023
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22. GenIDA: an international participatory database to gain knowledge on health issues related to genetic forms of neurodevelopmental disorders

Author

Pauline Burger, Florent Colin, Axelle Strehle, Timothée Mazzucotelli, Nicole Collot, Romain Coutelle, Benjamin Durand, Arianne Bouman, Daphna Landau Prat, Tjitske Kleefstra, Pierre Parrend, Amélie Piton, David A. Koolen, Jean-Louis Mandel, 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), Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg (UNISTRA), Neuropsychologie Cognitive et Physiopathologie de la Schizophrénie (NCPS), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Civil de Strasbourg, Les Hôpitaux Universitaires de Strasbourg (HUS), Service de génétique médicale, CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Department of Human Genetics [Nijmegen], Radboud University Medical Center [Nijmegen], Sackler Faculty of Medicine, Tel Aviv University (TAU), Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut d’Etudes Avancées de l’Université de Strasbourg - Institute for Advanced Study (USIAS), and univOAK, Archive ouverte

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], Psychiatry and Mental health, All institutes and research themes of the Radboud University Medical Center, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Neurology, Neurology (clinical), Biological Psychiatry, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract

Item does not contain fulltext Intellectual disability with or without manifestations of autism and/or epilepsy affects 1-2% of the population, and it is estimated that more than 30-50% of these cases have a single genetic cause. More than 1000 genes and recurrent chromosomal abnormalities are involved in these genetic forms of neurodevelopmental disorders, which often remain insufficiently described in terms of clinical spectrum, associated medical problems, etc., due to their rarity and the often-limited number of patients' phenotypes reported. GenIDA is an international online participatory database that aims to better characterise the clinical manifestations and natural histories of these rare diseases. Clinical information is reported by parents of affected individuals using a structured questionnaire exploring physical parameters, cognitive and behavioural aspects, the presence or absence of neurological disorders or problems affecting major physiological functions, as well as autonomy and quality of life. This strengthens the implication in research of the concerned families. GenIDA aims to construct international cohorts of significant size of individuals affected by a given condition. As of July 2022, GenIDA counts some 1545 documented patient records from over 60 nationalities and collaborates with clinicians and researchers around the world who have access to the anonymized data collected to generate new, medically meaningful information to improve patient care. We present the GenIDA database here, together with an overview of the possibilities it offers to affected individuals, their families, and professionals in charge of the management of genetic forms of neurodevelopmental disorders. Finally, case studies of cohorts will illustrate the usefulness of GenIDA.

Published
2022

24. Neurocognitive and neurobehavioral characterization of two frequent forms of neurodevelopmental disorders: the <scp>DYRK1A</scp> and the <scp>Wiedemann–Steiner</scp> syndromes

Author

Benjamin Durand, Elise Schaefer, Pauline Burger, Sarah Baer, Carmen Schroder, Jean‐Louis Mandel, Amélie Piton, and Romain Coutelle

Subjects
Autism Spectrum Disorder, Hypertrichosis, Histone-Lysine N-Methyltransferase, Syndrome, Craniofacial Abnormalities, Phenotype, Neurodevelopmental Disorders, Intellectual Disability, Genetics, Humans, Abnormalities, Multiple, Growth Disorders, Myeloid-Lymphoid Leukemia Protein, Genetics (clinical), Retrospective Studies
Abstract

DYRK1A and Wiedemann-Steiner syndromes (WSS) are two genetic conditions associated with neurodevelopmental disorders (NDDs). Although their clinical phenotype has been described, their behavioral phenotype has not systematically been studied using standardized assessment tools. To characterize the latter, we conducted a retrospective study, collecting data on developmental history, autism spectrum disorder (ASD), adaptive functioning, behavioral assessments, and sensory processing of individuals with these syndromes (n = 14;21). In addition, we analyzed information collected from families (n = 20;20) using the GenIDA database, an international patient-driven data collection aiming to better characterize natural history of genetic forms of NDDs. In the retrospective study, individuals with DYRK1A syndrome showed lower adaptive behavior scores compared to those with WSS, whose scores showed greater heterogeneity. An ASD diagnosis was established for 57% (8/14) of individuals with DYRK1A syndrome and 24% (5/21) of those with WSS. Language and communication were severely impaired in individuals with DYRK1A syndrome, which was also evident from GenIDA data, whereas in WSS patients, exploration of behavioral phenotypes revealed the importance of anxiety symptomatology and ADHD signs, also flagged in GenIDA. This study, describing the behavioral and sensorial profiles of individuals with WSS and DYRK1A syndrome, highlighted some specificities important to be considered for patients' management.

Published
2022

25. Lessons from two series by physicians and caregivers’ self-reported data, and DNA methylation profile in DDX3X-Related Disorders

Author

David Geneviève, Valentin Ruault, Pauline Burger, Johanna Gradels-Hauguel, Nathalie Ruiz-Pallares, Xtraordinaire Association, Rami Abou Jamra, Alexandra Afenjar, Yves Alembik, Jean-Luc Alessandri, Arpin Stéphanie, Giulia Barcia, Šárka Bendová, Ange-Line Bruel, Perrine Charles, Nicolas Chatron, Maya Chopra, Solène Conrad, Valérie Cormier-Daire, Auriane Cospain, Christine Coubes, Juliette Coursimault, Andrée Delahaye-Duriez, Martine Doco-Fenzy, William Dufour, Benjamin Durand, Camille ENGEL, Laurence Faivre, Fanny Ferroul, Mélanie FRADIN, Hélène Frenkiel, Carlo Fusco, Livia Garavelli, Aurore Garde, Bénédicte Gérard, David Germanaud, Louise Goujon, Aurélie Gouronc, Emmanuelle Ginglinger, Alice Goldenberg, Miroslava Hancarova, Delphine Héron, Bertrand Isidor, Nolwenn Jean Marçais, Boris Keren, Margarete Koch-Hogrebe, Paul Kuentz, Victoria Lamure, Anne-Sophie Lebre, François Lecoquierre, Natacha Lehman, Gaetan Lesca, Stanislas Lyonnet, Delphine Martin, Cyril Mignot, Teresa Neuhann, Gaël Nicolas, Mathilde Nizon, Florence Petit, Christophe Philippe, Amélie Piton, Marzia Pollazzon, Darina Prchalova, Audrey Putoux, Marlène RIO, Sophie Rondeau, Massimiliano Rossi, Quentin Sabbagh, Pascale Saugier-Veber, Ariane Schmetz, Julie Steffann, Christel Thauvin-Robinet, Annick Toutain, Frédéric Tran-Mau-Them, Gabriele Trimarchi, Marie Vincent, Marketa Vlckova, Dagmar Wieczorek, Marjolaine Willems, kevin yauy, Michaela Zelinová, Alban Ziegler, Boris Chaumette, Bekim Sadikovic, and Jean-Louis Mandel

Abstract

We report two series of individuals with DDX3X variations, one (48 individuals) from physicians and one (44 individuals) from caregivers. 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. Each of the two datasets provide complementary knowledge. We confirmed that symptoms are similar to those in the literature and provide more details on feeding difficulties. Caregivers considered that the symptom attention-deficit/hyperactivity disorder was 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. In addition, we demonstrate preliminary evidence of a mild genome-wide DNA methylation profile in patients carrying mutations in DDX3X.

Published
2023

33. Integrative approach to interpret DYRK1A variants, leading to a frequent neurodevelopmental disorder

Author

Marjolaine Willems, Benjamin Durand, Boris Keren, Kristina Pilekær Sørensen, Rosanna Weksberg, Magalie Barth, Christina Fagerberg, Cyril Mignot, Laurence Perrin, Lucas Bronicki, Nathalie Drouot, Imene Boujelbene, Marc Abramowicz, Maria Kibaek, Bertrand Isidor, Thierry Bienvenu, Mathilde Nizon, Perrine Charles, Laurent Pasquier, Yann Herault, Marie Christine Birling, Bruno Delobel, Michel Guipponi, Lydie Burglen, Mélanie Fradin, Anne Sophie Denommé, Florence Demurger, Benjamin Cogné, Sébastien Moutton, Allan Bayat, Frederic Tran Mau Them, Christèle Dubourg, Alice Goldenberg, Christine Francannet, Jean-Louis Mandel, Laurence Faivre, Jérémie Courraud, Anne Marie Guerrot, Julia Metreau, Loréline Genschik, Bénédicte Demeer, Marie Vincent, Mathilde Renaud, Julien Thevenon, Sandrine Passemard, Christine Coubes, Amélie Piton, David Geneviève, Maria del Mar Muniz Moreno, Bénédicte Gérard, Estelle Colin, Valérie Layet, Michèle Mathieu-Dramard, Salima El Chehadeh, Katrine M Johannesen, Julie D. Thompson, Cathrine Elisabeth Tronhjem, Pascale Saugier, Elise Schaefer, Eric Chater-Diehl, Séverine Drunat, Rikke S. Møller, Paul Kuentz, Claire Feger, Albert David, Antonio Vitobello, Marlène Rio, Khaoula Khachnaoui, Joane Svane, Stéphane Auvin, 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), The Hospital for sick children [Toronto] (SickKids), Centre hospitalier universitaire de Nantes (CHU Nantes), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Les Hôpitaux Universitaires de Strasbourg (HUS), Hôpital Universitaire de Genève, Children's hospital of Eastern Ontario Research Institute [Ottawa, canada] (CHEO), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Sorbonne Université (SU), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Hôpital Arnaud de Villeneuve [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Université de Montpellier (UM), Hôpital Saint Vincent de Paul de Lille, Groupe Hospitalier de l'Institut Catholique de Lille (GHICL), Centre hospitalier Bretagne Atlantique (Morbihan) (CHBA), Hôpital Robert Debré, CHU 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 Sud [CHU Rennes], CHU Pontchaillou [Rennes], CHU Clermont-Ferrand, 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), CHU Rouen, Normandie Université (NU), The Danish Epilepsy Centre Filadelfia [Dianalund, Denmark], University of Southern Denmark (SDU), Odense University Hospital (OUH), CHU Amiens-Picardie, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Odense University Hospital [Odense, Denmark], Centre Hospitalier Universitaire [Grenoble] (CHU), Groupe Hospitalier du Havre, Maladies neurodéveloppementales et neurovasculaires (NeuroDiderot (UMR_S_1141 / U1141)), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Centre Hospitalier Universitaire de Nice (CHU Nice), Institut Clinique de la Souris, Institut de Génétique et Développement de Rennes (IGDR), 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 ), Institut de psychiatrie et neurosciences de Paris (IPNP - U1266 Inserm), Hôpital Cochin [AP-HP], Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg (UNISTRA), University of Toronto, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université, Sorbonne Université, Sorbonne Université-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA), Centre for Integrative Biology - CBI (Inserm U964 - CNRS UMR7104 - IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche de l'institut du thorax (ITX-lab), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Laboratoire de Génétique Médicale (LGM), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), 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 ), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Agence de Biomédecine, Fondation APLM, Fondation Maladies Rares and Fondation Jérome Lejeune, univOAK, Archive ouverte, 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), 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), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), and Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], DYRK1A, [SDV]Life Sciences [q-bio], [SDV.GEN] Life Sciences [q-bio]/Genetics, Protein Serine-Threonine Kinases, Biology, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Mice, 03 medical and health sciences, 0302 clinical medicine, Neurodevelopmental disorder, Intellectual Disability, medicine, Animals, Humans, Missense mutation, Kinase activity, Gene, Genetics (clinical), Cellular localization, 030304 developmental biology, Genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Protein-Tyrosine Kinases, medicine.disease, Phenotype, Human genetics, 3. Good health, 030220 oncology & carcinogenesis, Microcephaly
Abstract

Purpose: DYRK1A syndrome is among the most frequent monogenic forms of intellectual disability (ID). We refined the molecular and clinical description of this disorder and developed tools to improve interpretation of missense variants, which remains a major challenge in human genetics. Methods: We reported clinical and molecular data for 50 individuals with ID harboring DYRK1A variants and developed (1) a specific DYRK1A clinical score; (2) amino acid conservation data generated from 100 DYRK1A sequences across different taxa; (3) in vitro overexpression assays to study level, cellular localization, and kinase activity of DYRK1A mutant proteins; and (4) a specific blood DNA methylation signature. Results: This integrative approach was successful to reclassify several variants as pathogenic. However, we questioned the involvement of some others, such as p.Thr588Asn, still reported as likely pathogenic, and showed it does not cause an obvious phenotype in mice. Conclusion: Our study demonstrated the need for caution when interpreting variants in DYRK1A, even those occurring de novo. The tools developed will be useful to interpret accurately the variants identified in the future in this gene. Graphic abstract: [Figure not available: see fulltext.]

Published
2021

35. Semi-symbolic inference for efficient streaming probabilistic programming

Author

Eric Atkinson, Charles Yuan, Guillaume Baudart, Louis Mandel, Michael Carbin, Massachusetts Institute of Technology (MIT), Parallélisme de Kahn Synchrone ( Parkas), Département d'informatique - ENS Paris (DI-ENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria), and IBM T. J. Watson Research Centre

Subjects
FOS: Computer and information sciences, Computer Science - Programming Languages, [INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL], Probabilistic programming, [INFO.INFO-ES]Computer Science [cs]/Embedded Systems, [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], Safety, Risk, Reliability and Quality, Streaming inference, Software, Programming Languages (cs.PL)
Abstract

A streaming probabilistic program receives a stream of observations and produces a stream of distributions that are conditioned on these observations. Efficient inference is often possible in a streaming context using Rao-Blackwellized particle filters (RBPFs), which exactly solve inference problems when possible and fall back on sampling approximations when necessary. While RBPFs can be implemented by hand to provide efficient inference, the goal of streaming probabilistic programming is to automatically generate such efficient inference implementations given input probabilistic programs. In this work, we propose semi-symbolic inference, a technique for executing probabilistic programs using a runtime inference system that automatically implements Rao-Blackwellized particle filtering. To perform exact and approximate inference together, the semi-symbolic inference system manipulates symbolic distributions to perform exact inference when possible and falls back on approximate sampling when necessary. This approach enables the system to implement the same RBPF a developer would write by hand. To ensure this, we identify closed families of distributions – such as linear-Gaussian and finite discrete models – on which the inference system guarantees exact inference. We have implemented the runtime inference system in the ProbZelus streaming probabilistic programming language. Despite an average 1.6× slowdown compared to the state of the art on existing benchmarks, our evaluation shows that speedups of 3×-87× are obtainable on a new set of challenging benchmarks we have designed to exploit closed families.

Published
2022

40. GenIDA : l’histoire naturelle et les comorbidités des troubles du neurodéveloppement d’origine génétique

Author

Axelle Strehle, David A. Koolen, Pauline Burger, Romain Coutelle, Nicole Collot, Florent Colin, Jean-Louis Mandel, and Tjitske Kleefstra

Subjects
Health (social science), Arts and Humanities (miscellaneous), Pediatrics, Perinatology and Child Health, Developmental and Educational Psychology, Education
Abstract

Au sein des troubles du neurodeveloppement, la deficience intellectuelle (DI), avec ou sans Trouble du spectre de l’autisme (TSA) et/ou epilepsie touche 1 a 2 % des enfants et jeunes adultes, et il est estime que plus de 50 % de ces cas ont une cause genetique unique. Plus de 1 000 genes et anomalies chromosomiques recurrentes sont impliques dans ces formes genetiques de DI ou TSA, correspondant a autant de maladies differentes, qui sont le plus souvent tres insuffisamment decrites, du fait de leur rarete, de leur decouverte en general recente, et du nombre souvent limite de patients.GenIDA est une base de donnees participative internationale initiee en 2016, dans le but de mieux caracteriser les manifestations cliniques et les histoires naturelles de ces formes genetiques de DI et/ou TSA, afin d’en tirer des informations pouvant etre utiles a la prise en charge des personnes atteintes. Pour cela, les parents de ces personnes sont sollicites pour repondre a un questionnaire structure portant sur les parametres physiques, medicaux, cognitifs et comportementaux.Les informations cliniques ainsi collectees sont analysees afin d’identifier de nouvelles informations ayant du sens pour les familles et les professionnels concernes par une maladie donnee. Disponible en 7 langues, le questionnaire a ete rempli pour plus de 1 150 patients : les principales cohortes correspondent aux syndromes de Koolen-de Vries (KdVS), Kleefstra et KBG. L’analyse des donnees collectees a notamment permis d’identifier des problemes respiratoires chez les patients KdVS non signales auparavant, et des profils cognitifs dans ces 3 syndromes. GenIDA permet egalement d’envisager, de par ses proprietes et les resultats precedemment obtenus, la realisation d’etudes longitudinales qui permettraient de suivre, en particulier, l’evolution des competences en socialisation et la typologie des troubles du comportement.

Published
2021

43. Molecular consequences of PQBP1 deficiency, involved in the X-linked Renpenning syndrome

Author

Jérémie Courraud, Camille Engel, Angélique Quartier, Nathalie Drouot, Ursula Houessou, Damien Plassard, Arthur Sorlin, Elise Brischoux-Boucher, Lionel Van Maldergem, Evan Gouy, Massimiliano Rossi, Patrick Edery, Audrey Putoux, Brigitte Gilbert-Dussardier, Vera Kalscheuer, Jean-Louis Mandel, and Amélie Piton

Abstract

Mutations in the PQBP1 gene (polyglutamine-binding protein 1) are responsible for a syndromic X-linked form of intellectual disability (XLID), the Renpenning syndrome. PQBP1 encodes a protein that plays a role in the regulation of gene expression, splicing and mRNA translation. To investigate the consequences of variants in PQBP1, we performed transcriptomic studies in 1) patients’ lymphoblastoid cell lines (LCL) carrying pathogenic variants in PQBP1 and 2) in human neural stem cells (hNSC) knocked-down (KD) for PQBP1. This led to the identification of a hundred dysregulated genes. In particular, we identified an increase in the expression of a non-canonical isoform of another XLID gene, UPF3B. UPF3B plays a crucial role during neurodevelopment by coding for an important actor of the nonsense mRNA mediated decay (NMD) system involved in regulation of protein translation, however, the exact function of the non-canonical isoform,UPF3B_S, is currently unknown. In order to investigate the role of UPF3B_S isoform, we compared the protein interactome of UPF3B_S to the canonical isoform (UPF3B_L). We confirmed that, on the contrary to UPF3B_L, UPF3B_S does not interact with the UPF2/UPF1 complex while it still interacts with exon junction complexes (EJC). However, no notable decrease of NMD pathways was observed in patient’s LCL or in hNSC KD for PQBP1. We identified several additional protein interactors specific to UPF3B_S. Moreover, we used the increase of UPF3B_S mRNA as a molecular marker to test the pathogenicity of variants of unknown clinical significance identified in individuals with ID in PQPB1. We analyzed patients’ LCL mRNA as well as blood mRNA samples and performed complementation studies in HeLa cells by overexpressing Wild-type and mutant PQBP1 cDNA. We showed that all these three approaches were efficient to test the effect of variants, at least for variants affecting the CTD domain of the protein. In conclusion, our study provides information on how PQBP1 deficiency may affect the expression of genes and isoforms, such as UPF3B. This informs about the pathological mechanisms involved in Renpenning syndrome but also allows to propose a functional test for variants of unknown significance identified in PQBP1.

Published
2022

44. A<scp>BBS1SVA</scp>F retrotransposon insertion is a frequent cause of<scp>Bardet‐Biedl</scp>syndrome

Author

Corinne Stoetzel, Richard Redon, Erica E. Davis, Véronique Geoffroy, Jean-Louis Mandel, Georgios Kellaris, Samuel Nicaise, Joakim Klar, Clarisse Delvallée, Anne Sophie Leuvrey, Florence Demurger, Manuela Antin, Emmanuelle Génin, Boris Keren, Nicholas Katsanis, Niklas Dahl, Sophie Scheidecker, Elsa Nourisson, Jean Muller, Hélène Dollfus, Jean-François Deleuze, Christel Depienne, Michèle Mathieu-Dramard, Christine Poitou-Bernert, Carmen C. Leitch, Koenraad Devriendt, Sylvie Odent, Laboratoire de Génétique Médicale (LGM), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Les Hôpitaux Universitaires de Strasbourg (HUS), Ann & Robert H. Lurie Children's Hospital of Chicago, 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), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institute of Human Genetics - Institut für Humangenetik [Essen], Universitätsklinikum Essen [Universität Duisburg-Essen] (Uniklinik Essen)-Universitat Duisberg-Essen, Uppsala University, Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Université de Nantes (UN), Centre hospitalier Bretagne Atlantique (Morbihan) (CHBA), Center for Human Genetics, University of Leuven School of Medicine, SCHOOL of MEDICINE [Louvain], Université Catholique de Louvain = Catholic University of Louvain (UCL)-Université Catholique de Louvain = Catholic University of Louvain (UCL), CHU Amiens-Picardie, Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), 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 ), 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), Northwestern University Feinberg School of Medicine, Agence Nationale de la Recherche, Grant/Award Number: Les Espoirs de l'Université de Strasbourg 2018, CREGEMES, Grant/Award Number: WGS 2016, Fondation pour la Recherche Médicale, Grant/Award Number: ECO20170637509, US National Institutes of Health grants, Grant/Award Numbers: DK072301, GM121317, HD042601, Chard-Hutchinson, Xavier, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), 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)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Nutrition et obésités: approches systémiques (nutriomics) (UMR-S 1269 INSERM - Sorbonne Université), 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), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
Male, 0301 basic medicine, congenital, hereditary, and neonatal diseases and abnormalities, Retroelements, BBS1, [SDV]Life Sciences [q-bio], Population, Medizin, 030105 genetics & heredity, Biology, Article, Cohort Studies, 03 medical and health sciences, Exon, Gene Frequency, Bardet–Biedl syndrome, Mobile element insertion, Bardet-Biedl syndrome, Genetics, medicine, Humans, Allele, SVA F, education, Genetics (clinical), Medicinsk genetik, education.field_of_study, Whole Genome Sequencing, Polydactyly, medicine.disease, Pedigree, [SDV] Life Sciences [q-bio], Mutagenesis, Insertional, Ciliopathy, founder effect, 030104 developmental biology, Female, Microtubule-Associated Proteins, Medical Genetics, Founder effect
Abstract

International audience; Bardet-Biedl syndrome (BBS) is a ciliopathy characterized by retinitis pigmentosa, obesity, polydactyly, cognitive impairment and renal failure. Pathogenic variants in 24 genes account for the molecular basis of >80% of cases. Toward saturated discovery of the mutational basis of the disorder, we carefully explored our cohorts and identified a hominid-specific SINE-R/VNTR/Alu type F (SVA-F) insertion in exon 13 of BBS1 in eight families. In six families, the repeat insertion was found in trans with c.1169 T > G, p.Met390Arg and in two families the insertion was found in addition to other recessive BBS loci. Whole genome sequencing, de novo assembly and SNP array analysis were performed to characterize the genomic event. This insertion is extremely rare in the general population (found in 8 alleles of 8 BBS cases but not in >10 800 control individuals from gnomAD-SV) and due to a founder effect. Its 2435 bp sequence contains hallmarks of LINE1 mediated retrotransposition. Functional studies with patient-derived cell lines confirmed that the BBS1 SVA-F is deleterious as evidenced by a significant depletion of both mRNA and protein levels. Such findings highlight the importance of dedicated bioinformatics pipelines to identify all types of variation.

Published
2020

45. De Novo and Bi-allelic Pathogenic Variants in NARS1 Cause Neurodevelopmental Delay Due to Toxic Gain-of-Function and Partial Loss-of-Function Effects

Author

Cheryl Cytrynbaum, Francesca Mattioli, Maria J. Guillen Sacoto, Federico Santoni, Rosanna Weksberg, Amina Nasar, Annemarie Fock, Henry Houlden, Shaikh Riazuddin, Tobias B. Haack, Roisin Sullivan, Mona Grimmel, Helen Griffin, Stylianos E. Antonarakis, Nuzhat Rana, Andreea Manole, Marisa I. Mendes, Ayca Dilruba Aslanger, Justyna Iwaszkiewicz, Julia Mohr, Rolph Pfundt, Muhammed Ilyas, Tina Duelund Hjortshøj, Kshitij Mankad, Muhammad Ansar, Katherine M. Christensen, Sonal Desai, Aida Telegrafi, Faisal Zafar, Helena Gásdal Karstensen, Dagan Jenkins, Yue Si, John F. Mantovani, Alice Goldenberg, Sylvain Debard, Muhammad T. Sarwar, Jagdeep S. Walia, Stephanie Efthymiou, Rita Horvath, Vincenzo Salpietro, Reza Maroofian, Jawad Ahmed, Joost Raaphorst, Lindsay B. Henderson, Benyekhlef Kara, Lauren Badalato, Adnan Y. Manzur, Desirée E.C. Smith, Ruben Portier, Marwan Shinawi, Marisa V. Andrews, Gajja S. Salomons, John B. Vincent, Amélie Piton, Felix Distelmaier, Emmanuelle Ranza, Jean-Louis Mandel, Sohail A. Paracha, Marybeth Hummel, Jürg Bähler, Dustin Baldridge, Muhammad A. Usmani, Lu Wang, Maria Rodriguez Lopez, Frédéric Fischer, Annette Seibt, Servi J. C. Stevens, Matthew J. Jennings, Majdi Kara, Amelia Kirby, Hubert Dominique Becker, Kristin W. Barañano, Christopher S. Francklyn, Saima Riazuddin, Rasim Ozgur Rosti, Emer O'Connor, Yalda Jamshidi, Barbara Oehl-Jaschkowitz, Ricardo Harripaul, Anne Marie Jelsig, Anna Sarkozy, Indran Davagnanam, Zubair M. Ahmed, David A. Koolen, Joseph G. Gleeson, Heinz Gabriel, Alkyoni Athanasiou-Fragkouli, Muhammad Ayub, Alejandro Horga, Conny van Ravenwaaij, Bruno Senger, Ingrid M. Wentzensen, Clinical Cognitive Neuropsychiatry Research Program (CCNP), Neurology, Laboratory Genetic Metabolic Diseases, ANS - Cellular & Molecular Mechanisms, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, ASLANGER, Ayça Dilruba, Université de Strasbourg (UNISTRA), MUMC+: DA KG Lab Centraal Lab (9), RS: FHML non-thematic output, Laboratory Medicine, AGEM - Endocrinology, metabolism and nutrition, AGEM - Inborn errors of metabolism, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Amsterdam Gastroenterology Endocrinology Metabolism, and Amsterdam Reproduction & Development (AR&D)

Subjects
Male, 0301 basic medicine, Microcephaly, Developmental delay, [SDV]Life Sciences [q-bio], Aspartate-tRNA Ligase, TRANSFER-RNA SYNTHETASE, RNA, Transfer, Amino Acyl, 0302 clinical medicine, RNA, Transfer, Loss of Function Mutation, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), next generation sequencing, chemistry.chemical_classification, Genetics, neurodevelopment, Stem Cells, Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], Neural stem cell, Pedigree, Amino acid, developmental delay, Gain of Function Mutation, Transfer RNA, Female, Amino Acyl, medicine.symptom, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], EXPRESSION, Ataxia, Biology, Article, Cell Line, Amino Acyl-tRNA Synthetases, 03 medical and health sciences, aminoacyl-tRNA synthetase, epilepsy, neuropathy, Alleles, Genetic Predisposition to Disease, Humans, Neurodevelopmental Disorders, 2 SIBLINGS, medicine, Allele, Epilepsy, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], MUTATIONS, medicine.disease, Transfer, 030104 developmental biology, Enzyme, chemistry, Aminoacyl-tRNA synthetase, RNA, 030217 neurology & neurosurgery, Function (biology)
Abstract

Aminoacyl-tRNA synthetases (ARSs) are ubiquitous, ancient enzymes that charge amino acids to cognate tRNA molecules, the essential first step of protein translation. Here, we describe 32 individuals from 21 families, presenting with microcephaly, neurodevelopmental delay, seizures, peripheral neuropathy, and ataxia, with de novo heterozygous and bi-allelic mutations in asparaginyl-tRNA synthetase (NARS1). We demonstrate a reduction in NARS1 mRNA expression as well as in NARS1 enzyme levels and activity in both individual fibroblasts and induced neural progenitor cells (iNPCs). Molecular modeling of the recessive c.1633C>T (p.Arg545Cys) variant shows weaker spatial positioning and tRNA selectivity. We conclude that de novo and bi-allelic mutations in NARS1 are a significant cause of neurodevelopmental disease, where the mechanism for de novo variants could be toxic gain-of-function and for recessive variants, partial loss-of-function.

Published
2020

46. Parotid swellings in an adolescent

Author

Louis Mandel, Daria Vasilyeva, Kun H. Yoon, and Scott M. Peters

Subjects
medicine.medical_specialty, Adolescent, business.industry, Diagnosis, Oral, MEDLINE, Humans, Medicine, business, General Dentistry, Dermatology
Published
2020

47. Systematic analysis and prediction of genes associated with disorders on chromosome X

Author

Elsa Leitão, Christopher Schröder, Ilaria Parenti, Carine Dalle, Agnès Rastetter, Theresa Kühnel, Alma Kuechler, Sabine Kaya, Bénédicte Gérard, Elise Schaefer, Caroline Nava, Nathalie Drouot, Camille Engel, Juliette Piard, Bénédicte Duban-Bedu, Laurent Villard, Alexander P.A. Stegmann, Els K. Vanhoutte, Job A.J Verdonshot, Frank J. Kaiser, Frédéric Tran Mau-Them, Marcello Scala, Pasquale Striano, Suzanna G.M. Frints, Emanuela Argilli, Elliott H. Sherr, Fikret Elder, Julien Buratti, Boris Keren, Cyril Mignot, Delphine Héron, Jean-Louis Mandel, Jozef Gecz, Vera M. Kalscheuer, Bernhard Horsthemke, Amélie Piton, and Christel Depienne

Abstract

Disease gene discovery on chromosome (chr) X is challenging owing to its unique modes of inheritance. We undertook a systematic analysis of human chrX genes. We observe a higher proportion of disorder-associated genes and an enrichment of genes involved in cognition, language, and seizures on chrX compared to autosomes. We analyze gene constraints, exon and promoter conservation, expression and paralogues, and report 127 genes sharing one or more attributes with known chrX disorder genes. Using a neural network trained to distinguish disease-associated from dispensable genes, we classify 235 genes, including 121 of the 127, as having high probability of being disease-associated. We provide evidence of an excess of variants in predicted genes in existing databases. Finally, we report damaging variants in CDK16 and TRPC5 in patients with intellectual disability or autism spectrum disorders. This study predicts large-scale gene-disease associations that could be used for prioritization of X-linked pathogenic variants.

Published
2022

49. Translating Canonical SQL to Imperative Code in Coq

Author

Véronique Benzaken, Évelyne Contejean, Mohammed Houssem Hachmaoui, Chantal Keller, Louis Mandel, Avraham Shinnar, Jérôme Siméon, Laboratoire Méthodes Formelles (LMF), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Centre National de la Recherche Scientifique (CNRS), IBM Watson Research Center, IBM, and IBM Thomas J. Watson Research Center

Subjects
FOS: Computer and information sciences, Computer Science - Programming Languages, Computer Science - Databases, [INFO.INFO-LO]Computer Science [cs]/Logic in Computer Science [cs.LO], InformationSystems_DATABASEMANAGEMENT, Databases (cs.DB), Safety, Risk, Reliability and Quality, Software, Programming Languages (cs.PL)
Abstract

SQL is by far the most widely used and implemented query language. Yet, on some key features, such as correlated queries and NULL value semantics, many implementations diverge or contain bugs. We leverage recent advances in the formalization of SQL and query compilers to develop DBCert, the first mechanically verified compiler from SQL queries written in a canonical form to imperative code. Building DBCert required several new contributions which are described in this paper. First, we specify and mechanize a complete translation from SQL to the Nested Relational Algebra which can be used for query optimization. Second, we define Imp, a small imperative language sufficient to express SQL and which can target several execution languages including JavaScript. Finally, we develop a mechanized translation from the nested relational algebra to Imp, using the nested relational calculus as an intermediate step., Comment: Version with appendix of a paper published at OOPSLA 2022

Published
2022
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50. CONTRIBUTORS

Author

Sara Ahmadi, Monika S. Akula, Erik K. Alexander, Trevor E. Angell, Maureen McCartney Anderson, John P. Bilezikian, Stefan Richard Bornstein, Jan Calissendorff, Stuart Campbell, Tariq Chukir, Tara Corrigan, Henrik Falhammar, Azeez Farooki, Chelsi Flippo, Lane L. Frasier, Vincent Gemma, Monica Girotra, Ansha Goel, Christopher G. Goodier, Heidi Guzman, Makoto Ishii, Yasuhiro Ito, Michael Kazim, Jane J. Keating, Anupam Kotwal, Svetlana L. Krasnova, David W. Lam, Melissa G. Lechner, Aundrea Eason Loftley, Sara E. Lubitz, Louis Mandel, Hiroo Masuoka, Jorge H. Mestman, Akira Miyauchi, Caroline T. Nguyen, Raquel Kristin Sanchez Ong, Randall P. Owen, Rodney F. Pommier, Jason D. Prescott, Ramya Punati, Gustavo Romero-Velez, Arthur B. Schneider, Alison P. Seitz, Alexander L. Shifrin, Adam Michael Shiroff, Marius N. Stan, Constantine A. Stratakis, Christina Tatsi, Daniel J. Toft, Arthur Topilow, Ann Q. Tran, Joseph G. Verbalis, Leonard Wartofsky, Sarah M. Wonn, Dorina Ylli, and William F. Young

Published
2022

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