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Couloigner L, Planes M, Ka C, Audebert-Bellanger S, Redon S, Benech C, Rouault K, Küry S, Peudenier S, Autret S, Gourlaouen I, Bonneau D, Odent S, Bézieau S, Gilbert-Dussardier B, Toutain A, Boland A, Deleuze JF, Le Marechal C, Le Gac G, Ferec C, Uguen K. A new case of Kaufman Oculocerebrofacial syndrome caused by two splicing variants in UBE3B and review of the literature. Clin Genet 2023; 103:377-379. [PMID: 36444497 DOI: 10.1111/cge.14270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Loïc Couloigner
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
| | - Marc Planes
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
| | - Chandran Ka
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Séverine Audebert-Bellanger
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
| | - Sylvia Redon
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | | | - Karen Rouault
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Sebastien Küry
- Service de Génétique Médicale, Nantes Université, CHU Nantes, Nantes, France
- INSERM, l'institut du thorax, Nantes Université, CHU Nantes, CNRS, Nantes, France
| | - Sylviane Peudenier
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
| | - Sandrine Autret
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | | | | | - Sylvie Odent
- Service de Génétique Clinique, CHU de Rennes, UMR6290 CNRS, Université Rennes, Rennes, France
| | - Stéphane Bézieau
- Service de Génétique Médicale, Nantes Université, CHU Nantes, Nantes, France
- INSERM, l'institut du thorax, Nantes Université, CHU Nantes, CNRS, Nantes, France
| | | | - Annick Toutain
- Service de Génétique, CHU de Tours, UMR1253 iBrain INSERM, Université de Tours, Tours, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, CEA, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, CEA, Evry, France
| | - Cédric Le Marechal
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Gérald Le Gac
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Claude Ferec
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Kevin Uguen
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
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Padhi EM, Hayeck TJ, Cheng Z, Chatterjee S, Mannion BJ, Byrska-Bishop M, Willems M, Pinson L, Redon S, Benech C, Uguen K, Audebert-Bellanger S, Le Marechal C, Férec C, Efthymiou S, Rahman F, Maqbool S, Maroofian R, Houlden H, Musunuri R, Narzisi G, Abhyankar A, Hunter RD, Akiyama J, Fries LE, Ng JK, Mehinovic E, Stong N, Allen AS, Dickel DE, Bernier RA, Gorkin DU, Pennacchio LA, Zody MC, Turner TN. Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism. Hum Genomics 2021; 15:44. [PMID: 34256850 PMCID: PMC8278787 DOI: 10.1186/s40246-021-00342-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. RESULTS We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10-3), and combined dataset (p = 1.1 × 10-4). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10-35, loss-of-function p = 2.26 × 10-13) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10-6, OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. CONCLUSIONS In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.
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Affiliation(s)
- Evin M Padhi
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA
| | - Tristan J Hayeck
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Zhang Cheng
- Center for Epigenomics, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sumantra Chatterjee
- Center for Human Genetics and Genomics, NYU School of Medicine, New York, NY, 10016, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Marjolaine Willems
- University of Montpellier, département de Génétique, maladies rares médecine personnalisée, U 1298, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Lucile Pinson
- University of Montpellier, département de Génétique, maladies rares médecine personnalisée, U 1298, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Sylvia Redon
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Caroline Benech
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Kevin Uguen
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | | | - Cédric Le Marechal
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Claude Férec
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Fatima Rahman
- Development and Behavioral Pediatrics Department, Institute of Child Health and Children Hospital, Lahore, Pakistan
| | - Shazia Maqbool
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Development and Behavioral Pediatrics Department, Institute of Child Health and Children Hospital, Lahore, Pakistan
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | | | | | | | - Riana D Hunter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Lauren E Fries
- Center for Human Genetics and Genomics, NYU School of Medicine, New York, NY, 10016, USA
| | - Jeffrey K Ng
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA
| | - Elvisa Mehinovic
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA
| | - Nick Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, 10027, USA
| | - Andrew S Allen
- Center for Statistical Genetics and Genomics, Duke University, Durham, NC, 27708, USA
- Division of Integrative Genomics, Duke University, Durham, NC, 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
| | - David U Gorkin
- Center for Epigenomics, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA.
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Guéguen P, Dupuis A, Py JY, Desprès A, Masson E, Le Marechal C, Cooper DN, Gachet C, Chen JM, Férec C. Pathogenic and likely pathogenic variants in at least five genes account for approximately 3% of mild isolated nonsyndromic thrombocytopenia. Transfusion 2020; 60:2419-2431. [PMID: 32757236 DOI: 10.1111/trf.15992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Thrombocytopenia has a variety of different etiologies, both acquired and hereditary. Inherited thrombocytopenia may be associated with other symptoms (syndromic forms) or may be strictly isolated. To date, only about half of all the familial forms of thrombocytopenia have been accounted for in terms of well-defined genetic abnormalities. However, data are limited on the nature and frequency of the underlying causative genetic variants in individuals with mild isolated nonsyndromic thrombocytopenia. STUDY DESIGN AND METHODS Thirteen known or candidate genes for isolated thrombocytopenia were included in a gene panel analysis in which targeted next-generation sequencing was performed on 448 French blood donors with mild isolated nonsyndromic thrombocytopenia. RESULTS A total of 68 rare variants, including missense, splice site, frameshift, nonsense, and in-frame variants (all heterozygous) were identified in 11 of the 13 genes screened. Twenty-nine percent (N = 20) of the variants detected were absent from both the French Exome Project and gnomAD exome databases. Using stringent criteria and an unbiased approach, we classified seven predicted loss-of-function variants (three in ITGA2B and four in TUBB1) and four missense variants (one in GP1BA, two in ITGB3 and one in ACTN1) as being pathogenic or likely pathogenic. Altogether, they were found in 13 members (approx. 3%) of our studied cohort. CONCLUSION We present the results of gene panel sequencing of known and candidate thrombocytopenia genes in mild isolated nonsyndromic thrombocytopenia. Pathogenic and likely pathogenic variants in five known thrombocytopenia genes were identified, accounting for approximately 3% of individuals with the condition.
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Affiliation(s)
- Paul Guéguen
- CHRU Brest, Brest, France.,EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France
| | - Arnaud Dupuis
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, Etablissement Français du Sang Grand Est, Unité Mixte de Recherche-S 1255, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Jean-Yves Py
- EFS Centre-Pays de la Loire, Site d'Orléans, Orléans, France
| | | | - Emmanuelle Masson
- CHRU Brest, Brest, France.,EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France
| | - Cédric Le Marechal
- CHRU Brest, Brest, France.,EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Christian Gachet
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, Etablissement Français du Sang Grand Est, Unité Mixte de Recherche-S 1255, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | | | - Claude Férec
- CHRU Brest, Brest, France.,EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France
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Loussert-Ajaka I, Damais-Cepitelli A, Zarnitsky C, Hurst JP, Le Marechal C, Manteau AC. Perte de l’Antigène RH5 (e) chez un patient suivi pour un Myélome multiple à chaînes légères lambda. Transfus Clin Biol 2018. [DOI: 10.1016/j.tracli.2018.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Redon S, Benech C, Schutz S, Despres A, Gueguen P, Le Berre P, Le Marechal C, Peudenier S, Meriot P, Parent P, Ferec C. Intragenic deletion of the WDR45
gene in a male with encephalopathy, severe psychomotor disability, and epilepsy. Am J Med Genet A 2017; 173:1444-1446. [DOI: 10.1002/ajmg.a.38180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 11/14/2016] [Accepted: 01/23/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Sylvia Redon
- Laboratoire de génétique moléculaire et d'histocompatibilité; CHRU Morvan; Brest France
- INSERM U1078; Brest France
| | - Caroline Benech
- INSERM U1078; Brest France
- Etablissement Français du Sang; Brest France
| | - Sacha Schutz
- Laboratoire de génétique moléculaire et d'histocompatibilité; CHRU Morvan; Brest France
| | - Aurore Despres
- Laboratoire de génétique moléculaire et d'histocompatibilité; CHRU Morvan; Brest France
| | - Paul Gueguen
- Laboratoire de génétique moléculaire et d'histocompatibilité; CHRU Morvan; Brest France
- INSERM U1078; Brest France
- Faculté de Médecine; UBO; Brest France
| | - Pauline Le Berre
- Laboratoire de génétique moléculaire et d'histocompatibilité; CHRU Morvan; Brest France
- INSERM U1078; Brest France
| | - Cédric Le Marechal
- Laboratoire de génétique moléculaire et d'histocompatibilité; CHRU Morvan; Brest France
- INSERM U1078; Brest France
- Etablissement Français du Sang; Brest France
- Faculté de Médecine; UBO; Brest France
| | - Sylviane Peudenier
- Service de pédiatrie et de génétique médicale; CHRU Morvan; Brest France
| | - Philippe Meriot
- Service de radiologie et d'imagerie médicale; CHRU Morvan; Brest France
| | - Philippe Parent
- Service de pédiatrie et de génétique médicale; CHRU Morvan; Brest France
| | - Claude Ferec
- Laboratoire de génétique moléculaire et d'histocompatibilité; CHRU Morvan; Brest France
- INSERM U1078; Brest France
- Etablissement Français du Sang; Brest France
- Faculté de Médecine; UBO; Brest France
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Dequeker EM, Keppens C, Egele C, Delen S, Lamy A, Lemoine A, Sabourin JC, Andrieu C, Ligtenberg M, Fetique D, Tops B, Descarpentries C, Blons H, Denoux Y, Aube C, Penault-Llorca F, Hofman P, Leroy K, Le Marechal C, Doucet L, Duranton-Tanneur V, Pedeutour F, Soubeyran I, Côté JF, Emile JF, Vignaud JM, Monhoven N, Haddad V, Laurent-Puig P, van Krieken H, Nowak F, Lonchamp E, Bellocq JP, Rouleau E. Three Rounds of External Quality Assessment in France to Evaluate the Performance of 28 Platforms for Multiparametric Molecular Testing in Metastatic Colorectal and Non-Small Cell Lung Cancer. J Mol Diagn 2016; 18:205-14. [DOI: 10.1016/j.jmoldx.2015.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/29/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022] Open
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Audrezet MP, Dabricot A, Le Marechal C, Ferec C. Validation of high-resolution DNA melting analysis for mutation scanning of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. J Mol Diagn 2008; 10:424-34. [PMID: 18687795 PMCID: PMC2518737 DOI: 10.2353/jmoldx.2008.080056] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2008] [Indexed: 01/08/2023] Open
Abstract
High-resolution melting analysis of polymerase chain reaction products for mutation scanning, which began in the early 2000s, is based on monitoring of the fluorescence released during the melting of double-stranded DNA labeled with specifically developed saturation dye, such as LC-Green. We report here the validation of this method to scan 98% of the coding sequence of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We designed 32 pairs of primers to amplify and analyze the 27 exons of the gene. Thanks to the addition of a small GC-clamp at the 5' ends of the primers, one single melting domain and one identical annealing temperature were obtained to co-amplify all of the fragments. A total of 307 DNA samples, extracted by the salt precipitation method, carrying 221 mutations and 21 polymorphisms, plus 20 control samples free from variations (confirmed by denaturing high-performance liquid chromatography analysis), was used. With the conditions described in this study, 100% of samples that carry heterozygous mutations and 60% of those with homozygous mutations were identified. The study of a cohort of 136 idiopathic chronic pancreatitis patients enabled us to prospectively evaluate this technique. Thus, high-resolution melting analysis is a robust and sensitive single-tube technique for screening mutations in a gene and promises to become the gold standard over denaturing high-performance liquid chromatography, particularly for highly mutated genes such as CFTR, and appears suitable for use in reference diagnostic laboratories.
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