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1. The diagnostic rate of inherited metabolic disorders by exome sequencing in a cohort of 547 individuals with developmental disorders

Author

Julian Delanne, Ange-Line Bruel, Frédéric Huet, Sébastien Moutton, Sophie Nambot, Margot Grisval, Nada Houcinat, Paul Kuentz, Arthur Sorlin, Patrick Callier, Nolwenn Jean-Marcais, Anne-Laure Mosca-Boidron, Frédéric Tran Mau-Them, Anne-Sophie Denommé-Pichon, Antonio Vitobello, Daphné Lehalle, Salima El Chehadeh, Christine Francannet, Marine Lebrun, Laetitia Lambert, Marie-Line Jacquemont, Marion Gerard-Blanluet, Jean-Luc Alessandri, Marjolaine Willems, Julien Thevenon, Mondher Chouchane, Véronique Darmency, Clémence Fatus-Fauconnier, Sébastien Gay, Marie Bournez, Alice Masurel, Vanessa Leguy, Yannis Duffourd, Christophe Philippe, François Feillet, Laurence Faivre, and Christel Thauvin-Robinet

Subjects
Inherited metabolic disorders, Exome sequencing, Intellectual disability, Developmental delay, Genotype first, Medicine (General), R5-920, Biology (General), QH301-705.5
Abstract

Considering that some Inherited Metabolic Disorders (IMDs) can be diagnosed in patients with no distinctive clinical features of IMDs, we aimed to evaluate the power of exome sequencing (ES) to diagnose IMDs within a cohort of 547 patients with unspecific developmental disorders (DD). IMDs were diagnosed in 12% of individuals with causative diagnosis (177/547). There are clear benefits of using ES in DD to diagnose IMD, particularly in cases where biochemical studies are unavailable. Synopsis: Exome sequencing and diagnostic rate of Inherited Metabolic Disorders in individuals with developmental disorders.

Published
2021
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2. The Severity of Congenital Hypothyroidism With Gland-In-Situ Predicts Molecular Yield by Targeted Next-Generation Sequencing

Author

Lucie Levaillant, Natacha Bouhours-Nouet, Frédéric Illouz, Jessica Amsellem Jager, Anne Bachelot, Pascal Barat, Sabine Baron, Candace Bensignor, Aude Brac De La Perriere, Yasmine Braik Djellas, Morgane Caillot, Emmanuelle Caldagues, Marie-Neige Campas, Marylène Caquard, Audrey Cartault, Julie Cheignon, Anne Decrequy, Brigitte Delemer, Katherine Dieckmann, Aurélie Donzeau, Emilie Doye, Mélanie Fradin, Mélanie Gaudillière, Frédérique Gatelais, Magali Gorce, Isabelle Hazart, Nada Houcinat, Laure Houdon, Marielle Ister-Salome, Lucie Jozwiak, Patrick Jeannoel, Francois Labarthe, Didier Lacombe, Anne-Sophie Lambert, Christine Lefevre, Bruno Leheup, Clara Leroy, Benedicte Maisonneuve, Isis Marchand, Emeline Marquant, Matthias Muszlak, Letitia Pantalone, Sandra Pochelu, Chloé Quelin, Catherine Radet, Peggy Renoult-Pierre, Rachel Reynaud, Stéphanie Rouleau, Cécile Teinturier, Julien Thevenon, Caroline Turlotte, Aline Valle, Melody Vierge, Carine Villanueva, Alban Ziegler, Xavier Dieu, Nathalie Bouzamondo, Patrice Rodien, Delphine Prunier-Mirebeau, and Régis Coutant

Subjects
Endocrinology, Endocrinology, Diabetes and Metabolism, Biochemistry (medical), Clinical Biochemistry, Biochemistry
Abstract

IntroductionCongenital hypothyroidism with gland-in-situ (CH-GIS) is usually attributed to mutations in the genes involved in thyroid hormone production. The diagnostic yield of targeted next-generation sequencing (NGS) varied widely between studies. We hypothesized that the molecular yield of targeted NGS would depend on the severity of CH.MethodsTargeted NGS was performed in 103 CH-GIS patients from the French national screening program referred to the Reference Center for Rare Thyroid Diseases of Angers University Hospital. The custom targeted NGS panel contained 48 genes. Cases were classified as solved or probably solved depending on the known inheritance of the gene, the classification of the variants according to the American College of Medical Genetics and Genomics, the familial segregation, and published functional studies. Thyroid-stimulating hormone at CH screening and at diagnosis (TSHsc and TSHdg) and free T4 at diagnosis (FT4dg) were recorded.ResultsNGS identified 95 variants in 10 genes in 73 of the 103 patients, resulting in 25 solved cases and 18 probably solved cases. They were mainly due to mutations in the TG (n = 20) and TPO (n = 15) genes. The molecular yield was, respectively, 73% and 25% if TSHsc was ≥ and < 80 mUI/L, 60% and 30% if TSHdg was ≥ and < 100 mUI/L, and 69% and 29% if FT4dg was ≤ and > 5 pmol/L.ConclusionNGS in patients with CH-GIS in France found a molecular explanation in 42% of the cases, increasing to 70% when TSHsc was ≥ 80 mUI/L or FT4dg was ≤ 5 pmol/L.

Published
2023

3. Second-tier trio exome sequencing after negative solo clinical exome sequencing: an efficient strategy to increase diagnostic yield and decipher molecular bases in undiagnosed developmental disorders

Author

Sebastien Moutton, Martin Chevarin, Nada Houcinat, Sophie Nambot, Yannis Duffourd, Laurence Faivre, Anne-Laure Mosca-Boidron, François Lecoquierre, Christel Thauvin-Robinet, Julian Delanne, Alice Masurel-Paulet, Arthur Sorlin, Charlotte Poe, Caroline Racine, Marjolaine Willems, Julien Thevenon, Steven A. Kushner, David Geneviève, Ange-Line Bruel, Patrick Callier, Frédéric Tran Mau-Them, Christophe Philippe, Emilie Tisserant, Thibaut Jouan, Christine Coubes, Antonio Vitobello, Nolwenn Jean-Marçais, Daphné Lehalle, Femke M.S. de Vrij, and Psychiatry

Subjects
Male, Candidate gene, Developmental Disabilities, Population, Biology, Compound heterozygosity, 03 medical and health sciences, Intellectual Disability, Genotype, Exome Sequencing, Genetics, Humans, Exome, Genetic Predisposition to Disease, education, Gene, Genetics (clinical), Exome sequencing, 030304 developmental biology, 0303 health sciences, education.field_of_study, 030305 genetics & heredity, Genomics, Phenotype, Human genetics, Female
Abstract

Developmental disorders (DD), characterized by malformations/dysmorphism and/or intellectual disability, affecting around 3% of worldwide population, are mostly linked to genetic anomalies. Despite clinical exome sequencing (cES) centered on genes involved in human genetic disorders, the majority of patients affected by DD remain undiagnosed after solo-cES. Trio-based strategy is expected to facilitate variant selection thanks to rapid parental segregation. We performed a second step trio-ES (not only focusing on genes involved in human disorders) analysis in 70 patients with negative results after solo-cES. All candidate variants were shared with a MatchMaking exchange system to identify additional patients carrying variants in the same genes and with similar phenotype. In 18/70 patients (26%), we confirmed causal implication of nine OMIM-morbid genes and identified nine new strong candidate genes (eight de novo and one compound heterozygous variants). These nine new candidate genes were validated through the identification of patients with similar phenotype and genotype thanks to data sharing. Moreover, 11 genes harbored variants of unknown significance in 10/70 patients (14%). In DD, a second step trio-based ES analysis appears an efficient strategy in diagnostic and translational research to identify highly candidate genes and improve diagnostic yield.

Published
2020

4. 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

5. Genotype-first in a cohort of 95 fetuses with multiple congenital abnormalities: when exome sequencing reveals unexpected fetal phenotype-genotype correlations

Author

Tania Attié-Bitach, Philippe Jonveaux, Alice Goldenberg, Antonio Vitobello, Nicole Laurent, Marjolaine Willems, Valérie Kremer, Dominique Gaillard, Chloé Quélin, Sebastien Moutton, Marion Aubert-Lenoir, Yannis Duffourd, Anne-Sophie Lebre, Anne-Claire Brehin, James Lespinasse, Yline Capri, Nolwenn Jean-Marçais, Maria Cristina Antal, Frédéric Tran Mau-Them, Nathalie Marle, Daphné Lehalle, Nicolas Bourgon, Sophie Blesson, Bernard Foliguet, Laetita Lambert, Nicole Bigi, Mélanie Fradin, Emilie Tisserant, Christel Thauvin-Robinet, Ange-Line Bruel, Elisabeth Alanio, Marie-Hélène Saint-Frison, Christine Francannet, Anne-Marie Guerrot, Paul Kuentz, Elise Schaefer, Anne-Marie Beaufrere, Sylvie Odent, Francine Arbez-Gindre, Laurence Faivre, Christophe Philippe, Julien Thevenon, Sophie Patrier-Sallebert, Nada Houcinat, Celine Poirisier, Sophie Nambot, Mathilde Lefebvre, Mirna Assoum, Françoise Girard-Lemaitre, Sophie Collardeau-Frachon, Marie-José Perez, Jean-Louis Mandel, Jean-Pierre Mazutti, Renaud Touraine, Philippe Loget, Salima El Chehadeh, Centre d’Investigation Clinique de Nantes (CIC Nantes), Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre hospitalier universitaire de Nantes (CHU Nantes), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), 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), Hospices Civils de Lyon (HCL), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Equipe GAD (LNC - U1231), 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), Laboratoire de Diagnostic Génétique [CHU Strasbourg], Université de Strasbourg (UNISTRA)-CHU Strasbourg, CHU Strasbourg, Hôpital de Hautepierre [Strasbourg], Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), European Organization for Nuclear Research (CERN), Service de Génétique [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Centre Hospitalier Universitaire de Reims (CHU Reims), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Service d'Anatomie pathologique [CHRU Besançon], Institut de Génétique et Développement de Rennes (IGDR), 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 de référence Maladies Rares CLAD-Ouest [Rennes], CHU Pontchaillou [Rennes], Hôpital Lapeyronie [Montpellier] (CHU), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut de Biomécanique Humaine Georges Charpak (IBHGC), Université Sorbonne Paris Nord-Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM), Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Service de Génétique Médicale [CHU Clermont-Ferrand], CHU Estaing [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, CHU Clermont-Ferrand, CHU Rouen, Normandie Université (NU), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Métropole Savoie [Chambéry], CHU Saint-Etienne, Département de génétique [Robert Debré], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP Hôpital universitaire Robert-Debré [Paris], Hôpital Robert Debré, Plateau technique de Biologie [CHU de Dijon], Centre Hospitalier Universitaire [Grenoble] (CHU), CarMeN, laboratoire, 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, 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 ), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), 14-013 FOETEX, Interregional French PHRC, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)

Subjects
Candidate gene, medicine.medical_specialty, Genotype, [SDV]Life Sciences [q-bio], Biology, Congenital Abnormalities, Cohort Studies, complex traits, 03 medical and health sciences, Fetus, Molecular genetics, medicine, Humans, Abnormalities, Multiple, Exome, Clinical significance, genetics, Gene, Genetic Association Studies, Genetics (clinical), Exome sequencing, 030304 developmental biology, Genetics, 0303 health sciences, 030305 genetics & heredity, Sequence Analysis, DNA, Phenotype, [SDV] Life Sciences [q-bio], molecular genetics, reproductive medicine
Abstract

PurposeMolecular diagnosis based on singleton exome sequencing (sES) is particularly challenging in fetuses with multiple congenital abnormalities (MCA). Indeed, some studies reveal a diagnostic yield of about 20%, far lower than in live birth individuals showing developmental abnormalities (30%), suggesting that standard analyses, based on the correlation between clinical hallmarks described in postnatal syndromic presentations and genotype, may underestimate the impact of the genetic variants identified in fetal analyses.MethodsWe performed sES in 95 fetuses with MCA. Blind to phenotype, we applied a genotype-first approach consisting of combined analyses based on variants annotation and bioinformatics predictions followed by reverse phenotyping. Initially applied to OMIM-morbid genes, analyses were then extended to all genes. We complemented our approach by using reverse phenotyping, variant segregation analysis, bibliographic search and data sharing in order to establish the clinical significance of the prioritised variants.ResultssES rapidly identified causal variant in 24/95 fetuses (25%), variants of unknown significance in OMIM genes in 8/95 fetuses (8%) and six novel candidate genes in 6/95 fetuses (6%).ConclusionsThis method, based on a genotype-first approach followed by reverse phenotyping, shed light on unexpected fetal phenotype-genotype correlations, emphasising the relevance of prenatal studies to reveal extreme clinical presentations associated with well-known Mendelian disorders.

Published
2020

6. 19p13 microduplications encompassing NFIX are responsible for intellectual disability, short stature and small head circumference

Author

Vanna Pecile, Didier Lacombe, Antonella Fabretto, Cécile Boucher, Clémence Vanlerberghe, Benoit Arveiler, Emma L. Baple, Nada Houcinat, Kate Robertshaw, Patricia Fergelot, Gemma Poke, Bruno Delobel, Aurélien Trimouille, Colina McKeown, Joris Andrieux, Paolo Gasparini, Bénédicte Duban, Jérôme Toutain, Marco Carrozzi, Mathilde Nizon, Sébastien Moutton, Marie Vincent, Sahar Mansour, Cédric Le Caignec, Caroline Rooryck, Eve Fifield, Marie Laure Vuillaume, Trimouille, Aurélien, Houcinat, Nada, Vuillaume, Marie-Laure, Fergelot, Patricia, Boucher, Cécile, Toutain, Jérôme, Caignec, Cédric Le, Vincent, Marie, Nizon, Mathilde, Andrieux, Jori, Vanlerberghe, Clémence, Delobel, Bruno, Duban, Bénédicte, Mansour, Sahar, Baple, Emma, Mckeown, Colina, Poke, Gemma, Robertshaw, Kate, Fifield, Eve, Fabretto, Antonella, Pecile, Vanna, Gasparini, Paolo, Carrozzi, Marco, Lacombe, Didier, Arveiler, Benoît, Rooryck, Caroline, and Moutton, Sébastien

Subjects
Male, 0301 basic medicine, Adolescent, Genetics, Genetics (clinical), Short stature, Article, 03 medical and health sciences, 0302 clinical medicine, Genetic, Intellectual Disability, Chromosome Duplication, Gene duplication, Intellectual disability, medicine, Humans, Abnormalities, Multiple, Copy-number variation, Child, biology, Sotos syndrome, Macrocephaly, Infant, Syndrome, medicine.disease, NFIX, NFI Transcription Factors, 030104 developmental biology, Child, Preschool, Chromosomal region, biology.protein, Female, medicine.symptom, Chromosomes, Human, Pair 19, 030217 neurology & neurosurgery
Abstract

Syndromes caused by copy number variations are described as reciprocal when they result from deletions or duplications of the same chromosomal region. When comparing the phenotypes of these syndromes, various clinical features could be described as reversed, probably due to the opposite effect of these imbalances on the expression of genes located at this locus. The NFIX gene codes for a transcription factor implicated in neurogenesis and chondrocyte differentiation. Microdeletions and loss of function variants of NFIX are responsible for Sotos syndrome-2 (also described as Malan syndrome), a syndromic form of intellectual disability associated with overgrowth and macrocephaly. Here, we report a cohort of nine patients harboring microduplications encompassing NFIX. These patients exhibit variable intellectual disability, short stature and small head circumference, which can be described as a reversed Sotos syndrome-2 phenotype. Strikingly, such a reversed phenotype has already been described in patients harboring microduplications encompassing NSD1, the gene whose deletions and loss-of-function variants are responsible for classical Sotos syndrome. Even though the type/contre-type concept has been criticized, this model seems to give a plausible explanation for the pathogenicity of 19p13 microduplications, and the common phenotype observed in our cohort.

Published
2017

7. First female prenatal case of osteopathia striata with cranial sclerosis in a fetus carrying a de-novo 1.9 Mbp interstitial deletion at Xq11.1q11.2

Author

Bruno Schaub, Jérôme Toutain, Nada Houcinat, Didier Lacombe, Clara Adenet, Anna-Gaelle Valard, Michèle Gueneret, Marie-Laure Vuillaume, S. Deves, Julie Bouron, Cécile Boucher, and Caroline Rooryck

Subjects
0301 basic medicine, Pathology, medicine.medical_specialty, Cranial sclerosis, 030105 genetics & heredity, Ultrasonography, Prenatal, Pathology and Forensic Medicine, Osteopathia striata, 03 medical and health sciences, Fetus, Humans, Medicine, Base Pairing, Genetics (clinical), Genetics, Chromosomes, Human, X, Comparative Genomic Hybridization, business.industry, General Medicine, Middle Aged, medicine.disease, 030104 developmental biology, Pediatrics, Perinatology and Child Health, Female, Chromosome Deletion, Anatomy, business, Osteosclerosis
Published
2017

8. Further delineation of a rare recessive encephalomyopathy linked to mutations in GFER thanks to data sharing of whole exome sequencing data

Author

C. Thauvin-Robinet, Nada Houcinat, Daphné Lehalle, A Vital, Laurence Faivre, Agnès Rötig, Jaak Jaeken, Fan Xia, Matthew N. Bainbridge, Marlène Rio, Sophie Nambot, Jean-Baptiste Rivière, Paul Kuentz, Julien Thevenon, D Gavrilov, Cyril Goizet, Ange-Line Bruel, Fanny Mochel, N Niu, Arthur L. Beaudet, Yannis Duffourd, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Lipides - Nutrition - Cancer [Dijon - U1231] ( LNC ), Université de Bourgogne ( UB ) -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 ), FHU TRANSLAD, Laboratoire de cytogénétique (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), 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), and FHU TRANSLAD (CHU de Dijon)

Subjects
Adult, Male, 0301 basic medicine, Heterozygote, Candidate gene, Adolescent, data sharing, Mitochondrial disease, Compound heterozygosity, Bioinformatics, Young Adult, 03 medical and health sciences, Mitochondrial myopathy, Mitochondrial Encephalomyopathies, Exome Sequencing, Genetics, Humans, Medicine, Genetic Predisposition to Disease, Oxidoreductases Acting on Sulfur Group Donors, whole-exome sequencing, Child, Exome, Cytochrome Reductases, Genetics (clinical), Exome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, business.industry, GFER, Disease gene identification, medicine.disease, Pedigree, 3. Good health, 030104 developmental biology, mitochondrial condition, Mutation, Congenital cataracts, Female, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, business
Abstract

Background Alterations in GFER gene have been associated with progressive mitochondrial myopathy, congenital cataracts, hearing loss, developmental delay, lactic acidosis and respiratory chain deficiency in 3 siblings born to consanguineous Moroccan parents by homozygosity mapping and candidate gene approach (OMIM#613076). Next generation sequencing recently confirmed this association by the finding of compound heterozygous variants in 19-year-old girl with a strikingly similar phenotype, but this ultra-rare entity remains however unknown from most of the scientific community. Materials and methods Whole exome sequencing was performed as part of a "diagnostic odyssey" for suspected mitochondrial condition in 2 patients, presenting congenital cataracts, progressive encephalomyopathy and hypotrophy and detected unreported compound heterozygous variants in GFER. Results Thanks to an international data sharing, we found 2 additional patients carrying compound heterozygous variants in GFER. Reverse phenotyping confirmed the phenotypical similarities between the 4 patients. Together with the first literature reports, the review of these 8 cases from 4 unrelated families enables us to better describe this apparently homogeneous disorder, with the clinical and biological stigmata of mitochondrial disease. Conclusion This report highlights the clinical utility of whole exome sequencing and reverse phenotyping for the diagnosis of ultra-rare diseases and underlines the importance of a broad data sharing for accurate clinical delineation of previously unrecognized entities.

Published
2017

9. Hearing impairment as an early sign of alpha-mannosidosis in children with a mild phenotype: Report of seven new cases

Author

Sebastien Moutton, Aurore Garde, Laurence Faivre, François Feillet, Christel Thauvin-Robinet, Paul Kuentz, Antonio Vitobello, Frédéric Huet, Arthur Sorlin, Roberto Colombo, Nada Houcinat, Yannis Duffourd, Caroline Racine, Julian Delanne, Christophe Philippe, Daphné Lehalle, Michael J. O'Grady, Julien Thevenon, Frédéric Tran Mau-Them, Bénédicte Héron, Sandrine Marlin, and Sophie Nambot

Subjects
Adult, Male, Pediatrics, medicine.medical_specialty, Adolescent, Hearing loss, Alpha-mannosidosis, Urinary system, Young Adult, alpha-Mannosidase, Intellectual Disability, Intellectual disability, Exome Sequencing, Genetics, medicine, Humans, Child, Hearing Loss, Genetics (clinical), Exome sequencing, Coarse facial features, business.industry, Siblings, Enzyme replacement therapy, medicine.disease, Hypotonia, Phenotype, Child, Preschool, alpha-Mannosidosis, Female, medicine.symptom, business, Lysosomes
Abstract

Alpha-mannosidosis (AM) is a very rare (prevalence: 1/500000 births) autosomal recessive lysosomal storage disorder. It is characterized by multi-systemic involvement associated with progressive intellectual disability, hearing loss, skeletal anomalies, and coarse facial features. The spectrum is wide, from very severe and lethal to a milder phenotype that usually progresses slowly. AM is caused by a deficiency of lysosomal alpha-mannosidase. A diagnosis can be established by measuring the activity of lysosomal alpha-mannosidase in leucocytes and screening for abnormal urinary excretion of mannose-rich oligosaccharides. Genetic confirmation is obtained with the identification of MAN2B1 mutations. Enzyme replacement therapy (LAMZEDER ) was approved for use in Europe in August 2018. Here, we describe seven individuals from four families, diagnosed at 3-23 years of age, and who were referred to a clinical geneticist for etiologic exploration of syndromic hearing loss, associated with moderate learning disabilities. Exome sequencing had been used to establish the molecular diagnosis in five cases, including a two-sibling pair. In the remaining two patients, the diagnosis was obtained with screening of urinary oligosaccharides excretion and the association of deafness and hypotonia. These observations emphasize that the clinical diagnosis of AM can be challenging, and that it is likely an underdiagnosed rare cause of syndromic hearing loss. Exome sequencing can contribute significantly to the early diagnosis of these nonspecific mild phenotypes, with advantages for treatment and management.

Published
2019

10. NBEA : developmental disease gene with early generalized epilepsy phenotypes

Author

Hermine E. Veenstra-Knol, Rolph Pfundt, Nada Houcinat, Gregory M. Cooper, James J. Riviello, Frédéric Bilan, Servi J. C. Stevens, Susan M. Hiatt, Mary K. Kukolich, Anna Lehman, Brigitte Gilbert-Dussardier, Cédric Le Caignec, Christian Korff, Catharina M L Volker-Touw, Eva H. Brilstra, Louise Bier, Alexander P.A. Stegmann, Evan H. Baugh, Berten Ceulemans, David Goldstein, Magalie Barth, Heather C. Mefford, Elaine Pereira, Han G. Brunner, Lot Snijders Blok, E. Lopez-Rangel, Rob P.W. Rouhl, Anya Revah-Politi, Bertrand Isidor, Mathilde Pacault, Constance T. R. M. Stumpel, E. Martina Bebin, Dana Craiu, Aida Telegrafi, Marlies Kempers, Jolien Roovers, Erin L. Heinzen, Candace T. Meyers, D Barca, Tania Djémié, Nicholas Stong, Zsuzsanna Siegler, Maureen S. Mulhern, Johannes R. Lemke, Tristan T. Sands, Natalie Lippa, Nicolette S. den Hollander, Danielle McBrian, Ellen van Binsbergen, Sarah Weckhuysen, Mariëtte J.V. Hoffer, CAUSES Study, EuroEPINOMICS-RES-MAE Working Grp, MUMC+: DA KG Polikliniek (9), Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA Klinische Genetica (5), Klinische Neurowetenschappen, RS: MHeNs - R1 - Cognitive Neuropsychiatry and Clinical Neuroscience, MUMC+: MA Med Staf Spec Neurologie (9), MUMC+: DA KG Lab Centraal Lab (9), Columbia University Medical Center (CUMC), Columbia University [New York], Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], Radboud University Medical Center [Nijmegen], Donders Institute for Brain, Cognition and Behaviour, Radboud university [Nijmegen], GeneDx [Gaithersburg, MD, USA], 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), 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 Bourgogne Franche-Comté [COMUE] (UBFC), Service de génétique [Angers], Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Department of Human Genetics, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium, University of Antwerp (UA), University of Medicine and Pharmacy 'Carol Davila' Bucharest (UMPCD), Dpt de l'Enfant et de l'Adolescent, Neuropédiatrie [Genève], Hôpitaux Universitaires de Genève (HUG), University Medical Center [Utrecht], Department of Medical Genetics, Department of Medicine, Karolinska Institutet [Stockholm], Service de génétique médicale - Unité de génétique clinique [Nantes], Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), and Centre hospitalier universitaire de Nantes (CHU Nantes)

Subjects
Male, 0301 basic medicine, Carrier Proteins/genetics, Candidate gene, Disease, Neurodevelopmental Disorders/genetics, Epilepsy, 0302 clinical medicine, Nerve Tissue Proteins/genetics, Child, Atonic seizure, Genetics, ddc:618, Phenotype, Neurology, Child, Preschool, Epilepsy, Generalized, Female, NEUROBEACHIN, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Adolescent, Genotype, Generalized/genetics, Nerve Tissue Proteins, Biology, PATIENT, Article, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, medicine, Journal Article, Humans, Generalized epilepsy, AUTISM, Preschool, Gene, SPECTRUM, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], DELETION, NBEA encodes neurobeachin, medicine.disease, FRAMEWORK, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Neurodevelopmental Disorders, DE-NOVO MUTATIONS, Mutation, Autism, Neurology (clinical), Human medicine, Carrier Proteins, 030217 neurology & neurosurgery
Abstract

NBEA is a candidate gene for autism, and de novo variants have been reported in neurodevelopmental disease (NDD) cohorts. However, NBEA has not been rigorously evaluated as a disease gene, and associated phenotypes have not been delineated. We identified 24 de novo NBEA variants in patients with NDD, establishing NBEA as an NDD gene. Most patients had epilepsy with onset in the first few years of life, often characterized by generalized seizure types, including myoclonic and atonic seizures. Our data show a broader phenotypic spectrum than previously described, including a myoclonic-astatic epilepsy-like phenotype in a subset of patients. Ann Neurol 2018;84:796-803

Published
2018

11. In utero seizures revealing dentato-olivary dysplasia caused by SCN2A mutation

Author

Dominique Carles, Christophe Pécheux, Gwenaëlle André, Fanny Sauvestre, Bernard Broussin, Caroline Lacoste, Laurent Villard, Fanny Pelluard, Sébastien Moutton, Nada Houcinat, Annie Laquerrière, Catherine Badens, Florent Marguet, 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), Centre de référence maladie rare Thalassémie, Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)

Subjects
Pathology, medicine.medical_specialty, Histology, Encephalopathy, medicine.disease_cause, Bioinformatics, Pathology and Forensic Medicine, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Genetic linkage, Physiology (medical), medicine, Gene, ComputingMilieux_MISCELLANEOUS, Mutation, 030219 obstetrics & reproductive medicine, business.industry, medicine.disease, 3. Good health, Neurology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Dysplasia, In utero, Autism, Neurology (clinical), business, 030217 neurology & neurosurgery
Abstract

Most early-onset epileptic encephalopathies (EOEE) are caused by genetic defects. In the past, mutations, especially in genes encoding sodium channels, have been identified using linkage studies, array-CGH and more recently next-generation sequencing (NGS) [1]. Mutations in SCN2A gene have been identified in a wide variety of early-onset epileptic syndromes including benign familial neonatal infantile seizures (BFNIS) [2] and more severe forms leading to encephalopathy such as Ohtahara or West syndromes [3], epilepsy of infancy with migrating focal seizures (EIMFS) [4] and autism spectrum disorders [5]. In 2013, mutations in SCN2A gene were reported with dentato-olivary dysplasia (DOD) in a single family [6] but the link between DOD and severe EOEE needs to be confirmed [6]. This article is protected by copyright. All rights reserved.

Published
2017

12. New practical definitions for the diagnosis of autosomal recessive spastic ataxia of Charlevoix-Saguenay

Author

Rodrigue Rossignol, Isabelle Coupry, Michel Koenig, Magalie Barth, Cyril Goizet, Nadège Bellance, Dominique Bonneau, Agnès Guichet, Diana Rodriguez, Christelle M. Durand, Nada Houcinat, Julie Bouron, Sébastien Moutton, Julie Lavie, Sandra Chantot-Bastaraud, Julie Pilliod, Alexandra Durr, Karine Nguyen, Alexis Brice, Didier Hannequin, Giovanni Benard, Mathieu Anheim, Perrine Charles, Christel Thauvin-Robinet, Alexandra Afenjar, Elise Maurat, Guillaume Fromager, Patrick Berquin, Didier Lacombe, Caroline Rooryck, Dan Milea, Sylvie Forlani, Philippe Convers, Elisabeth Maillart, Christophe Verny, Stéphanie Valence, Julien Van-Gils, Fanny Mochel, Christophe Hubert, Giovanni Stevanin, Lucie Guyant-Maréchal, Lydie Burglen, and Gaetan Lesca

Subjects
Genetics, Mutation, Ataxia, Mitochondrion, Biology, medicine.disease_cause, medicine.disease, 3. Good health, Neurology, medicine, Spinocerebellar ataxia, Biomarker (medicine), Missense mutation, Neurology (clinical), medicine.symptom, Gene, Exome sequencing
Abstract

Objective Autosomal recessive spastic ataxia of Charlevoix–Saguenay (ARSACS) is caused by mutations in the SACS gene. SACS encodes sacsin, a protein whose function remains unknown, despite the description of numerous protein domains and the recent focus on its potential role in the regulation of mitochondrial physiology. This study aimed to identify new mutations in a large population of ataxic patients and to functionally analyze their cellular effects in the mitochondrial compartment. Methods A total of 321 index patients with spastic ataxia selected from the SPATAX network were analyzed by direct sequencing of the SACS gene, and 156 patients from the ATAXIC project presenting with congenital ataxia were investigated either by targeted or whole exome sequencing. For functional analyses, primary cultures of fibroblasts were obtained from 11 patients carrying either mono- or biallelic variants, including 1 case harboring a large deletion encompassing the entire SACS gene. Results We identified biallelic SACS variants in 33 patients from SPATAX, and in 5 nonprogressive ataxia patients from ATAXIC. Moreover, a drastic and recurrent alteration of the mitochondrial network was observed in 10 of the 11 patients tested. Interpretation Our results permit extension of the clinical and mutational spectrum of ARSACS patients. Moreover, we suggest that the observed mitochondrial network anomalies could be used as a trait biomarker for the diagnosis of ARSACS when SACS molecular results are difficult to interpret (ie, missense variants and heterozygous truncating variant). Based on our findings, we propose new diagnostic definitions for ARSACS using clinical, genetic, and cellular criteria. Ann Neurol 2015;78:871–886

Published
2015

13. Homozygous 16p13.11 duplication associated with mild intellectual disability and urinary tract malformations in two siblings born from consanguineous parents

Author

Benoit Arveiler, Jérôme Toutain, Dorothée Cailley, Sébastien Moutton, Didier Lacombe, Caroline Rooryck, Nada Houcinat, B. Llanas, and C. Combe

Subjects
Adult, Male, Parents, Pediatrics, medicine.medical_specialty, DNA Copy Number Variations, Urinary system, Consanguinity, Intellectual Disability, Chromosome Duplication, Gene duplication, Intellectual disability, Genetics, Humans, Medicine, Copy-number variation, Urinary Tract, Genetics (clinical), Comparative Genomic Hybridization, Kidney, business.industry, Siblings, Homozygote, Infant, Newborn, Infant, Chronic renal disease, medicine.disease, Phenotype, Pedigree, medicine.anatomical_structure, Female, business, Chromosomes, Human, Pair 16, Cohort study
Abstract

The use of array-comparative genomic hybridization (array-CGH) in routine clinical work has allowed the identification of many new copy number variations (CNV). The 16p13.11 duplication has been implicated in various congenital anomalies and neurodevelopmental disorders, but it has also been identified in healthy individuals. We report a clinical observation of two brothers from related parents each carrying a homozygous 16p13.11 duplication. The propositus had mild intellectual disability and posterior urethral valves with chronic renal disease. His brother was considered a healthy child with only learning disabilities and poor academic performances. However, a routine medical examination at 25-years-old revealed a mild chronic renal disease and ureteropelvic junction obstruction. Furthermore, the father presented with a unilateral renal agenesis, thus it seemed that a “congenital anomalies of kidney and urinary tract” (CAKUT) phenotype segregated in this family. This may be related to the duplication, but we cannot exclude the involvement of additional genetic or non-genetic factors in the urological phenotype. Several cohort studies showed association between this chromosomal imbalance and different clinical manifestations, but rarely with CAKUT. The duplication reported here was similar to the larger one of 3.4 Mb previously described versus the more common of 1.6 Mb. It encompassed at least 11 known genes, including the five ohnologs previously identified. Our observation, in addition to expanding the clinical spectrum of the duplication provides further support to understanding the underlying pathogenic mechanism. © 2015 Wiley Periodicals, Inc.

Published
2015

14. 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

15. Diagnostic approach to neurotransmitter monoamine disorders: experience from clinical, biochemical, and genetic profiles

Author

Alice, Kuster, Jean-Baptiste, Arnoux, Magalie, Barth, Delphine, Lamireau, Nada, Houcinat, Cyril, Goizet, Bérénice, Doray, Stéphanie, Gobin, Manuel, Schiff, Aline, Cano, Daniel, Amsallem, Christine, Barnerias, Boris, Chaumette, Marion, Plaze, Abdelhamid, Slama, Christine, Ioos, Isabelle, Desguerre, Anne-Sophie, Lebre, Pascale, de Lonlay, Laurence, Christa, Jean-François, Benoist, Physiopathologie des Adaptations Nutritionnelles (PhAN), Institut National de la Recherche Agronomique (INRA)-Université de Nantes (UN), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Université de Bordeaux (UB), Genetic Department, Institut de l'élevage (IDELE), AP-HP Hôpital universitaire Robert-Debré [Paris], Hôpital de la Timone [CHU - APHM] (TIMONE), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Centre Hospitalier Sainte Anne [Paris], AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Hôpital Raymond Poincaré [AP-HP], and Université de Reims Champagne-Ardenne (URCA)

Subjects
0301 basic medicine, Oncology, Genetic Markers, medicine.medical_specialty, Neurotransmitter disorders, DNA Mutational Analysis, Pharmacology, 03 medical and health sciences, 0302 clinical medicine, Predictive Value of Tests, ATP1A3, Internal medicine, Genetics, Medicine, Humans, Biogenic Monoamines, Genetic Predisposition to Disease, Registries, Genetics (clinical), Dopamine transporter, Retrospective Studies, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, biology, business.industry, Gene Expression Profiling, Brain Diseases, Metabolic, Inborn, Prognosis, 3. Good health, QDPR, 030104 developmental biology, Monoamine neurotransmitter, Phenotype, Methylenetetrahydrofolate reductase, Primary and secondary diagnoses, dup, Mutation, Etiology, biology.protein, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], SDHD, business, 030217 neurology & neurosurgery, Biomarkers
Abstract

International audience; Background and aim To improve the diagnostic work‐up of patients with diverse neurological diseases, we have elaborated specific clinical and CSF neurotransmitter patterns. Methods Neurotransmitter determinations in CSF from 1200 patients revealed abnormal values in 228 (19%) cases. In 54/228 (24%) patients, a final diagnosis was identified. Results We have reported primary (30/54, 56%) and secondary (24/54, 44%) monoamine neurotransmitter disorders. For primary deficiencies, the most frequently mutated gene was DDC (n = 9), and the others included PAH with neuropsychiatric features (n = 4), PTS (n = 5), QDPR (n = 3), SR (n = 1), and TH (n = 1). We have also identified mutations in SLC6A3, FOXG1 (n = 1 of each), MTHFR (n = 3), FOLR1, and MTHFD (n = 1 of each), for dopamine transporter, neuronal development, and folate metabolism disorders, respectively. For secondary deficiencies, we have identified POLG (n = 3), ACSF3 (n = 1), NFU1, and SDHD (n = 1 of each), playing a role in mitochondrial function. Other mutated genes included: ADAR, RNASEH2B, RNASET2, SLC7A2‐IT1 A/B lncRNA, and EXOSC3 involved in nuclear and cytoplasmic metabolism; RanBP2 and CASK implicated in post‐traductional and scaffolding modifications; SLC6A19 regulating amino acid transport; MTM1, KCNQ2 (n = 2), and ATP1A3 playing a role in nerve cell electrophysiological state. Chromosome abnormalities, del(8)(p23)/dup(12) (p23) (n = 1), del(6)(q21) (n = 1), dup(17)(p13.3) (n = 1), and non‐genetic etiologies (n = 3) were also identified. Conclusion We have classified the final 54 diagnoses in 11 distinctive biochemical profiles and described them through 20 clinical features. To identify the specific molecular cause of abnormal NT profiles, (targeted) genomics might be used, to improve diagnosis and allow early treatment of complex and rare neurological genetic diseases.

Published
2017

16. 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

17. A novel FTL mutation responsible for neuroferritinopathy with asymmetric clinical features and brain anomalies

Author

Violaine Plante-Bordeneuve, Cyril Goizet, J.-M. Trocello, Emilie Wenisch, Pierre Brugières, Patricia Fergelot, Didier Lacombe, Vincent Larue, Fabienne Clot, Benoit Arveiler, Sébastien Moutton, and Nada Houcinat

Subjects
Dystonia, Neurology, business.industry, Neurodegeneration with brain iron accumulation, Mutation (genetic algorithm), Medicine, Neuroferritinopathy, Neurology (clinical), Geriatrics and Gerontology, business, medicine.disease, Neuroscience
Published
2014

18. Otopalatodigital spectrum disorders: refinement of the phenotypic and mutational spectrum

Author

Pierre Sarda, Guilhem Solé, Fabienne Giuliano, Cyril Goizet, Marie-Ange Delrue, Eva-Lena Stattin, Patricia Fergelot, Nada Houcinat, Hubert Journel, Jacqueline Vigneron, Elisabeth Sarrazin, Benoit Arveiler, S. Deves, Laurence Faivre, Albert David, Clarisse Baumann, Martine Le Merrer, Caroline Abadie, Caroline Rooryck, Elodie Guerineau, Sophie Naudion, Marie-Laure Vuillaume, Nicolas Chassaing, Julie Bouron, Sébastien Moutton, Isabelle Coupry, David Geneviève, Marie-Pierre Cordier, Julie Deforges, Christine Francannet, Didier Lacombe, Danielle Leclair, André Mégarbané, Christophe Hubert, Service de génétique médicale, Université de Bordeaux (UB)-CHU Bordeaux [Bordeaux]-Groupe hospitalier Pellegrin, Maladies rares, génétique et métabolisme / Rare Diseases, Genetics and Metabolism, École de sage femme - Groupe hospitalier Pellegrin - CHU de Bordeaux-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Génomique Fonctionnelle Bordeaux [Bordeaux] (CGFB), Institut Polytechnique de Bordeaux-Université de Bordeaux Ségalen [Bordeaux 2], Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Hospices Civils de Lyon (HCL), Service de neurologie [Bordeaux], CHU Bordeaux [Bordeaux]-Groupe hospitalier Pellegrin, Service de Génétique Médicale [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de génétique médicale - Unité de génétique clinique [Nantes], Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), Département de génétique médicale, maladies rares et médecine personnalisée [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Dpt génétique médicale [CHU Nice], Centre Hospitalier Universitaire de Nice (CHU Nice), Centre hospitalier Bretagne Atlantique (Morbihan) (CHBA), Arabian Gulf University, 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), Unité différenciation épidermique et auto-immunité rhumatoïde (UDEAR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de génétique médicale [Toulouse], CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], Service de Génétique Médicale [CHU Clermont-Ferrand], CHU Estaing [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Hôpital Pierre Zobda-Quitman [CHU de la Martinique], CHU de la Martinique [Fort de France], Service de Génétique Médicale [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service de médecine physique et réadaptation [CHU Raymond-Poincaré], Hôpital Raymond Poincaré [AP-HP], AP-HP Hôpital universitaire Robert-Debré [Paris], Institut National de la Santé et de la Recherche Médicale (INSERM)-École de sage femme - Groupe hospitalier Pellegrin - CHU de Bordeaux, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Necker - Enfants Malades [AP-HP], Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de génétique médicale, maladies rares et médecine personnalisée [CHRU de Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre Hospitalier Bretagne Atlantique [Vannes], Service de génétique médicale [Clermont-Ferrand], CHU Clermont-Ferrand, and AP-HP Hôpital Raymond Poincaré [Garches]

Subjects
0301 basic medicine, Proband, Male, MESH: Sequence Analysis, DNA, 030105 genetics & heredity, Bioinformatics, medicine.disease_cause, Craniofacial Abnormalities, FLNA, Missense mutation, Genetics (clinical), Genetics, MESH: Osteochondrodysplasias / genetics, Mutation, MESH: Hand Deformities, Congenital / genetics, Exons, MESH: Amino Acid Substitution, Pedigree, Phenotype, MESH: Facies, Statistical genetics, Medical genetics, Female, MESH: Osteochondrodysplasias / diagnosis, MESH: Genetic Association Studies, Hand Deformities, Congenital, medicine.medical_specialty, MESH: Pedigree, MESH: Phenotype, Filamins, Biology, Osteochondrodysplasias, MESH: Craniofacial Abnormalities / diagnosis, 03 medical and health sciences, medicine, Humans, MESH: Filamins / genetics, Alleles, Genetic Association Studies, MESH: Hand Deformities, Congenital / diagnosis, MESH: Humans, MESH: Alleles, Facies, Sequence Analysis, DNA, medicine.disease, MESH: Craniofacial Abnormalities / genetics, Human genetics, MESH: Male, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Amino Acid Substitution, Dysplasia, MESH: Mutation, MESH: Exons, MESH: Female
Abstract

International audience; Otopalatodigital spectrum disorders (OPDSD) constitute a group of dominant X-linked osteochondrodysplasias including four syndromes: otopalatodigital syndromes type 1 and type 2 (OPD1 and OPD2), frontometaphyseal dysplasia, and Melnick-Needles syndrome. These syndromes variably associate specific facial and extremities features, hearing loss, cleft palate, skeletal dysplasia and several malformations, and show important clinical overlap over the different entities. FLNA gain-of-function mutations were identified in these conditions. FLNA encodes filamin A, a scaffolding actin-binding protein. Here, we report phenotypic descriptions and molecular results of FLNA analysis in a large series of 27 probands hypothesized to be affected by OPDSD. We identified 11 different missense mutations in 15 unrelated probands (n=15/27, 56%), of which seven were novel, including one of unknown significance. Segregation analyses within families made possible investigating 20 additional relatives carrying a mutation. This series allows refining the phenotypic and mutational spectrum of FLNA mutations causing OPDSD, and providing suggestions to avoid the overdiagnosis of OPD1.

Published
2015

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