Search

Your search keyword '"Thibaud Jouan"' showing total 15 results
Start Over Author "Thibaud Jouan" Topic male
15 results on '"Thibaud Jouan"'

1. Further clinical and molecular characterization of an XLID syndrome associated with BRWD3 variants, a gene implicated in the leukemia-related JAK-STAT pathway

Author

Julian Delanne, Magaly Lecat, Patrick R. Blackburn, Eric W. Klee, Constance T.R.M. Stumpel, Sander Stegmann, Servi J.C. Stevens, Caroline Nava, Delphine Heron, Boris Keren, Sonal Mahida, Sakkubai Naidu, Dusica Babovic-Vuksanovic, Johanna C. Herkert, Pernille M. Torring, Maria Kibæk, Isabelle De Bie, Rolph Pfundt, Yvonne M.C. Hendriks, Lilian Bomme Ousager, Renee Bend, Hannah Warren, Steven A. Skinner, Michael J. Lyons, Charlotte Pöe, Martin Chevarin, Thibaud Jouan, Aurore Garde, Quentin Thomas, Paul Kuentz, Emilie Tisserant, Yannis Duffourd, Christophe Philippe, Laurence Faivre, Christel Thauvin-Robinet, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA KG Polikliniek (9), Klinische Genetica, and MUMC+: DA KG Lab Specialisten (9)

Subjects
Male, General Medicine, Syndrome, Megalencephaly, STAT Transcription Factors, Phenotype, Intellectual Disability, Mutation, Genetics, Humans, Female, Language Development Disorders, Genetics (clinical), Janus Kinases, Signal Transduction, Transcription Factors
Abstract

Since the first description of a BRWD3-associated nonsydromic intellectual disability (ID) disorder in 2007, 21 additional families have been reported in the literature.Using exome sequencing (ES) and international data sharing, we identified 14 additional unrelated individuals with pathogenic BRWD3 variants (12 males and 2 females, including one with skewed X-inactivation). We reviewed the 31 previously published cases in the literature with clinical data available, and describe the collective phenotypes of 43 males and 2 females, with 33 different BRWD3 variants.The most common features in males (excluding one patient with a mosaic variant) included ID (39/39 males), speech delay (24/25 males), postnatal macrocephaly (28/35 males) with prominent forehead (18/25 males) and large ears (14/26 males), and obesity (12/27 males). Both females presented with macrocephaly, speech delay, and epilepsy, while epilepsy was only observed in 4/41 males. Among the 28 variants with available segregation reported, 19 were inherited from unaffected mothers and 9 were de novo.This study demonstrates that the BRWD3-related phenotypes are largely non-specific, leading to difficulty in clinical recognition of this disorder. A genotype-first approach, however, allows for the more efficient diagnosis of the BRWD3-related nonsyndromic ID. The refined clinical features presented here may provide additional diagnostic assistance for reverse phenotyping efforts.

Published
2023

2. Variant recurrence in neurodevelopmental disorders: the use of publicly available genomic data identifies clinically relevant pathogenic missense variants

Author

Sebastien Moutton, Antonio Vitobello, Laurence Faivre, Christophe Philippe, Christel Thauvin-Robinet, Philippine Garret, Thibaud Jouan, Martin Chevarin, Benoit Urteaga, Yannis Duffourd, Sophie Nambot, Frédéric Tran-Mau-Them, Arthur Sorlin, François Lecoquierre, Ange-Line Bruel, and Christine Coubes

Subjects
Male, 0301 basic medicine, Candidate gene, Developmental Disabilities, Mutation, Missense, 030105 genetics & heredity, Biology, 03 medical and health sciences, Neurodevelopmental disorder, Intellectual Disability, Databases, Genetic, Intellectual disability, medicine, Humans, Missense mutation, Exome, Genetic Predisposition to Disease, Genetic Testing, Autistic Disorder, Gene, Genetics (clinical), Exome sequencing, Genetics, Computational Biology, High-Throughput Nucleotide Sequencing, Genomics, Sequence Analysis, DNA, medicine.disease, Phenotype, 030104 developmental biology, Neurodevelopmental Disorders, Autism, Female, Transcription Factors
Abstract

Next-generation sequencing has revealed the major impact of de novo variants (DNVs) in developmental disorders (DD) such as intellectual disability, autism, and epilepsy. However, a substantial fraction of these predicted pathogenic DNVs remains challenging to distinguish from background DNVs, notably the missense variants acting via nonhaploinsufficient mechanisms on specific amino acid residues. We hypothesized that the detection of the same missense variation in at least two unrelated individuals presenting with a similar phenotype could be a powerful approach to reveal novel pathogenic variants. We looked for variations independently present in both our database of >1200 solo exomes and in denovo-db, a large, publicly available collection of de novo variants identified in patients with DD. This approach identified 30 variants with strong evidence of pathogenicity, including variants already classified as pathogenic or probably pathogenic by our team, and also several new variants of interest in known OMIM genes or in novel genes. We identified FEM1B and GNAI2 as good candidate genes for syndromic intellectual disability and confirmed the implication of ACTL6B in a neurodevelopmental disorder. Annotation of local variants with denovo-db can highlight missense variants with high potential for pathogenicity, both facilitating the time-consuming reanalysis process and allowing novel DD gene discoveries.

Published
2019

3. Increased diagnostic and new genes identification outcome using research reanalysis of singleton exome sequencing

Author

Martin Chevarin, Sophie Nambot, Sebastien Moutton, Mirna Assoum, C. Thauvin-Robinet, Quéré, Charlotte Poe, Them Ftm, Ange-Line Bruel, Nolwenn Jean-Marçais, Daphné Lehalle, Nada Houcinat, Yannis Duffourd, Thibaud Jouan, Patrick Callier, Antonio Vitobello, Laurence Faivre, Christophe Philippe, Julien Thevenon, and Tisserand E

Subjects
Male, Candidate gene, medicine.medical_specialty, Adolescent, Sequence analysis, Genomics, Disease, Bioinformatics, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Exome Sequencing, Intellectual disability, Genetics, medicine, Humans, Genetic Predisposition to Disease, Child, Genetic Association Studies, Genetics (clinical), Exome sequencing, 0303 health sciences, business.industry, Research, 030305 genetics & heredity, Computational Biology, Sequence Analysis, DNA, medicine.disease, Molecular Diagnostic Techniques, Child, Preschool, Cohort, Medical genetics, Female, business
Abstract

In clinical exome sequencing (cES), the American College of Medical Genetics and Genomics recommends limiting variant interpretation to established human-disease genes. The diagnostic yield of cES in intellectual disability and/or multiple congenital anomalies (ID/MCA) is currently about 30%. Though the results may seem acceptable for rare diseases, they mean that 70% of affected individuals remain genetically undiagnosed. Further analysis extended to all mutated genes in a research environment is a valuable strategy for improving diagnostic yields. This study presents the results of systematic research reanalysis of negative cES in a cohort of 313 individuals with ID/MCA. We identified 17 new genes not related to human disease, implicated 22 non-OMIM disease-causing genes recently or previously rarely related to disease, and described 1 new phenotype associated with a known gene. Twenty-six candidate genes were identified and are waiting for future recurrence. Overall, we diagnose 15% of the individuals with initial negative cES, increasing the diagnostic yield from 30% to more than 40% (or 46% if strong candidate genes are considered). This study demonstrates the power of such extended research reanalysis to increase scientific knowledge of rare diseases. These novel findings can then be applied in the field of diagnostics.

Published
2019

4. Secondary actionable findings identified by exome sequencing: expected impact on the organisation of care from the study of 700 consecutive tests

Author

Aurore Pélissier, Anne-Laure Mosca-Boidron, Thibaud Jouan, Elodie Cretin, Maxime Luu, Pierre Vabres, Jean-François Deleuze, Chritine Peyron, Nolwenn Jean-Marçais, Julien Thevenon, Christine Binquet, Frédéric Tran Mau-Them, Ange-Line Bruel, Patrick Callier, Elodie Gautier, Laurent Demougeot, Daphné Lehalle, Christophe Philippe, Paul Kuentz, Martin Chevarin, Sophie Nambot, Aline Chassagne, Charlotte Poe, Christel Thauvin-Robinet, Mathilde Lefebvre, Marc Bardou, Céline Verstuyft, Antonio Vitobello, Laurence Faivre, Julian Delanne, Emilie Tisserant, Arthur Sorlin, and Yannis Duffourd

Subjects
Adult, Male, Proband, PharmGKB, Genotype, Genetic counseling, Disease, Bioinformatics, Article, 03 medical and health sciences, Exome Sequencing, Genetics, Humans, Medicine, Genetic Predisposition to Disease, Genetic Testing, Child, Exome, Genetics (clinical), Exome sequencing, Retrospective Studies, Incidental Findings, 0303 health sciences, Genome, Human, business.industry, 030305 genetics & heredity, Genetic Variation, Genomics, Cohort, Female, business, Pharmacogenetics
Abstract

With exome/genome sequencing (ES/GS) integrated into the practice of medicine, there is some potential for reporting incidental/secondary findings (IFs/SFs). The issue of IFs/SFs has been studied extensively over the last 4 years. In order to evaluate their implications in care organisation, we retrospectively evaluated, in a cohort of 700 consecutive probands, the frequency and burden of introducing the search for variants in a maximum list of 244 medically actionable genes (genes that predispose carriers to a preventable or treatable disease in childhood/adulthood and genes for genetic counselling issues). We also focused on the 59 PharmGKB class IA/IB pharmacogenetic variants. We also compared the results in different gene lists. We identified variants (likely) affecting protein function in genes for care in 26 cases (3.7%) and heterozygous variants in genes for genetic counselling in 29 cases (3.8%). Mean time for the 700 patients was about 6.3 min/patient for medically actionable genes and 1.3 min/patient for genes for genetic counselling, and a mean time of 37 min/patients for the reinterpreted variants. These results would lead to all 700 pre-test counselling sessions being longer, to 55 post-test genetic consultations and to 27 secondary specialised medical evaluations. ES also detected 42/59 pharmacogenetic variants or combinations of variants in the majority of cases. An extremely low metabolizer status in genes relevant for neurodevelopmental disorders (CYP2C9 and CYP2C19) was found in 57/700 cases. This study provides information regarding the need to anticipate the implementation of genomic medicine, notably the work overload at various steps of the process.

Published
2019

5. Whole-exome sequencing identifies the first French MODY 6 family with a new mutation in the NEUROD1 gene

Author

P. Callier, Bruno Vergès, E. Crevisy, S. Baillot-Rudoni, Benjamin Bouillet, Jean-Michel Petit, D. Gallegarine, Yannis Duffourd, Thibaud Jouan, Service d'Endocrinologie, Diabétologie et Maladies Métaboliques (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, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), and CCSD, Accord Elsevier

Subjects
Adult, Male, Proband, Heterozygote, Endocrinology, Diabetes and Metabolism, [SDV]Life Sciences [q-bio], Mutation, Missense, Mothers, 030209 endocrinology & metabolism, 030204 cardiovascular system & hematology, Biology, 03 medical and health sciences, symbols.namesake, 0302 clinical medicine, Endocrinology, Diabetic Neuropathies, Exome Sequencing, Basic Helix-Loop-Helix Transcription Factors, Internal Medicine, medicine, Humans, Hypoglycemic Agents, Insulin, Missense mutation, Diabetic Nephropathies, Age of Onset, Gene, Exome sequencing, Aged, Sanger sequencing, Genetics, Diabetic Retinopathy, Siblings, General Medicine, medicine.disease, [SDV] Life Sciences [q-bio], Diabetes Mellitus, Type 2, Mutation (genetic algorithm), symbols, Female, France, MODY 6, NEUROD1 Gene
Abstract

Aim The aim of the present study was to identify the affected gene in a French family with maturity-onset diabetes of the young (MODY) using whole-exome sequencing (WES). Methods WES was performed in one patient with MODY, and candidate variants were confirmed in members of the immediate family by Sanger sequencing. Results In the proband, a new heterozygous missense mutation (c.340A>C) was identified in the NEUROD1 gene by WES analysis and confirmed by Sanger sequencing. Additional Sanger sequencing of the proband's sister and mother revealed the same heterozygous mutation. The proband and his sister displayed typical clinical characteristics of MODY, while their mother had the same typical MODY features except for later onset. When clinical and biological profiles were established for all three patients, the severity of diabetes-related complications varied substantially from one family member to another. Conclusion A novel missense mutation found in NEUROD1 was associated with MODY 6 features in a single French family.

Published
2020

6. Further delineation of the female phenotype with KDM5C disease causing variants: 19 new individuals and review of the literature

Author

Christiane Zweier, Jamal Ghoumid, Cornelia Kraus, Sophie Nambot, Laurence Faivre, Antonio Vitobello, Stéphanie Moortgat, Thierry Bienvenu, Christel Thauvin-Robinet, Virginie Carmignac, Benjamin Cogné, Frédéric Tran Mau-Them, Julien Thevenon, Patrick Callier, Alain Verloes, Christophe Philippe, Sophie Naudion, Renaud Touraine, André Reis, Arthur Sorlin, Caroline Thuillier, Bruno Delobel, Thibaud Jouan, Francis Ramond, Cécile Zordan, Daphné Lehalle, Valérie Benoit, Yannis Duffourd, Mathilde Nizon, Emilie Tisserant, and Thomas Smol

Subjects
0301 basic medicine, Proband, Adult, Male, Heterozygote, X-linked intellectual disability, Genetic counseling, Disease, 030105 genetics & heredity, Biology, Short stature, 03 medical and health sciences, Young Adult, Genes, X-Linked, Intellectual Disability, Intellectual disability, Genetics, medicine, Humans, 10. No inequality, Exome, Genetics (clinical), Histone Demethylases, Epilepsy, Genetic heterogeneity, Genetic Variation, medicine.disease, 3. Good health, 030104 developmental biology, Phenotype, Child, Preschool, Mental Retardation, X-Linked, Female, medicine.symptom
Abstract

X-linked intellectual disability (XLID) is a genetically heterogeneous condition involving more than 100 genes. To date, 35 pathogenic variants have been reported in the lysine specific demethylase 5C (KDM5C) gene. KDM5C variants are one of the major causes of moderate to severe XLID. Affected males present with short stature, distinctive facial features, behavioral disorders, epilepsy, and spasticity. For most of these variants, related female carriers have been reported, but phenotypic descriptions were poor. Here, we present clinical and molecular features of 19 females carrying 10 novel heterozygous variants affecting KDM5C function, including five probands with de novo variants. Four heterozygous females were asymptomatic. All affected individuals presented with learning disabilities or ID (mostly moderate), and four also had a language impairment mainly affecting expression. Behavioral disturbances were frequent, and endocrine disorders were more frequent in females. In conclusion, our findings provide evidence of the role of KDM5C in ID in females highlighting the increasing implication of XLID genes in females, even in sporadic affected individuals. Disease expression of XLID in females should be taken into consideration for genetic counseling.

Published
2020

7. Excess of de novo variants in genes involved in chromatin remodelling in patients with marfanoid habitus and intellectual disability

Author

Florence Demurger, Christine Binquet, Muriel Holder, Frédéric Tran Mau-Them, Salima El Chehadeh, Martine Doco-Fenzy, Geneviève Baujat, Delphine Héron, Judith St-Onge, Christophe Philippe, Elodie Gautier, Robert Olaso, Rebecca A. Barnard, Paul Kuentz, François Lecoquierre, Stanislas Lyonnet, Gwenaëlle Collod-Béroud, Dominique Martin-Coignard, Isabelle Missotte, Anne Boland, Cyril Goizet, Laurence Perrin, Valérie Cormier-Daire, Sébastien Moutton, Nadine Hanna, Jean-François Deleuze, Audrey Putoux, Guillaume Jondeau, Sylvie Odent, Doris Lechner, Arnold Munnich, Thibaud Jouan, Aurélia Jacquette, Pierre-Simon Jouk, Martin Chevarin, Virginie Carmignac, Elisabetta Lapi, Alice Goldenberg, Christel Thauvin-Robinet, Sujatha Jagadeesh, P. Callier, Fatma Daoud, Yannis Duffourd, Frédéric Huet, Nathalie Marle, Charlotte Poe, Gipsy Lopez, Cyril Mignot, Florence Petit, Khadija Amarof, Brian J. O'Roak, Caroline Cabret, Fanny Morice-Picard, Jean Baptiste Rivière, Mirna Assoum, Marie Ange Delrue, Julien Thevenon, Laurence Faivre, David Geneviève, Elisabeth Sarrazin, Ange Line Bruel, Pauline Arnaud, Catherine Boileau, Christine Coubes, Didier Lacombe, Laurence Duplomb, Alice Masurel, Patrick Collignon, Antonio Vitobello, Julien Van-Gils, Bruno Leheup, Nolwenn Jean-Marçais, 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, FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), CHU Bordeaux [Bordeaux], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Centre Hospitalier Universitaire [Rennes], Centre Hospitalier Universitaire [Grenoble] (CHU), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Centre Hospitalier Le Mans (CH Le Mans), CHU Pitié-Salpêtrière [AP-HP], Hôpital Robert Debré Paris, Hôpital Robert Debré, Hospices Civils de Lyon (HCL), CHU de la Martinique [Fort de France], Hôpital Pierre Zobda-Quitman [CHU de la Martinique], Centre hospitalier territorial Gaston-Bourret [Nouméa], CHU Rouen, Normandie Université (NU), Centre Hospitalier Universitaire de Reims (CHU Reims), Hémostase et Remodelage Vasculaire Post-Ischémie (HERVI - EA 3801), Université de Reims Champagne-Ardenne (URCA), 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), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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), Université Paris-Saclay, and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)

Subjects
Proband, Male, [SDV]Life Sciences [q-bio], intellectual deficiency, MESH: NFI Transcription Factors, chromatin remodeling, Marfan Syndrome, Craniofacial Abnormalities, MESH: Child, Intellectual disability, MESH: Craniofacial Abnormalities, MESH: Mental Retardation, X-Linked, Exome, Child, de novo variants, Genetics (clinical), Exome sequencing, Genetics, MESH: Exome, MESH: Middle Aged, biology, MESH: Genetic Predisposition to Disease, Middle Aged, NFIX, MESH: Young Adult, Female, Adult, MESH: Mutation, Adolescent, Chromatin remodeling, MESH: Intellectual Disability, MESH: Marfan Syndrome, EHMT1, Young Adult, MESH: Whole Exome Sequencing, Intellectual Disability, Exome Sequencing, medicine, Humans, Genetic Predisposition to Disease, marfanoid habitus, Gene, MESH: Neurodevelopmental Disorders, MESH: Adolescent, MESH: Humans, Genetic heterogeneity, MESH: Chromatin Assembly and Disassembly, MESH: Histone-Lysine N-Methyltransferase, MESH: Adult, Histone-Lysine N-Methyltransferase, medicine.disease, Chromatin Assembly and Disassembly, MESH: Male, NFI Transcription Factors, Neurodevelopmental Disorders, Mutation, biology.protein, Mental Retardation, X-Linked, MESH: Female
Abstract

PurposeMarfanoid habitus (MH) combined with intellectual disability (ID) (MHID) is a clinically and genetically heterogeneous presentation. The combination of array CGH and targeted sequencing of genes responsible for Marfan or Lujan–Fryns syndrome explain no more than 20% of subjects.MethodsTo further decipher the genetic basis of MHID, we performed exome sequencing on a combination of trio-based (33 subjects) or single probands (31 subjects), of which 61 were sporadic.ResultsWe identified eight genes with de novo variants (DNVs) in at least two unrelated individuals (ARID1B, ATP1A1, DLG4, EHMT1, NFIX, NSD1, NUP205 and ZEB2). Using simulation models, we showed that five genes (DLG4, NFIX, EHMT1, ZEB2 and ATP1A1) met conservative Bonferroni genomewide significance for an excess of the observed de novo point variants. Overall, at least one pathogenic or likely pathogenic variant was identified in 54.7% of subjects (35/64). These variants fell within 27 genes previously associated with Mendelian disorders, including NSD1 and NFIX, which are known to be mutated in overgrowth syndromes.ConclusionWe demonstrated that DNVs were enriched in chromatin remodelling (p=2×10−4) and genes regulated by the fragile X mental retardation protein (p=3×10−8), highlighting overlapping genetic mechanisms between MHID and related neurodevelopmental disorders.

Published
2019

8. De novo truncating variants in the intronless IRF2BPL are responsible for developmental epileptic encephalopathy

Author

Laurent Guibaud, Kristin Lindstrom, F. Tran Mau-Them, Alice Masurel, John M. Graham, Yannis Duffourd, Renske Oegema, A. A. Sharkov, Markus Zweier, M. J. van den Boogaard, Thibaud Jouan, Ekaterina R. Lozier, Agnes Chen, M. T. Cho, Sergey Korostelev, Laurence Faivre, Henry J. Lin, F. A. Konovalov, Anaïs Begemann, Patricia I. Dickson, Jennifer Friedman, K.L.I. van Gassen, Boris Keren, Laurence Duplomb, C. Thauvin-Robinet, Moin Vera, Isabelle Marey, Margaret G. Au, Christophe Philippe, Thomas Schmitt-Mechelke, Floor E. Jansen, B. Urteaga, Caroline Nava, Stan F. Nelson, Julian A. Martinez-Agosto, Anita Rauch, Fanny Mochel, and Antonio Vitobello

Subjects
0301 basic medicine, Adult, Central Nervous System, Male, Heterozygote, Adolescent, data sharing, 030105 genetics & heredity, Biology, developmental epileptic encephalopathies, 03 medical and health sciences, Epilepsy, Young Adult, Neurodevelopmental disorder, Seizures, medicine, Transcriptional regulation, Humans, Genetics(clinical), Child, Gene, Genetics (clinical), Exome sequencing, Genetics, Genetic heterogeneity, Neurodegeneration, High-Throughput Nucleotide Sequencing, Nuclear Proteins, Electroencephalography, Middle Aged, medicine.disease, 030104 developmental biology, Phenotype, Neurodevelopmental Disorders, Mutation, IRF2BPL, Female, Carrier Proteins, exome sequencing, Interferon regulatory factors
Abstract

Purpose: Developmental and epileptic encephalopathies (DEEs) are severe clinical conditions characterized by stagnation or decline of cognitive and behavioral abilities preceded, accompanied or followed by seizures. Because DEEs are clinically and genetically heterogeneous, next-generation sequencing, especially exome sequencing (ES), is becoming a first-tier strategy to identify the molecular etiologies of these disorders. Methods: We combined ES analysis and international data sharing. Results: We identified 11 unrelated individuals with DEE and de novo heterozygous truncating variants in the interferon regulatory factor 2–binding protein-like gene (IRF2BPL). The 11 individuals allowed for delineation of a consistent neurodevelopmental disorder characterized by mostly normal initial psychomotor development followed by severe global neurological regression and epilepsy with nonspecific electroencephalogram (EEG) abnormalities and variable central nervous system (CNS) anomalies. IRF2BPL, also known as enhanced at puberty protein 1 (EAP1), encodes a transcriptional regulator containing a C-terminal RING-finger domain common to E3 ubiquitin ligases. This domain is required for its repressive and transactivating transcriptional properties. The variants identified are expected to encode a protein lacking the C-terminal RING-finger domain. Conclusions: These data support the causative role of truncating IRF2BPL variants in pediatric neurodegeneration and expand the spectrum of transcriptional regulators identified as molecular factors implicated in genetic developmental and epileptic encephalopathies.

Published
2019

9. Application of whole-exome sequencing to unravel the molecular basis of undiagnosed syndromic congenital neutropenia with intellectual disability

Author

Jean Donadieu, Delphine Héron, Laurence Faivre, Salima El Chehadeh, Daphné Lehalle, Claire Briandet, Elodie Gautier, Julien Thevenon, Daniel Amram, Thibaud Jouan, Jean-Baptiste Rivière, Judith Melki, Laurence Duplomb-Jego, Frédéric Huet, Christine Bellanné-Chantelot, Christel Thauvin-Robinet, Ange-Line Bruel, Yannis Duffourd, Lucile Pinson, Isabelle Maystadt, Judith St-Onge, Sophia Julia, Alexandra Gauthier-Vasserot, Paul Kuentz, Institut d'hématologie et d'oncologie pédiatrique [CHU - HCL] (IHOPe), Hospices Civils de Lyon (HCL), Génétique des Anomalies du Développement (GAD), IFR100 - Structure fédérative de recherche Santé-STIC-Université de Bourgogne (UB), 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), CHU Dijon, CHU Pitié-Salpêtrière [AP-HP], 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), Service d'hématologie-immunologie-oncologie pédiatrique [CHU Trousseau], CHU Trousseau [APHP], 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], Immuno-hématologie pédiatrique (MaRIH), Laboratoire de géographie physique : Environnements Quaternaires et Actuels (LGP), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Université de Namur [Namur] (UNamur), Service de génétique médicale [Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Arnaud de Villeneuve, Unité fonctionnelle de génétique clinique, Université Paris Diderot - Paris 7 (UPD7)-Hôpital Robert Debré-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de génétique médicale, CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Hôpital Bicêtre, Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, Centre hospitalier universitaire de Toulouse-Purpan, Institut d'hématologie et d'oncologie pédiatrique [CHU - HCL] ( IHOPe ), Hospices Civils de Lyon ( HCL ), Génétique des Anomalies du Développement ( GAD ), Université de Bourgogne ( UB ) -IFR100 - Structure fédérative de recherche Santé-STIC, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Centre de Référence des Déficiences Intellectuelles de Causes Rares, Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Pitié-Salpêtrière [APHP], Groupe de Recherche Clinique : Déficience Intellectuelle et Autisme ( GRC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ), Service d’oncologie hématologie pédiatrique [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Trousseau [APHP], Immuno-hématologie pédiatrique ( MaRIH ), Laboratoire de géographie physique ( LGP ), Université Panthéon-Sorbonne ( UP1 ) -Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Namur, Centre Hospitalier Régional Universitaire [Montpellier] ( CHRU Montpellier ) -Hôpital Arnaud de Villeneuve, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 ( UPD7 ), Université Paris-Sud - Paris 11 ( UP11 ) -Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Bicêtre, Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, Service de pédiatrie (CHU de Dijon), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7), CHU Toulouse [Toulouse], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)

Subjects
Male, 0301 basic medicine, Pediatrics, medicine.medical_specialty, Neutropenia, Adolescent, Neonatal onset, 03 medical and health sciences, 0302 clinical medicine, congenital neutropenia, [ SDV.MHEP ] Life Sciences [q-bio]/Human health and pathology, Intellectual Disability, Intellectual disability, Genetics, medicine, Congenital Bone Marrow Failure Syndromes, Humans, Exome, Child, Congenital Neutropenia, Genetic Association Studies, Genetics (clinical), Exome sequencing, Retrospective Studies, business.industry, High-Throughput Nucleotide Sequencing, Infant, Syndrome, medicine.disease, 3. Good health, Phenotype, 030104 developmental biology, CHD2, Child, Preschool, 030220 oncology & carcinogenesis, Cohort, Etiology, Female, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Biomarkers
Abstract

International audience; Neutropenia can be qualified as congenital when of neonatal onset or when associated with extra-hematopoietic manifestations. Overall, 30% of patients with congenital neutropenia (CN) remain without a molecular diagnosis after a multidisciplinary consultation and tedious diagnostic strategy. In the rare situations when neutropenia is identified and associated with intellectual disability (ID), there are few diagnostic hypotheses to test. This retrospective multicenter study reports on a clinically heterogeneous cohort of 10 unrelated patients with CN associated with ID and no molecular diagnosis prior to whole-exome sequencing (WES). WES provided a diagnostic yield of 40% (4/10). The results suggested that in many cases neutropenia and syndromic manifestations could not be assigned to the same molecular alteration. Three sub-groups of patients were highlighted: (i) severe, symptomatic chronic neutropenia, detected early in life, and related to a known mutation in the CN spectrum (ELANE); (ii) mild to moderate benign intermittent neutropenia, detected later, and associated with mutations in genes implicated in neurodevelopmental disorders (CHD2, HUWE1); and (iii) moderate to severe intermittent neutropenia as a probably undiagnosed feature of a newly reported syndrome (KAT6A). Unlike KAT6A, which seems to be associated with a syndromic form of CN, the other reported mutations may not explain the entire clinical picture. Although targeted gene sequencing can be discussed for the primary diagnosis of severe CN, we suggest that performing WES for the diagnosis of disorders associating CN with ID will not only provide the etiological diagnosis but will also pave the way towards personalized care and follow-up. (C) 2016 Wiley Periodicals, Inc., (C) 2016 John Wiley & Sons, Ltd

Published
2016

10. Recessive loss of function PIGN alleles, including an intragenic deletion with founder effect in La Réunion Island, in patients with Fryns syndrome

Author

Asma Chebil, Duksha Ramful, Thibaud Jouan, Hanitra Randrianaivo, Norbert F. Ajeawung, Nicolas Gruchy, Yannis Duffourd, Bérénice Doray, Christopher T. Gordon, Francesca Filippini, Christine Bole-Feysot, Philippe M. Campeau, Asma Omarjee, Julien Thevenon, Paul Kuentz, Jean-Luc Alessandri, Patrick Nitschke, Laurence Faivre, Jeanne Amiel, Coralie Dumont, Thi Tuyet Mai Nguyen, Marion Gérard, Myriam Oufadem, Guillaume Benoist, Olivier Alibeu, Marie-Line Jacquemont, Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Sud Saint Pierre [Ile de la Réunion], Service de Génétique [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), Centre de recherche du CHU Sainte-Justine, CHU Sainte Justine [Montréal], Centre Hospitalier de Mayotte, 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, 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, FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Laboratoire de Génétique Médicale (LGM), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche du CHU Sainte-Justine [Montreal], Université de Montréal (UdeM)-CHU Sainte Justine [Montréal], Service de réanimation néonatologique et pédiatrique [La Réunion], Groupe Hospitalier Sud-CHR La réunion, Embryology and genetics of human malformation (Equipe Inserm U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique et épigénétique des maladies métaboliques, neurosensorielles et du développement (Inserm U781), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Biologie, génétique et thérapies ostéoarticulaires et respiratoires (BIOTARGEN), Normandie Université (NU)-Normandie Université (NU), Pôle Gynécologie Obstétrique [CHM, Mayotte], Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), 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), Pôle Femme-Mère-Enfant [CHU La Réunion, Saint-Pierre, La Réunion], Plateforme de génomique [SFR Necker], Structure Fédérative de Recherche Necker (SFR Necker - UMS 3633 / US24), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Plate Forme Paris Descartes de Bioinformatique (BIP-D), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Biologie moléculaire et cellulaire de la différenciation, Université Joseph Fourier - Grenoble 1 (UJF)-Institut Albert Bonniot-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de La Réunion ( CHU La Réunion ), Imagine - Institut des maladies génétiques ( IMAGINE - U1163 ), Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Paris Descartes - Paris 5 ( UPD5 ), Service de Génétique Clinique [Caen], Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -CHU Caen, Lipides - Nutrition - Cancer [Dijon - U1231] ( LNC ), 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 ), 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 ), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Laboratoire de Génétique Médicale ( LGM ), Université de Strasbourg ( UNISTRA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Service de Réanimation Néonatale et Pédiatrique, CHD Félix Guyon, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Université de Lausanne (UNIL), Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Equipe NuTox (LNC - U1231) (NUTOX), Service de Médecine Néonatale [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Université de Maurice, Service de médecine foetale et foetopathologie, Service de Génétique, Hôpital de Hautepierre [Strasbourg], Department of Experimental Cardiology, Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), and University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA)-Heart Failure Research Center (HFRC)

Subjects
0301 basic medicine, Male, MESH: Limb Deformities, Congenital, Limb Deformities, Congenital, MESH: Phosphotransferases, [SDV.CAN]Life Sciences [q-bio]/Cancer, 030105 genetics & heredity, Biology, MESH: Founder Effect, Article, 03 medical and health sciences, Pulmonary hypoplasia, 0302 clinical medicine, Fryns syndrome, Loss of Function Mutation, Genetics, medicine, Missense mutation, Humans, Allele, [ SDV.GEN.GH ] Life Sciences [q-bio]/Genetics/Human genetics, Genetics (clinical), Loss function, Hernia, Diaphragmatic, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, Phosphotransferases, MESH: Infant, Newborn, Infant, Newborn, Congenital diaphragmatic hernia, Facies, Infant, MESH: Loss of Function Mutation, medicine.disease, MESH: Infant, Hypoplasia, Founder Effect, MESH: Male, MESH: Hernia, Diaphragmatic, MESH: Facies, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, MESH: Gene Deletion, Female, MESH: Female, 030217 neurology & neurosurgery, Gene Deletion, Founder effect
Abstract

International audience; Fryns syndrome (FS) is a multiple malformations syndrome with major features of congenital diaphragmatic hernia, pulmonary hypoplasia, craniofacial dysmorphic features, distal digit hypoplasia, and a range of other lower frequency malformations. FS is typically lethal in the fetal or neonatal period. Inheritance is presumed autosomal recessive. Although no major genetic cause has been identified for FS, biallelic truncating variants in PIGN, encoding a component of the glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway, have been identified in a limited number of cases with a phenotype compatible with FS. Biallelic variants in PIGN, typically missense or compound missense with truncating, also cause multiple congenital anomalies-hypotonia-seizures syndrome 1 (MCAHS1). Here we report six further patients with FS with or without congenital diaphragmatic hernia and recessive loss of function PIGN alleles, including an intragenic deletion with a likely founder effect in La Réunion and other Indian Ocean islands. Our results support the hypothesis that a spectrum of phenotypic severity is associated with recessive PIGN variants, ranging from FS at the extreme end, caused by complete loss of function, to MCAHS1, in which some residual PIGN function may remain. Our data add FS resulting from PIGN variants to the catalog of inherited GPI deficiencies caused by the disruption of the GPI-anchor biosynthesis pathway.

Published
2018

11. Reducing diagnostic turnaround times of exome sequencing for families requiring timely diagnoses

Author

Judith St-Onge, Anne-Laure Mosca-Boidron, Thibaud Jouan, Frédéric Tran-Mau-Them, Ange-Line Bruel, Laetitia Lambert, Sebastien Moutton, Aurélie Bourchany, Nolwenn Jean, Aurélia Jaquette, Christel Thauvin-Robinet, Daphné Lehalle, Elise Schaefer, Nada Houcinat, Charlotte Poe, Yannis Duffourd, Paul Kuentz, Salima El Chehadeh-Djebbar, Alice Masurel-Paulet, Martin Chevarin, Laurence Faivre, Sophie Nambot, Marjorie Willems, Mathilde Lefebvre, Nicole Laurent, Antonio Vitobello, Frédéric Huet, Julien Thevenon, Patrick Callier, Jean-Baptiste Rivière, Christophe Philippe, Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] ( LNC ), 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 ), Service de pédiatrie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), FHU TRANSLAD, Département de Génétique Clinique [CHRU de Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] ( CHRU Montpellier ), Service de Médecine Infantile III et Génétique Clinique [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy ( CHRU Nancy ), Service de Génétique Médicale, Hôpital Civil, Strasbourg, Centre de Génétique (Hôpital de la Pitié-Salpétrière, Paris), Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques, Université Montpellier 1 ( UM1 ) -IFR3-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ), Service de Pathologie [CHU de 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-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, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), FHU TRANSLAD (CHU de Dijon), Département génétique méd, mal rares et médecine personnalisée [CHRU de Montpellier], Pôle Biologie-Pathologie [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), Université Montpellier 1 (UM1)-IFR3, and Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)

Subjects
0301 basic medicine, Adult, Male, Exome sequencing, medicine.medical_specialty, Time Factors, Adolescent, Genetic counseling, Bioinformatics, Turnaround time, Sensitivity and Specificity, Undiagnosed genetic conditions, 03 medical and health sciences, Genetics, medicine, Humans, Exome, Genetic Testing, Medical diagnosis, Intensive care medicine, Child, Genetics (clinical), Genetic testing, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, medicine.diagnostic_test, business.industry, Infant, Newborn, Infant, General Medicine, Sequence Analysis, DNA, Diagnostic turnaround time, 3. Good health, Clinical trial, 030104 developmental biology, Early Diagnosis, Child, Preschool, Female, business, [ SDV.GEN ] Life Sciences [q-bio]/Genetics
Abstract

IF 2.137; International audience; BACKGROUND AND OBJECTIVE:Whole-exome sequencing (WES) has now entered medical practice with powerful applications in the diagnosis of rare Mendelian disorders. Although the usefulness and cost-effectiveness of WES have been widely demonstrated, it is essential to reduce the diagnostic turnaround time to make WES a first-line procedure. Since 2011, the automation of laboratory procedures and advances in sequencing chemistry have made it possible to carry out diagnostic whole genome sequencing from the blood sample to molecular diagnosis of suspected genetic disorders within 50 h. Taking advantage of these advances, the main objective of the study was to improve turnaround times for sequencing results.METHODS:WES was proposed to 29 patients with severe undiagnosed disorders with developmental abnormalities and faced with medical situations requiring rapid diagnosis. Each family gave consent. The extracted DNA was sequenced on a NextSeq500 (Illumina) instrument. Data were analyzed following standard procedures. Variants were interpreted using in-house software. Each rare variant affecting protein sequences with clinical relevance was tested for familial segregation.RESULTS:The diagnostic rate was 45% (13/29), with a mean turnaround time of 40 days from reception of the specimen to delivery of results to the referring physician. Besides permitting genetic counseling, the rapid diagnosis for positive families led to two pre-natal diagnoses and two inclusions in clinical trials.CONCLUSIONS:This pilot study demonstrated the feasibility of rapid diagnostic WES in our primary genetics center. It reduced the diagnostic odyssey and helped provide support to families.Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Published
2017

12. Autosomal recessive variations of TBX6 , from congenital scoliosis to spondylocostal dysostosis

Author

Yannis Duffourd, Nolwenn Jean-Marçais, Charlotte Poe, Julien Thevenon, Geneviève Pierquin, P. Callier, B. Demeer, Mathilde Lefebvre, Jean-Baptiste Rivière, Christel Thauvin-Robinet, Laurence Faivre, Thibaud Jouan, Florence Petit, Alain Verloes, Judith St-Onge, Génétique des Anomalies du Développement ( GAD ), Université de Bourgogne ( UB ) -IFR100 - Structure fédérative de recherche Santé-STIC, FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), AP-HP Hôpital universitaire Robert-Debré [Paris], CHU Dijon, Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université ( AMU ) -Université d'Avignon et des Pays de Vaucluse ( UAPV ), Anthropologie bio-culturelle, Droit, Ethique et Santé ( ADES ), Aix Marseille Université ( AMU ) -EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique ( CNRS ), Centre de Génétique Humaine, Université de Liège-CHU Liège, CHU Amiens-Picardie, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Génétique des Anomalies du Développement (GAD), Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU)

Subjects
0301 basic medicine, Male, Pediatrics, medicine.medical_specialty, Candidate gene, Genotype, Scoliosis, 030105 genetics & heredity, Compound heterozygosity, 03 medical and health sciences, [ SDV.MHEP ] Life Sciences [q-bio]/Human health and pathology, Genetics, medicine, Inheritance Mode, Missense mutation, Humans, Abnormalities, Multiple, Genetic Predisposition to Disease, Child, Genetics (clinical), Hernia, Diaphragmatic, business.industry, Haplotype, Infant, medicine.disease, Spondylocostal dysostosis, Spine, 3. Good health, Pedigree, 030104 developmental biology, Haplotypes, Child, Preschool, Mutation, Female, business, Haploinsufficiency, T-Box Domain Proteins, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; Proximal 16p11.2 microdeletions are recurrent microdeletions with an overall prevalence of 0.03%. In patients with segmentation defects of the vertebra (SDV), a burden of this microdeletion was observed with TBX6 as a candidate gene for SDV. In a published cohort of patients with congenital scoliosis (CS), TBX6 haploinsufficiency was compound heterozygous with a common haplotype. Besides, a single three-generation family with spondylocostal dysostosis (SCD) was reported with a heterozygous stop-loss of TBX6. These observations questioned both on the inheritance mode and on the variable expressivity associated with TBX6-associated SDV. Based on a national recruitment of 56 patients with SDV, we describe four patients with variable SDV ranging from CS to SCD associated with biallelic variations of TBX6. Two patients with CS were carrying a proximal 16p11.2 microdeletion associated with the previously reported haplotype. One patient with extensive SDV was carrying a proximal 16p11.2 microdeletion associated with a TBX6 rare missense change. One patient with a clinical diagnosis of SCD was compound heterozygous for two TBX6 rare missense changes. The three rare variants were affecting the chromatin-binding domain. Our data illustrate the variable expressivity of recessive TBX6 ranging from CS to SCD.

Published
2017

13. Autosomal-Recessive Mutations in AP3B2, Adaptor-Related Protein Complex 3 Beta 2 Subunit, Cause an Early-Onset Epileptic Encephalopathy with Optic Atrophy

Author

Catherine Nowak, Kamiar Mireskandari, Masano Amamoto, Jean-Baptiste Rivière, Amber Begtrup, Thibaud Jouan, Laurence Faivre, Aline Saunier, Nicolas Chatron, Noriko Miyake, Mitsuhiro Kato, Dorothée Ville, Jessica Douglas, Stéphane Auvin, Bertrand Isidor, Guylène Lemeur, Stylianos E. Antonarakis, Naomichi Matsumoto, Mathieu Milh, Philippe Jonveaux, Hanan Hamamy, Neal Sondheimer, Mirna Assoum, Paolo Milani, Mitsuko Nakashima, Amira Masri, Gaetan Lesca, Julien Thevenon, Yannis Duffourd, Laurence Perrin, Caroline Paris, Christel Thauvin-Robinet, Christophe Philippe, Periklis Makrythanasis, Génétique des Anomalies du Développement ( GAD ), IFR100 - Structure fédérative de recherche Santé-STIC-Université de Bourgogne ( UB ), Nutrition-Génétique et Exposition aux Risques Environnementaux ( NGERE ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Lorraine ( UL ), Centre hospitalier universitaire de Nantes ( CHU Nantes ), Service de génétique [Robert Debré], Assistance publique - Hôpitaux de Paris (AP-HP), University of Geneva, Division of Clinical and Metabolic Genetics [Toronto], The Hospital for sick children [Toronto] ( SickKids ), Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ), Boston Children's Hospital, Centre de recherche en neurosciences de Lyon ( 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 ), Université de Lyon, Service de Génétique Médicale [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy ( CHRU Nancy ), GeneDx, Service de Neurologie Pédiatrique [CHU Lyon], Hôpital Femme Mère Enfant [CHU - HCL] ( HFME ), Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ), Service de Neurologie Pédiatrique, HFME, Bron, France, Service d'ophtalmologie [Nantes], Hôtel-Dieu, 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 ), Génétique Médicale et Génomique Fonctionnelle ( GMGF ), 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 National de la Recherche Scientifique ( CNRS ), Pediatric Emergency Centre, Kitakyushu Municipal Yahata Hospital, Yokohama City University School of Medecine ( YCUSM ), University School of Medecine, University of Amman, 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 ), Regional Council of Burgundy Dijon University Hospital Association Française du Syndrome de Rett, Génétique des Anomalies du Développement (GAD), Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, Nutrition-Génétique et Exposition aux Risques Environnementaux (NGERE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Centre hospitalier universitaire de Nantes (CHU Nantes), Département de génétique [Robert Debré], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), The Hospital for sick children [Toronto] (SickKids), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Centre de recherche en neurosciences de Lyon (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), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), GeneDx [Gaithersburg, MD, USA], Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Université de la Méditerranée - Aix-Marseille 2-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Génétique Médicale et Génomique Fonctionnelle (GMGF), 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 National de la Recherche Scientifique (CNRS), Yokohama City University School of Medecine (YCUSM), Yokohama University School of Medecine, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), and 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)

Subjects
0301 basic medicine, Male, Microcephaly, Developmental Disabilities, Postnatal microcephaly, copper-metabolism, Epilepsy, 0302 clinical medicine, expansion, hermansky-pudlak-syndrome, ddc:576.5, Age of Onset, Child, disorders, Genetics (clinical), seizures, Genetics, MEDNIK syndrome, Syndrome, 3. Good health, Pedigree, intellectual disability, Child, Preschool, mednik syndrome, Female, Developmental regression, Adaptor Protein Complex 3, Genes, Recessive, Biology, AP3B1, 03 medical and health sciences, Atrophy, Report, [ SDV.MHEP ] Life Sciences [q-bio]/Human health and pathology, medicine, Humans, Adaptor Protein Complex beta Subunits, mouse, disease, ap-4 deficiency, Infant, Newborn, Infant, medicine.disease, Optic Atrophy, 030104 developmental biology, Mutation, Hermansky–Pudlak syndrome, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; Early-onset epileptic encephalopathy (EOEE) represents a heterogeneous group of severe disorders characterized by seizures, interictal epileptiform activity with a disorganized electroencephalography background, developmental regression or retardation, and onset before 1 year of age. Among a cohort of 57 individuals with epileptic encephalopathy, we ascertained two unrelated affected individuals with EOEE associated with developmental impairment and autosomal-recessive variants in AP3B2 by means of whole-exome sequencing. The targeted sequencing of AP3B2 in 86 unrelated individuals with EOEE led to the identification of an additional family. We gathered five additional families with eight affected individuals through the Matchmaker Exchange initiative by matching autosomal- recessive mutations in AP3B2. Reverse phenotyping of 12 affected individuals from eight families revealed a homogeneous EOEE phenotype characterized by severe developmental delay, poor visual contact with optic atrophy, and postnatal microcephaly. No spasticity, albinism, or hematological symptoms were reported. AP3B2 encodes the neuron-specific subunit of the AP-3 complex. Autosomal-recessive variations of AP3B1, the ubiquitous isoform, cause Hermansky-Pudlak syndrome type 2. The only isoform for the delta subunit of the AP-3 complex is encoded by AP3D1. Autosomal-recessive mutations in AP3D1 cause a severe disorder cumulating the symptoms of the AP3B1 and AP3B2 defects.

Published
2016

14. Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3

Author

Paul Kuentz, Magali Avila, Jean Baptiste Rivière, Pierre Vabres, Marietta Zinner, Julien Thevenon, Judith St-Onge, David Geneviève, Eveline S. J. M. de Bont, Florian Villegas, Floor A. M. Duijkers, Mieke M. van Haelst, Laurence Duplomb-Jego, Sébastien A. Smallwood, Silvana van Koningsbruggen, Daniel Olivieri, Nada Houcinat, Yannis Duffourd, Thibaud Jouan, Christel Thauvin-Robinet, Koen L.I. van Gassen, Daphné Lehalle, Melanie Rittirsch, Michael B. Stadler, Laurence Faivre, Daniel Hess, Klaske D. Lichtenbelt, Joerg Betschinger, Daniela Mayer, Friedrich Miescher Institute for Biomedical Research (FMI), Novartis Research Foundation, University of Basel (Unibas), FHU TRANSLAD (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)-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), Université Bourgogne Franche-Comté [COMUE] (UBFC), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Service de Dermatologie (CHU de Dijon), Beatrix Children's Hospital, Department of Clinical Genetics (Academic Medical Center, University of Amsterdam), VU University Medical Center [Amsterdam], Département de génétique médicale, maladies rares et médecine personnalisée [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), University Medical Center [Utrecht], Research Institute of the McGill University Hospital Centre, Human genetics, Cancer Center Amsterdam, Amsterdam Reproduction & Development (AR&D), Human Genetics, and ACS - Pulmonary hypertension & thrombosis

Subjects
Male, Transcription, Genetic, GTPase, GTP Phosphohydrolases, PATHWAY, Mice, 0302 clinical medicine, Neural Stem Cells, CRISPR, TUMOR-SUPPRESSOR, Cell Self Renewal, Phosphorylation, SPECIFICATION, developmental disorder, 0303 health sciences, Genome, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Cell Differentiation, Mouse Embryonic Stem Cells, Flcn, differentiation, Cell biology, medicine.anatomical_structure, mTOR, Molecular Medicine, Female, Signal transduction, Protein Binding, Signal Transduction, RECRUITMENT, Biology, 03 medical and health sciences, Rag GTPases, Lysosome, Genetics, medicine, Animals, Humans, Point Mutation, NAIVE PLURIPOTENCY, AMINO-ACID LEVELS, Transcription factor, Alleles, PI3K/AKT/mTOR pathway, 030304 developmental biology, COMPLEX, FOLLICULIN, Ragulator, Cell Biology, pluripotency, embryonic stem cell, Embryonic stem cell, Tfe3, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Cytoplasm, Lysosomes, 030217 neurology & neurosurgery
Abstract

International audience; Self-renewal and differentiation of pluripotent murine embryonic stem cells (ESCs) is regulated by extrinsic signaling pathways. It is less clear whether cellular metabolism instructs developmental progression. In an unbiased genome-wide CRISPR/Cas9 screen, we identified components of a conserved amino-acid-sensing pathway as critical drivers of ESC differentiation. Functional analysis revealed that lysosome activity, the Ragulator protein complex, and the tumor-suppressor protein Folliculin enable the Rag GTPases C and D to bind and seclude the bHLH transcription factor Tfe3 in the cytoplasm. In contrast, ectopic nuclear Tfe3 represses specific developmental and metabolic transcriptional programs that are associated with peri-implantation development. We show differentiation-specific and non-canonical regulation of Rag GTPase in ESCs and, importantly, identify point mutations in a Tfe3 domain required for cytoplasmic inactivation as potentially causal for a human developmental disorder. Our work reveals an instructive and biomedically relevant role of metabolic signaling in licensing embryonic cell fate transitions.

Published
2019

15. Molecular diagnosis of PIK3CA-related overgrowth spectrum (PROS) in 162 patients and recommendations for genetic testing

Author

Judith St-Onge, Yannis Duffourd, Sandra Whalen, Marjolaine Willems, Anne-Claire Bursztejn, Massimiliano Rossi, Bertrand Isidor, Patrick Edery, Odile Boute, Virginie Carmignac, J. Miquel, Sébastien Barbarot, Daniel Amram, Fanny Morice-Picard, A. Phan, Pierre Vabres, Didier Lacombe, Maryse Bonnière, Jean-Baptiste Rivière, Nadia Bahi-Buisson, Catherine Vincent-Delorme, Thibaud Jouan, Paul Kuentz, Caroline Michot, Renaud Touraine, Jean-Benoît Courcet, Christine Francannet, Marie Vincent, Smail Hadj-Rabia, Valérie Cormier-Daire, Christine Coubes, Cyril Mignot, Nathalie Marle, Jeanne Amiel, Michèle Mathieu-Dramard, Philippe Khau Van Kien, Juliette Mazereeuw-Hautier, Annabel Maruani, Salima El Chehadeh, Geneviève Baujat, Christine Chiaverini, Daphné Lehalle, Arthur Sorlin, Florence Petit, Bruno Delobel, Laurence Faivre, Julien Thevenon, Stéphanie Arpin, Didier Bessis, Damien Haye, David Geneviève, Tania Attié-Bitach, Claire Abasq-Thomas, Jelena Martinovic, Alain Verloes, Christel Thauvin-Robinet, Juliette Albuisson, Marie-Line Jacquemont, Alice Goldenberg, Olivia Boccara, and Ludovic Martin

Subjects
0301 basic medicine, Adult, Male, Pathology, medicine.medical_specialty, Adolescent, Genotype, Class I Phosphatidylinositol 3-Kinases, Prenatal diagnosis, Bioinformatics, medicine.disease_cause, DNA sequencing, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Prenatal Diagnosis, medicine, Humans, Genetic Predisposition to Disease, Genetic Testing, Allele, Child, Genetics (clinical), Alleles, Genetic Association Studies, Growth Disorders, Genetic testing, Mutation, medicine.diagnostic_test, business.industry, Mosaicism, Infant, Newborn, Disease Management, High-Throughput Nucleotide Sequencing, Infant, Sequence Analysis, DNA, Phenotype, 030104 developmental biology, Amino Acid Substitution, Child, Preschool, Allelic heterogeneity, Female, business, 030217 neurology & neurosurgery
Abstract

Postzygotic activating mutations of PIK3CA cause a wide range of mosaic disorders collectively referred to as PIK3CA-related overgrowth spectrum (PROS). We describe the diagnostic yield and characteristics of PIK3CA sequencing in PROS. We performed ultradeep next-generation sequencing (NGS) of PIK3CA in various tissues from 162 patients referred to our clinical laboratory and assessed diagnostic yield by phenotype and tissue tested. We identified disease-causing mutations in 66.7% (108/162) of patients, with mutant allele levels as low as 1%. The diagnostic rate was higher (74%) in syndromic than in isolated cases (35.5%; P = 9.03 × 10−5). We identified 40 different mutations and found strong oncogenic mutations more frequently in patients without brain overgrowth (50.6%) than in those with brain overgrowth (15.2%; P = 0.00055). Mutant allele levels were higher in skin and overgrown tissues than in blood and buccal samples (P = 3.9 × 10−25), regardless of the phenotype. Our data demonstrate the value of ultradeep NGS for molecular diagnosis of PROS, highlight its substantial allelic heterogeneity, and confirm that optimal diagnosis requires fresh skin or surgical samples from affected regions. Our findings may be of value in guiding future recommendations for genetic testing in PROS and other mosaic conditions. Genet Med advance online publication 02 February 2017

Published
2016

Catalog

Books, media, physical & digital resources
See catalog results