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Bergougnoux A, Billet A, Ka C, Heller M, Degrugillier F, Vuillaume ML, Thoreau V, Sasorith S, Bareil C, Thèze C, Ferec C, Gac GL, Bienvenu T, Bieth E, Gaston V, Lalau G, Pagin A, Malinge MC, Dufernez F, Lemonnier L, Koenig M, Fergelot P, Claustres M, Taulan-Cadars M, Kitzis A, Reboul MP, Becq F, Fanen P, Mekki C, Audrezet MP, Girodon E, Raynal C. The multi-faceted nature of 15 CFTR exonic variations: Impact on their functional classification and perspectives for therapy. J Cyst Fibros 2022:S1569-1993(22)01423-0. [PMID: 36567205 DOI: 10.1016/j.jcf.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/30/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The majority of variants of unknown clinical significance (VUCS) in the CFTR gene are missense variants. While change on the CFTR protein structure or function is often suspected, impact on splicing may be neglected. Such undetected splicing default of variants may complicate the interpretation of genetic analyses and the use of an appropriate pharmacotherapy. METHODS We selected 15 variants suspected to impact CFTR splicing after in silico predictions on 319 missense variants (214 VUCS), reported in the CFTR-France database. Six specialized laboratories assessed the impact of nucleotide substitutions on splicing (minigenes), mRNA expression levels (quantitative PCR), synthesis and maturation (western blot), cellular localization (immunofluorescence) and channel function (patch clamp) of the CFTR protein. We also studied maturation and function of the truncated protein, consecutive to in-frame aberrant splicing, on additional plasmid constructs. RESULTS Six of the 15 variants had a major impact on CFTR splicing by in-frame (n = 3) or out-of-frame (n = 3) exon skipping. We reclassified variants into: splicing variants; variants causing a splicing defect and the impairment of CFTR folding and/or function related to the amino acid substitution; deleterious missense variants that impair CFTR folding and/or function; and variants with no consequence on the different processes tested. CONCLUSION The 15 variants have been reclassified by our comprehensive approach of in vitro experiments that should be used to properly interpret very rare exonic variants of the CFTR gene. Targeted therapies may thus be adapted to the molecular defects regarding the results of laboratory experiments.
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Affiliation(s)
- A Bergougnoux
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - A Billet
- Laboratoire STIM, Université de Poitiers, Poitiers, France
| | - C Ka
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - M Heller
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France
| | - F Degrugillier
- Université Paris-Est Créteil, INSERM, IMRB, Créteil F-94010, France
| | - M-L Vuillaume
- Génétique Moléculaire, CHU Bordeaux, Bordeaux, France
| | - V Thoreau
- Laboratoire NEUVACOD-3808, Université de Poitiers, Poitiers, France
| | - S Sasorith
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France
| | - C Bareil
- Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Thèze
- Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Ferec
- Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - G Le Gac
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - T Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France
| | - E Bieth
- Génétique Médicale, CHU Toulouse, Toulouse, France
| | - V Gaston
- Génétique Médicale, CHU Toulouse, Toulouse, France
| | - G Lalau
- Biochimie et Biologie Moléculaire, CHU Lille, Lille, France
| | - A Pagin
- Biochimie et Biologie Moléculaire, CHU Lille, Lille, France
| | - M-C Malinge
- Biochimie et Génétique, CHU Angers, Angers, France
| | - F Dufernez
- Génétique, CHU Poitiers, Poitiers, France
| | - L Lemonnier
- Association Vaincre la Mucoviscidose, Paris, France
| | - M Koenig
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - P Fergelot
- MRGM, INSERM UMR 1211 Université de Bordeaux, Bordeaux, France
| | - M Claustres
- Université de Montpellier, Montpellier, France
| | - M Taulan-Cadars
- PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - A Kitzis
- Génétique, CHU Poitiers, Poitiers, France
| | - M-P Reboul
- Génétique Moléculaire, CHU Bordeaux, Bordeaux, France
| | - F Becq
- Laboratoire STIM, Université de Poitiers, Poitiers, France
| | - P Fanen
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, Créteil F-94010, France
| | - C Mekki
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, Créteil F-94010, France
| | - M-P Audrezet
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - E Girodon
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France; INSERM U1151, Institut Necker Enfants Malades, Université de Paris, Paris, France
| | - C Raynal
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France.
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Abstract
Pathogenic variants of the CFTR gene are responsible for a broad phenotypic spectrum characterized by malfunction of some exocrine tissues, with an autosomal recessive mode of inheritance. More than 2,000 variants, distributed throughout the CFTR gene, have been identified, with different effects on the gene and protein expression and function. Genotype-phenotype correlation studies have associated severe variants with a typical multi-organ form of cystic fibrosis, while mild variants are involved in monosymptomatic or adult-onset diseases, called CFTR-related disorders. However, the interpretation of rare variants remains challenging. This review presents an overview of the epidemiology of CFTR variants worldwide and in France and describes the functional classification. Finally, some frequent cystic fibrosis-causing and mild CFTR variants are used as example to depict the molecular pathology of the CFTR locus. Finally, we give the recommendations concerning nomenclature and classification that are useful for appropriate genetic counseling. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- C Bareil
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
| | - A Bergougnoux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France; EA7402 Laboratoire de Génétique de Maladies Rares, Institut Universitaire de Recherche Clinique, Université de Montpellier, Montpellier, France..
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Sasorith S, Bareil C, Lemonnier L, Dehillotte C, Farge A, Audrezet MP, Ferec C, Girodon E, Bienvenu T, Fanen P, Mekki C, Bieth E, Gaston V, Fergelot P, Reboul MP, Dufernez F, Pagin A, Lalau G, Malinge MC, Cabet F, Bergougnoux A, Claustres M, Raynal C. WS21.3 Overview of shared benefits from the 6-year long collaboration between the French Cystic Fibrosis Registry and the CFTR-France genetics database. J Cyst Fibros 2020. [DOI: 10.1016/s1569-1993(20)30271-x] [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: 11/28/2022]
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Sasorith S, Baux D, Bergougnoux A, Paulet D, Lahure A, Bareil C, Taulan-Cadars M, Roux AF, Koenig M, Claustres M, Raynal C. The CYSMA web server: An example of integrative tool for in silico analysis of missense variants identified in Mendelian disorders. Hum Mutat 2019; 41:375-386. [PMID: 31674704 DOI: 10.1002/humu.23941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 05/10/2019] [Revised: 10/02/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022]
Abstract
Exome sequencing used for molecular diagnosis of Mendelian disorders considerably increases the number of missense variants of unclear significance, whose pathogenicity can be assessed by a variety of prediction tools. As the performance of algorithms may vary according to the datasets, complementary specific resources are needed to improve variant interpretation. As a model, we were interested in the cystic fibrosis transmembrane conductance regulator gene (CFTR) causing cystic fibrosis, in which at least 40% of missense variants are reported. Cystic fibrosis missense analysis (CYSMA) is a new web server designed for online estimation of the pathological relevance of CFTR missense variants. CYSMA generates a set of computationally derived data, ranging from evolutionary conservation to functional observations from three-dimensional structures, provides all available allelic frequencies, clinical observations, and references for functional studies. Compared to software classically used in analysis pipelines on a dataset of 141 well-characterized missense variants, CYSMA was the most efficient tool to discriminate benign missense variants, with a specificity of 85%, and very good sensitivity of 89%. These results suggest that such integrative tools could be adapted to numbers of genes involved in Mendelian disorders to improve the interpretation of missense variants identified in the context of diagnosis.
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Affiliation(s)
- Souphatta Sasorith
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - Damien Paulet
- EA 7402, Université de Montpellier, Montpellier, France
| | - Alan Lahure
- EA 7402, Université de Montpellier, Montpellier, France
| | - Corinne Bareil
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | | | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - Michel Koenig
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | | | - Caroline Raynal
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
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Bareil C, Sasorith S, Lemattre C, Ducharlet J, Baux D, Varilh J, Altieri JP, Stremler-le-Bel N, Sermet I, Sands D, Girodon E, Audrézet MP, Koenig M, Claustres M, Taulan-Cadars M, Raynal C, Bergougnoux A. P012 CFTR-NGS, an expanded version of the CFTR-France database for the interpretation of whole CFTR next generation sequencing data. J Cyst Fibros 2019. [DOI: 10.1016/s1569-1993(19)30307-8] [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: 10/26/2022]
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Bergougnoux A, Bareil C, Thèze C, Sasorith S, Audrézet MP, Férec C, Bienvenu T, Girodon E, Heller M, Fanen P, Mekki C, Bieth E, Fergelot P, Gaston V, Reboul MP, Winter ML, Kitzis A, Thoreau V, Becq F, Lalau G, Pagin A, Malinge MC, Lemonnier L, Koenig M, Claustres M, Raynal C. WS17.1 The multi-faceted nature of CFTR exonic mutations: impact on their functional classification. J Cyst Fibros 2018. [DOI: 10.1016/s1569-1993(18)30214-5] [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: 11/17/2022]
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Claustres M, Thèze C, des Georges M, Baux D, Girodon E, Bienvenu T, Audrezet MP, Dugueperoux I, Férec C, Lalau G, Pagin A, Kitzis A, Thoreau V, Gaston V, Bieth E, Malinge MC, Reboul MP, Fergelot P, Lemonnier L, Mekki C, Fanen P, Bergougnoux A, Sasorith S, Raynal C, Bareil C. CFTR-France, a national relational patient database for sharing genetic and phenotypic data associated with rare CFTR variants. Hum Mutat 2017; 38:1297-1315. [PMID: 28603918 DOI: 10.1002/humu.23276] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [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: 04/04/2017] [Revised: 05/31/2017] [Accepted: 06/04/2017] [Indexed: 11/09/2022]
Abstract
Most of the 2,000 variants identified in the CFTR (cystic fibrosis transmembrane regulator) gene are rare or private. Their interpretation is hampered by the lack of available data and resources, making patient care and genetic counseling challenging. We developed a patient-based database dedicated to the annotations of rare CFTR variants in the context of their cis- and trans-allelic combinations. Based on almost 30 years of experience of CFTR testing, CFTR-France (https://cftr.iurc.montp.inserm.fr/cftr) currently compiles 16,819 variant records from 4,615 individuals with cystic fibrosis (CF) or CFTR-RD (related disorders), fetuses with ultrasound bowel anomalies, newborns awaiting clinical diagnosis, and asymptomatic compound heterozygotes. For each of the 736 different variants reported in the database, patient characteristics and genetic information (other variations in cis or in trans) have been thoroughly checked by a dedicated curator. Combining updated clinical, epidemiological, in silico, or in vitro functional data helps to the interpretation of unclassified and the reassessment of misclassified variants. This comprehensive CFTR database is now an invaluable tool for diagnostic laboratories gathering information on rare variants, especially in the context of genetic counseling, prenatal and preimplantation genetic diagnosis. CFTR-France is thus highly complementary to the international database CFTR2 focused so far on the most common CF-causing alleles.
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Affiliation(s)
- Mireille Claustres
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Corinne Thèze
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Marie des Georges
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Emmanuelle Girodon
- Service de Génétique et Biologie Moléculaires, Groupe Hospitalier Cochin-Broca-Hotel Dieu, Paris, France
| | - Thierry Bienvenu
- Service de Génétique et Biologie Moléculaires, Groupe Hospitalier Cochin-Broca-Hotel Dieu, Paris, France
| | - Marie-Pierre Audrezet
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Ingrid Dugueperoux
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Guy Lalau
- Centre de Biologie Pathologie Génétique, Centre Hospitalier Régional Universitaire, Lille, France
| | - Adrien Pagin
- Centre de Biologie Pathologie Génétique, Centre Hospitalier Régional Universitaire, Lille, France
| | - Alain Kitzis
- Département de Génétique, Centre Hospitalier Universitaire, Poitiers, France
| | - Vincent Thoreau
- Département de Génétique, Centre Hospitalier Universitaire, Poitiers, France
| | - Véronique Gaston
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Toulouse, France
| | - Eric Bieth
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Toulouse, France
| | - Marie-Claire Malinge
- Département de Biochimie Génétique, Institut de Biologie en Santé, Centre Hospitalier Universitaire, Angers, France
| | - Marie-Pierre Reboul
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Régional Universitaire, Bordeaux, France
| | - Patricia Fergelot
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux, France
| | - Lydie Lemonnier
- Registre français de la mucoviscidose, Vaincre la Mucoviscidose, Paris, France
| | - Chadia Mekki
- Laboratoire de Génétique, Hôpital Henri Mondor, Créteil, France
| | - Pascale Fanen
- Laboratoire de Génétique, Hôpital Henri Mondor, Créteil, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Souphatta Sasorith
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Caroline Raynal
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Corinne Bareil
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
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Sasorith S, Baux D, Bareil C, Bergougnoux A, Colomb-Jung V, Thèze C, Audrézet MP, Férec C, Bienvenu T, Girodon E, Fanen P, Mekki C, Bieth E, Gaston V, Fergelot P, Reboul MP, Kitzis A, Lalau G, Pagin A, Malinge MC, Claustres M, Raynal C. WS15.1 CysMA, a new tool for the interpretation of rare CFTR missense variants. J Cyst Fibros 2017. [DOI: 10.1016/s1569-1993(17)30243-6] [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: 11/28/2022]
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Colomb S, Bareil C, Baccino E, Berthet JP, Knabe L, Vachier I, Bourdin A. LIFE BEYOND LIFE - An Easy Way to Derive Lung Fibroblasts from Cadavers. J Forensic Sci 2017; 62:1339-1344. [PMID: 28185266 DOI: 10.1111/1556-4029.13445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/17/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 11/28/2022]
Abstract
Several protocols have illustrated the possibility of deriving cells, such as fibroblasts, from different organs. These techniques generally concern organs sampled from living persons, but have already been described for cadavers, especially concerning the skin and tendons. We present, for the first time, an easy way to derive pulmonary fibroblasts from a lung tissue sampled from a cadaver and directly culture plated. The fibroblast output was checked daily. We obtained lung fibroblasts from 3 (60%) cadavers and 2 (100%) living persons. The fibroblast output took about 3 days for cells from living persons and took up to 39 days for those from cadavers. We did not clearly identify any parameters that could explain these differences. Nevertheless, these derived cells had the same features as the source cells, especially in terms of morphology and proliferation, and could potentially be used in different research domains such as forensic or regeneration medicine.
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Affiliation(s)
- Sophie Colomb
- Emergency Pole, Forensic Medicine Department, Montpellier University Hospital, 371 Avenue du Doyen Gaston Giraud, Montpellier, 34285, France
| | - Corinne Bareil
- Molecular Genetics Laboratory - IURC, Montpellier University Hospital, 641 Avenue du Doyen Gaston Giraud, Montpellier, 34093, France
| | - Eric Baccino
- Emergency Pole, Forensic Medicine Department, Montpellier University Hospital, 371 Avenue du Doyen Gaston Giraud, Montpellier, 34285, France
| | - Jean-Philippe Berthet
- Heart-Lung Pole, Cardiac, Thoracic and Vascular Surgery, Montpellier University Hospital, 375 Avenue du Doyen Gaston Giraud, Montpellier, 34295, France
| | - Lucie Knabe
- Heart-Lung Pole, Department of Lung Diseases and Addictology, Montpellier University Hospital, 375 Avenue du Doyen Gaston Giraud, Montpellier, 34295, France
| | - Isabelle Vachier
- Heart-Lung Pole, Department of Lung Diseases and Addictology, Montpellier University Hospital, 375 Avenue du Doyen Gaston Giraud, Montpellier, 34295, France
| | - Arnaud Bourdin
- Heart-Lung Pole, Department of Lung Diseases and Addictology, Montpellier University Hospital, 375 Avenue du Doyen Gaston Giraud, Montpellier, 34295, France
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Bareil C, Lemonnier L, Dehillotte C, Colomb-Jung V, Thèze C, Audrézet MP, Férec C, Bienvenu T, Girodon E, Fanen P, Mekki C, Bieth E, Gaston V, Fergelot P, Reboul MP, Kitzis A, Lalau G, Pagin A, Malinge MC, Raynal C, Claustres M. 4 Valuable collaboration between a molecular CFTR database and a national CF registry: the French experience. J Cyst Fibros 2016. [DOI: 10.1016/s1569-1993(16)30244-2] [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: 11/26/2022]
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Guissart C, Debant V, Desgeorges M, Bareil C, Raynal C, Toga C, Pritchard V, Koenig M, Claustres M, Vincent MC. Non-invasive prenatal diagnosis of monogenic disorders: an optimized protocol using MEMO qPCR with miniSTR as internal control. Clin Chem Lab Med 2015; 53:205-15. [PMID: 25274949 DOI: 10.1515/cclm-2014-0501] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/02/2014] [Indexed: 11/15/2022]
Abstract
BACKGROUND Analysis of circulating cell-free fetal DNA (cffDNA) in maternal plasma is very promising for early diagnosis of monogenic diseases. However, this approach is not yet available for routine use and remains technically challenging because of the low concentration of cffDNA, which is swamped by the overwhelming maternal DNA. METHODS To make clinical applications more readily accessible, we propose a new approach based on mutant enrichment with 3'-modified oligonucleotides (MEMO) PCR along with real-time PCR to selectively amplify from the maternal blood the paternally inherited fetal allele that is not present in the maternal genome. RESULTS The first proof of concept of this strategy was displayed for cystic fibrosis by the accuracy of our detection of the p.Gly542* mutation used as the initial developmental model. Subsequently, a retrospective study of plasmas originating from two pregnant women carrying a fetus with private mutation confirmed the effectiveness of our method. We confirmed the presence of cffDNA in the studied samples by the identification of a tri-allelic DNA profile using a miniSTR kit. CONCLUSIONS This new non-invasive prenatal diagnosis test offers numerous advantages over current methods: it is simple, cost effective, time efficient and does not require complex equipment or bioinformatics settings. Moreover, our assays for different private mutations demonstrate the viability of this approach in clinical settings for monogenic disorders.
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Raynal C, Guittard C, Bergougnoux A, Aufray M, Taulan M, Chiron R, Bareil C, Claustres M, des Georges M. 11 A new multiplex PCR method for the quantification of aberrant transcripts from nasal epithelial cells of patients. J Cyst Fibros 2013. [DOI: 10.1016/s1569-1993(13)60154-x] [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: 10/26/2022]
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13
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Raynal C, Baux D, Theze C, Bareil C, Taulan M, Roux AF, Claustres M, Tuffery-Giraud S, des Georges M. A classification model relative to splicing for variants of unknown clinical significance: application to the CFTR gene. Hum Mutat 2013; 34:774-84. [PMID: 23381846 DOI: 10.1002/humu.22291] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/29/2013] [Indexed: 12/24/2022]
Abstract
Molecular diagnosis of cystic fibrosis and cystic fibrosis transmembrane regulator (CFTR)-related disorders led to the worldwide identification of nearly 1,900 sequence variations in the CFTR gene that consist mainly of private point mutations and small insertions/deletions. Establishing their effect on the function of the encoded protein and therefore their involvement in the disease is still challenging and directly impacts genetic counseling. In this context, we built a decision tree following the international guidelines for the classification of variants of unknown clinical significance (VUCS) in the CFTR gene specifically focused on their consequences on splicing. We applied general and specific criteria, including comprehensive review of literature and databases, familial genetics data, and thorough in silico studies. This model was tested on 15 intronic and exonic VUCS identified in our cohort. Six variants were classified as probably nonpathogenic considering their impact on splicing and eight as probably pathogenic, which include two apparent missense mutations. We assessed the validity of our method by performing minigenes studies and confirmed that 93% (14/15) were correctly classified. We provide in this study a high-performance method that can play a full role in interpreting the results of molecular diagnosis in emergency context, when functional studies are not achievable.
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Affiliation(s)
- Caroline Raynal
- CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, Montpellier, France.
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14
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Theze C, Bareil C, Audrézet MP, Duguépéroux I, Férec C, Girodon E, de Becdelièvre A, Bienvenu T, Malinge MC, Reboul MP, Fergelot P, Lalau G, Fresquet F, Kitzis A, Gaston V, Bieth E, Claustres M, Des Georges M. WS8.5 Help for the interpretation of unclassified variants: example of the UMD-CFTR-France Locus Specific Database. J Cyst Fibros 2012. [DOI: 10.1016/s1569-1993(12)60054-x] [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: 10/28/2022]
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15
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Raynal C, Baux D, Thèze C, Bareil C, Roux A, Tuffery-Giraud S, Claustres M, Des Georges M. WS8.6 Decision algorithm and scoring method for the classification of variants of unknown clinical significance in the CFTR gene. J Cyst Fibros 2012. [DOI: 10.1016/s1569-1993(12)60055-1] [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: 10/28/2022]
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16
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Bareil C, Thèze C, Béroud C, Hamroun D, Guittard C, René C, Paulet D, Georges MD, Claustres M. UMD-CFTR: A database dedicated to CF and CFTR-related disorders. Hum Mutat 2010; 31:1011-9. [DOI: 10.1002/humu.21316] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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Bareil C, Thèze C, Audrezet MP, Bienvenu T, Girodon E, Gaston V, Reboul MP, Fresquet F, Leclerc J, Malinge MC, des Georges M, Claustres M. UMD-CFTR-France: a model of national database for collection and analysis of extensive molecular data in CF and CFTR-related diseases (CFTR-RD). J Cyst Fibros 2010. [DOI: 10.1016/s1569-1993(10)60440-7] [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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18
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Barat-Houari M, Nguyen K, Bernard R, Fernandez C, Vovan C, Bareil C, Khau Van Kien P, Thorel D, Tuffery-Giraud S, Vasseur F, Attarian S, Pouget J, Girardet A, Lévy N, Claustres M. New multiplex PCR-based protocol allowing indirect diagnosis of FSHD on single cells: can PGD be offered despite high risk of recombination? Eur J Hum Genet 2010; 18:533-8. [PMID: 19935833 PMCID: PMC2987324 DOI: 10.1038/ejhg.2009.207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 10/01/2009] [Accepted: 10/14/2009] [Indexed: 01/23/2023] Open
Abstract
Molecular pathophysiology of facioscapulohumeral muscular dystrophy (FSHD) involves the heterozygous contraction of the number of tandemly repeated D4Z4 units at chromosome 4q35.2. FSHD is associated with a range of 1-10 D4Z4 units instead of 11-150 in normal controls. Several factors complicate FSHD molecular diagnosis, especially the cis-segregation of D4Z4 contraction with a 4qA allele, whereas D4Z4 shortening is silent both on alleles 4qB and 10q. Discrimination of pathogenic 4q-D4Z4 alleles from highly homologous 10q-D4Z4 arrays requires the use of the conventional Southern blot, which is not suitable at the single-cell level. Preimplantation genetic diagnosis (PGD) is a frequent request from FSHD families with several affected relatives. We aimed to develop a rapid and sensitive PCR-based multiplex approach on single cells to perform an indirect familial segregation study of pathogenic alleles. Among several available polymorphic markers at 4q35.2, the four most proximal (D4S2390, D4S1652, D4S2930 and D4S1523, <1.23 Mb) showing the highest heterozygote frequencies (67-91%) were selected. Five recombination events in the D4S2390-D4S1523 interval were observed among 144 meioses. In the D4S2390-D4Z4 interval, no recombination event occurred among 28 FSHD meioses. Instead, a particular haplotype segregated with both clinical and molecular status, allowing the characterization of an at-risk allele in each tested FSHD family (maximal LOD score 2.98 for theta=0.0). This indirect protocol can easily complement conventional techniques in prenatal diagnosis. Although our multiplex PCR-based approach technically fulfils guidelines for single-cell analysis, the relatively high recombination risk hampers its application to PGD.
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Affiliation(s)
- Mouna Barat-Houari
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France.
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Bareil C, Béroud C, Thèze C, Paulet D, René C, Hamroun D, des Georges M, Claustres M. UMD-CFTR: a database dedicated to CF and CFTR-related diseases. J Cyst Fibros 2009. [DOI: 10.1016/s1569-1993(09)60408-2] [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: 11/28/2022]
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20
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Bareil C, Guittard C, Altieri JP, Templin C, Claustres M, des Georges M. Comprehensive and rapid genotyping of mutations and haplotypes in congenital bilateral absence of the vas deferens and other cystic fibrosis transmembrane conductance regulator-related disorders. J Mol Diagn 2008; 9:582-8. [PMID: 17975025 DOI: 10.2353/jmoldx.2007.070040] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Available commercial kits only screen for the most common cystic fibrosis transmembrane conductance regulator (CFTR) mutations causing classic cystic fibrosis and for the Tn variant in IVS8. However, full scanning of CFTR is needed for the diagnosis of patients with cystic fibrosis or CFTR-related disorders (including congenital bilateral absence of the vas deferens) bearing rare mutations. Standard strategies for detecting point mutations rely on extensive scanning of the gene by denaturing gradient gel electrophoresis or denaturing high performance liquid chromatography, which are time-consuming. Moreover, the haplotyping of IVS8-(TG)m and Tn tracts is still challenging despite several recent improvements. We have optimized both the detection of mutations and the haplotyping of IVS8 polyvariants in developing two methods: i) a rapid and robust direct sequence analysis of all exons/flanking introns of the CFTR gene based on single condition touchdown amplification/sequencing in 96-well plates, and ii) a fluorescent assay that allows haplotyping of IVS8-(TG)mTn even without family linkage study. Combined with search for rare large rearrangements, this strategy detected 87.9% of CFTR defects in congenital bilateral absence of the vas deferens patients, a proportion considerably higher than those usually reported. These highly efficient tests, scanning each sample in a few days, greatly improve the genotyping of patients with CFTR-related symptoms and may be particularly important in emergency situations such as fetus with hyperechogenic bowel suggestive of cystic fibrosis.
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Affiliation(s)
- Corinne Bareil
- Laboratoire de Génétique Moléculaire, Institut Universitaire de Recherche Clinique, 641 av du doyen Gaston Giraud, Montpellier cedex 5, France
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21
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Del Rio M, Molina F, Bascoul-Mollevi C, Copois V, Bibeau F, Chalbos P, Bareil C, Kramar A, Salvetat N, Fraslon C, Conseiller E, Granci V, Leblanc B, Pau B, Martineau P, Ychou M. Gene expression signature in advanced colorectal cancer patients select drugs and response for the use of leucovorin, fluorouracil, and irinotecan. J Clin Oncol 2007; 25:773-80. [PMID: 17327601 PMCID: PMC2257989 DOI: 10.1200/jco.2006.07.4187] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
PURPOSE In patients with advanced colorectal cancer, leucovorin, fluorouracil, and irinotecan (FOLFIRI) is considered as one of the reference first-line treatments. However, only about half of treated patients respond to this regimen, and there is no clinically useful marker that predicts response. A major clinical challenge is to identify the subset of patients who could benefit from this chemotherapy. We aimed to identify a gene expression profile in primary colon cancer tissue that could predict chemotherapy response. PATIENTS AND METHODS Tumor colon samples from 21 patients with advanced colorectal cancer were analyzed for gene expression profiling using Human Genome GeneChip arrays U133. At the end of the first-line treatment, the best observed response, according to WHO criteria, was used to define the responders and nonresponders. Discriminatory genes were first selected by the significance analysis of microarrays algorithm and the area under the receiver operating characteristic curve. A predictor classifier was then constructed using support vector machines. Finally, leave-one-out cross validation was used to estimate the performance and the accuracy of the output class prediction rule. RESULTS We determined a set of 14 predictor genes of response to FOLFIRI. Nine of nine responders (100% specificity) and 11 of 12 nonresponders (92% sensitivity) were classified correctly, for an overall accuracy of 95%. CONCLUSION After validation in an independent cohort of patients, our gene signature could be used as a decision tool to assist oncologists in selecting colorectal cancer patients who could benefit from FOLFIRI chemotherapy, both in the adjuvant and the first-line metastatic setting.
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Affiliation(s)
- Maguy Del Rio
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 5160, Service d'Anatomie pathologique, Service d'Oncologie Digestive, Montpellier, France.
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22
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Copois V, Bibeau F, Bascoul-Mollevi C, Salvetat N, Chalbos P, Bareil C, Candeil L, Fraslon C, Conseiller E, Granci V, Mazière P, Kramar A, Ychou M, Pau B, Martineau P, Molina F, Del Rio M. Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. J Biotechnol 2006; 127:549-59. [PMID: 16945445 DOI: 10.1016/j.jbiotec.2006.07.032] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 07/21/2006] [Accepted: 07/27/2006] [Indexed: 11/24/2022]
Abstract
DNA microarray technology enables investigators to measure the expression of several 1000 mRNA species simultaneously in a biological specimen. However, the reliability of the microarray technology to detect transcriptional differences representative of the original samples is affected by the quality of the extracted RNA. Thus, it is of critical importance to standardize sample-handling protocols and to perform a quality assessment of RNA preparations. In this report, 59 human tissue samples were used to evaluate the relationships between RNA quality and gene expression. From Affymetrix GeneChip array data analysis of these samples, we compared the performance of the 28S/18S ratio, two computer methods (RIN and degradometer) and our in-house RNA quality scale (RQS) in assessing RNA quality. The optimal RNA reliability threshold was determined for each method using statistical discrimination measures. We showed that RQS, RIN and degradometer have a similar capacity to detect reliable RNA samples whereas the 28S/18S ratio leads to a misleading categorization. Furthermore, we developed a new approach, based on clustering analyses of full chip expression, to control RNA quality after hybridization experiments. The combination of these methods, allowing monitoring of RNA quality prior to and after the hybridization experiments, ensured reliable and reproducible microarray data.
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23
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des Georges M, Guittard C, Altiéri J, Templin C, Bareil C, Claustres M. 12 Rapid and reliable analysis of the CFTR locus in CBAVD patients. J Cyst Fibros 2006. [DOI: 10.1016/s1569-1993(06)80013-5] [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: 11/17/2022]
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24
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Delague V, Bareil C, Bouvagnet P, Salem N, Chouery E, Loiselet J, Mégarbané A, Claustres M. A new autosomal recessive non-progressive congenital cerebellar ataxia associated with mental retardation, optic atrophy, and skin abnormalities (CAMOS) maps to chromosome 15q24-q26 in a large consanguineous Lebanese Druze Family. Neurogenetics 2002; 4:23-7. [PMID: 12030328 DOI: 10.1007/s10048-001-0127-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Congenital cerebellar ataxias are a heterogeneous group of non-progressive disorders characterized by hypotonia and developmental delay followed by the appearance of ataxia, and often associated with dysarthria, mental retardation, and atrophy of the cerebellum. We report the mapping of a disease gene in a large inbred Lebanese Druze family, with five cases of a new form of non-progressive autosomal recessive congenital ataxia associated with optic atrophy, severe mental retardation, and structural skin abnormalities, to a 3.6-cM interval on chromosome 15q24-15q26.
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Affiliation(s)
- Valérie Delague
- Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
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25
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Delague V, Bareil C, Bouvagnet P, Salem N, Chouery E, Loiselet J, Mégarbané A, Claustres M. Nonprogressive autosomal recessive ataxia maps to chromosome 9q34-9qter in a large consanguineous Lebanese family. Ann Neurol 2001; 50:250-3. [PMID: 11506409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Congenital ataxias are a heterogeneous group of predominantly nonprogressive disorders characterized by hypotonia, developmental delay followed by the appearance of ataxia, and often associated with dysarthria, mental retardation, and atrophy of the cerebellum. We performed a genome-wide screen on a large inbred Lebanese family presenting a nonprogressive autosomal recessive congenital cerebellar ataxia associated with short stature (MIM 213200), already described by Mégarbané and colleagues. The disease locus was assigned to a 12.1 cM interval on chromosome 9q34-9qter between D9S67 and D9S312. Differential diagnosis with other hereditary ataxias linked to the same region is discussed.
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Affiliation(s)
- V Delague
- Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
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26
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Delague V, Bareil C, Bouvagnet P, Salem N, Chouery E, Loiselet J, Mégarbané A, Claustres M. Nonprogressive autosomal recessive ataxia maps to chromosome 9q34-9qter in a large consanguineous lebanese family. Ann Neurol 2001. [DOI: 10.1002/ana.1286] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bareil C, Hamel CP, Delague V, Arnaud B, Demaille J, Claustres M. Segregation of a mutation in CNGB1 encoding the beta-subunit of the rod cGMP-gated channel in a family with autosomal recessive retinitis pigmentosa. Hum Genet 2001; 108:328-34. [PMID: 11379879 DOI: 10.1007/s004390100496] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of retinal diseases leading to blindness. By performing full genome linkage analysis in a consanguineous French family affected with severe autosomal recessive RP, we have excluded linkage to known loci involved in RP and mapped a novel locus to chromosome 16q13-q21 (Zmax=2.83 at theta=0 at the D16S3089 locus). Two candidate genes KIFC3 and CNGB1 mapping to this critical interval have been screened for mutations. The CNGB1 gene, which encodes the beta-subunit of the rod cGMP-gated channel, is mutated in the family presented in this study.
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Affiliation(s)
- C Bareil
- Laboratoire de Génétique Moléculaire, IURC, and CNRS UPR 1142, Montpellier, France
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Guilbot A, Williams A, Ravisé N, Verny C, Brice A, Sherman DL, Brophy PJ, LeGuern E, Delague V, Bareil C, Mégarbané A, Claustres M. A mutation in periaxin is responsible for CMT4F, an autosomal recessive form of Charcot-Marie-Tooth disease. Hum Mol Genet 2001; 10:415-21. [PMID: 11157804 DOI: 10.1093/hmg/10.4.415] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Charcot-Marie-Tooth (CMT) disease is a heterogeneous group of inherited peripheral motor and sensory neuropathies characterized by chronic distal weakness with progressive muscular atrophy and sensory loss in the distal extremities. Inheritance can be autosomal dominant, X-linked or autosomal recessive (ARCMT). Recently, a locus responsible for a demyelinating form of ARCMT disease, named CMT4F, has been mapped on 19q13 in a large consanguineous Lebanese family. L- and S-periaxin are proteins of myelinating Schwann cells and homozygous periaxin-null mice display extensive demyelination of myelinated fibers in the peripheral nervous system, which suggests that the periaxin gene is a good candidate gene for an ARCMT disease. The human gene encoding the periaxins (PRX) was mapped to 19q13, in the CMT4F candidate interval. After characterizing the human PRX gene, we identified a nonsense R196X mutation in the Lebanese family which cosegregated with CMT. Histopathological and immunohistochemical analysis of a sural nerve biopsy of one patient revealed common features with the mouse mutant and the absence of L-periaxin from the myelin sheath. These data confirm the importance of the periaxin proteins to normal Schwann cell function and substantiate the utility of the periaxin-null mouse as a model of ARCMT disease.
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Affiliation(s)
- A Guilbot
- INSERM U289, Hôpital de la Salpêtrière, 47 Boulevard de l'Hôpital, Paris, France.
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Hamel CP, Griffoin JM, Bazalgette C, Lasquellec L, Duval PA, Bareil C, Beaufrère L, Bonnet S, Eliaou C, Marlhens F, Schmitt-Bernard CF, Tuffery S, Claustres M, Arnaud B. [Molecular genetics of pigmentary retinopathies: identification of mutations in CHM, RDS, RHO, RPE65, USH2A and XLRS1 genes]. J Fr Ophtalmol 2000; 23:985-95. [PMID: 11139690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
PURPOSE To evaluate the occurrence and inheritance of various types of pigmentary retinopathy in patients followed at the outpatient clinic in the university hospital, Montpellier, France. To characterize genes and mutations causing these conditions. METHODS Ophthalmic examination and various visual tests were performed. Mutations were sought from genomic DNA by PCR amplification of exons associated with single-strand conformation analysis and/or direct sequencing. RESULTS Among 315 patients over an 8-year period, cases of retinitis pigmentosa (63.2%), Usher's syndrome (10.2%), Stargardt's disease (5.4%), choroideremia (3.2%), Leber's congenital amaurosis (3.2%), congenital stationary night blindness (2.9%), cone dystrophy (2.5%), dominant optic atrophy (1.9%), X-linked juvenile retinoschisis (1.6%), Best's disease (1.6%), and others (4.3%) were diagnosed. In retinitis pigmentosa, inheritance could be determined in 54.2% of the cases including dominant autosomic (26.6%), recessive autosomic (22.6%), and X-linked cases (5%) while it could not be confirmed in 45.7% of the cases (simplex cases in the majority). For the 6 examined genes, mutations were found in 22 out of 182 propositus (12.1%). Analysis of phenotype-genotype correlations indicates that in retinitis pigmentosa, RDS is more frequently associated with macular involvement and retinal flecks, RHO with regional disease, and RPE65 with the great severity of the disease with some cases of Leber's congenital amaurosis. CONCLUSIONS Identification of genes may help in diagnosis and in genetic counseling, especially in simplex cases with retinitis pigmentosa. In this latter condition, molecular diagnosis will be necessary to rationalize future treatments.
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Affiliation(s)
- C P Hamel
- Laboratoire de Neurobiologie, Inserm U. 254, 71, rue de Navacelles, 34090 Montpellier.
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Delague V, Bareil C, Tuffery S, Bouvagnet P, Chouery E, Koussa S, Maisonobe T, Loiselet J, Mégarbané A, Claustres M. Mapping of a new locus for autosomal recessive demyelinating Charcot-Marie-Tooth disease to 19q13.1-13.3 in a large consanguineous Lebanese family: exclusion of MAG as a candidate gene. Am J Hum Genet 2000; 67:236-43. [PMID: 10848494 PMCID: PMC1287083 DOI: 10.1086/302980] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2000] [Accepted: 05/08/2000] [Indexed: 11/04/2022] Open
Abstract
Autosomal recessive Charcot-Marie-Tooth disease (CMT) type 4 (CMT4) is a complex group of demyelinating hereditary motor and sensory neuropathies presenting genetic heterogeneity. Five different subtypes that correspond to six different chromosomal locations have been described. We hereby report a large inbred Lebanese family affected with autosomal recessive CMT4, in whom we have excluded linkage to the already-known loci. The results of a genomewide search demonstrated linkage to a locus on chromosome 19q13.1-13.3, over an 8.5-cM interval between markers D19S220 and D19S412. A maximum pairwise LOD score of 5.37 for marker D19S420, at recombination fraction [theta].00, and a multipoint LOD score of 10.3 for marker D19S881, at straight theta = .00, strongly supported linkage to this locus. Clinical features and the results of histopathologic studies confirm that the disease affecting this family constitutes a previously unknown demyelinating autosomal recessive CMT subtype known as "CMT4F." The myelin-associated glycoprotein (MAG) gene, located on 19q13.1 and specifically expressed in the CNS and the peripheral nervous system, was ruled out as being the gene responsible for this form of CMT.
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Affiliation(s)
- Valérie Delague
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
| | - Corinne Bareil
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
| | - Sylvie Tuffery
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
| | - Patrice Bouvagnet
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
| | - Eliane Chouery
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
| | - Salam Koussa
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
| | - Thierry Maisonobe
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
| | - Jacques Loiselet
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
| | - André Mégarbané
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
| | - Mireille Claustres
- Unité de Génétique Médicale, Laboratoire de Génétique Moléculaire, Faculté de Médecine, Université Saint-Joseph, and Service de Neurologie, Hôtel Dieu de France, Beirut; Laboratoire de Génétique Moléculaire, Institut de Biologie, Montpellier, France; Laboratoire de Génétique Moléculaire Humaine, Institut Nétien, Université Claude Bernard, Lyon; and Service de Neurologie, Hôpital la Pitié Salpêtrière, Paris
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Delague V, Bareil C, Tuffery S, Bouvagnet P, Chouery E, Koussa S, Maisonobe T, Loiselet J, Mégarbané A, Claustres M. Mapping of a new locus for autosomal recessive demyelinating Charcot-Marie-Tooth disease to 19q13.1-13.3 in a large consanguineous Lebanese family: exclusion of MAG as a candidate gene. Am J Hum Genet 2000. [PMID: 10848494 DOI: 10.1086/302980/s0002-9297(07)62450-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Autosomal recessive Charcot-Marie-Tooth disease (CMT) type 4 (CMT4) is a complex group of demyelinating hereditary motor and sensory neuropathies presenting genetic heterogeneity. Five different subtypes that correspond to six different chromosomal locations have been described. We hereby report a large inbred Lebanese family affected with autosomal recessive CMT4, in whom we have excluded linkage to the already-known loci. The results of a genomewide search demonstrated linkage to a locus on chromosome 19q13.1-13.3, over an 8.5-cM interval between markers D19S220 and D19S412. A maximum pairwise LOD score of 5.37 for marker D19S420, at recombination fraction [theta].00, and a multipoint LOD score of 10.3 for marker D19S881, at straight theta = .00, strongly supported linkage to this locus. Clinical features and the results of histopathologic studies confirm that the disease affecting this family constitutes a previously unknown demyelinating autosomal recessive CMT subtype known as "CMT4F." The myelin-associated glycoprotein (MAG) gene, located on 19q13.1 and specifically expressed in the CNS and the peripheral nervous system, was ruled out as being the gene responsible for this form of CMT.
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Affiliation(s)
- V Delague
- Unité de Génétique Médicale, Faculté de Médecine, Université Saint-Joseph, Paris, France
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Bareil C, Delague V, Arnaud B, Demaille J, Hamel C, Claustres M. W179R: a novel missense mutation in the peripherin/RDS gene in a family with autosomal dominant retinitis pigmentosa. Hum Mutat 2000; 15:583-4. [PMID: 10862101 DOI: 10.1002/1098-1004(200006)15:6<583::aid-humu24>3.0.co;2-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- C Bareil
- Laboratoire de Génétique Moléculaire et CNRS UPR 1142
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Bareil C, Hamel C, Pallarès-Ruiz N, Arnaud B, Demaille J, Claustres M. Molecular analysis of the rhodopsin gene in southern France: identification of the first duplication responsible for retinitis pigmentosa, c.998999ins4. Ophthalmic Genet 1999; 20:173-82. [PMID: 10521250 DOI: 10.1076/opge.20.3.173.2282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PURPOSE Mutations in the gene encoding rhodopsin, the visual pigment in rod photoreceptors, were shown to be the most common cause of autosomal retinitis pigmentosa (RP). In order to determine the prevalence of rhodopsin alterations in southern French populations, we examined 52 unrelated patients/families with autosomal dominant RP (adRP=29), RP simplex (6), or unclassified RP (17). METHODS The full coding and flanking sequences of the rhodopsin (RHO) gene were scanned using an improved DGGE (denaturing gradient gel electrophoresis) assay, followed by sequencing of abnormal fragments. RESULTS This study revealed three RHO mutations in patients with adRP (G106R, R135W, and c.998999ins4) and a number of frequent or rare polymorphisms. No disease-causing sequence variation was found in simplex and unclassified RP pedigrees. Mutation c.998999ins4 has not been previously reported, and appears as the first duplication identified so far in the RHO gene. This frameshift mutation, which is associated with a severe RP, alters the carboxy terminus and predicts a 353-amino acid mutant rhodopsin instead of 348. DISCUSSION Our study demonstrates that rhodopsin mutations are responsible for only 10.3% of adRP in French populations living in the Mediterranean area in contrast to the 25-35% reported in other populations.
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Affiliation(s)
- C Bareil
- Laboratoire de Génétique Moléculaire, CNRS UPR 1142, Montpellier, France
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34
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Marlhens F, Griffoin JM, Bareil C, Arnaud B, Claustres M, Hamel CP. Autosomal recessive retinal dystrophy associated with two novel mutations in the RPE65 gene. Eur J Hum Genet 1998; 6:527-31. [PMID: 9801879 DOI: 10.1038/sj.ejhg.5200205] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Retinal dystrophies are a complex set of hereditary diseases of the retina that result in the degeneration of photoreceptors. Recent studies have shown that mutations in RPE65, a gene that codes for a retinal pigment epithelium (RPE)-specific protein thought to be involved in the 11-cis-retinoid metabolism, a key process in vision, cause severe, early onset retinal dystrophy. We describe two novel missense RPE65 mutations, L22P and H68Y, in a compound heterozygote with autosomal recessive retinal dystrophy. The relatively mild phenotype associated with these mutations suggests a possible link between the severity of the disease and the type of mutations in the RPE65 gene.
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Affiliation(s)
- F Marlhens
- Laboratoire de Neurobiologie de l'Audition, Plasticité Synaptique, Hôpital Gui de Chauliac, Montpellier, France
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Schmitt-Bernard CF, Bareil C, Hamel CP, Beaufrere L, Arnaud B, Claustres M, de Meeus A. [Clinical features and genetic analysis in a family with X-linked incomplete congenital stationary night blindness (CSNBi)]. J Fr Ophtalmol 1998; 21:251-6. [PMID: 9759413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE We describe particular clinical features in a three-generation family with X-linked CSNBi and present the genetic analysis. METHOD The diagnosis of CSNBi was established on clinical and electrophysiological criteria. Polymorphic DNA markers of the Xp region were analyzed by fluorescent polymerase chain reaction. RESULTS Clinical findings evidenced an atypical association of both myopia and hyperopia in the same brotherhood. The most interesting feature in this family was the observation of major worsening of the clinical shape between the first and the third generation of affected individuals. DNA analysis did not show significant linkage between the disease and markers of the Xp11-p21 region. Southern analysis did not show expansion of trinucleotide repeat CAG/CTG and CCG/CGG over the three generation. CONCLUSION Haplotypic analysis together with clinical observations allow to exclude the existence of a myopia gene closely linked to the CSNB2 locus. The clinical anticipation observed in this family does not seem to be linked with trinucleotide repeat expansion CAG/CTG or CCG/CGG.
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Beaufrère L, Tuffery S, Hamel C, Bareil C, Arnaud B, Demaille J, Claustres M. [Rapid genetic diagnosis of females carriers related to patients with choroideremia]. J Fr Ophtalmol 1998; 20:534-8. [PMID: 9499978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE By using the single strand conformation analysis to search for point mutations in the choroideremia gene, we had previously identified the first truncative mutation responsible for CHM in France. The aim of the present study was to perform a simple and nonisotopic routine test to identify carriers and non carriers in the relevant family. METHODS We used a PCR-based restriction analysis to detect the presence or absence of the mutation in the family members, as the mutation creates a restriction site in the coding sequence of the CHM gene. RESULTS We could follow the segregation of the mutation in the pedigree, and unambiguously determine the genetic status of the females. CONCLUSION When a mutation responsible for choroideremia modifies a restriction site, the PCR-restriction provides an efficient and unexpensive one-day test to detect heterozygosity in the family.
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Affiliation(s)
- L Beaufrère
- Laboratoire de Biochimie Génétique, CNRS UPR-9008, Institut de Biologie, CHU de Montpellier
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Tuffery S, Chambert S, Bareil C, Sarda P, Coubes C, Echenne B, Demaille J, Claustres M. Mutation analysis of the dystrophin gene in Southern French DMD or BMD families: from Southern blot to protein truncation test. Hum Genet 1998; 102:334-42. [PMID: 9544849 DOI: 10.1007/s004390050702] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Data from 6 years of experience in molecular diagnosis of Duchenne (DMD) and Becker (BMD) muscular dystrophy in Southern France are reported. DMD and BMD patients have been extensively analyzed for deletions and for point mutations in the dystrophin gene. By scanning the whole coding sequence as reverse-transcribed from lymphocytes or muscular RNA by the protein truncation test, we have reached a minimum of an 86% detection rate for point mutations responsible for DMD; these mutations consist of nonsense, frameshifting, and splicing mutations. Four of 12 small alterations identified in our sample are novel and described in this study. We also present an improved protocol for the automated detection of fluorescently labeled duplex polymerase chain reactions of six known intragenic microsatellites (Dys II, TG 15, STRs 44, 45, 49, and 50). Accurate sizing of the alleles at each locus was performed, and we elucidated the sequence of several repeat units. Allele frequencies at each of the six microsatellite loci and at one restriction fragment length polymorphism site (intron 16/TaqI) were defined in a sample of normal, DMD, and BMD X chromosomes from Southern France. The determination of the grandparental origin of either deletions or point mutations revealed differences depending on the type of the mutation, with most of the deletions occurring in oogenesis and most of the point mutations occurring in spermatogenesis.
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Affiliation(s)
- S Tuffery
- Laboratoire de Biochimie Génétique, CHU et CNRS ERS 155, Institut de Biologie, Montpellier, France
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Maugard C, Tuffery S, Beaufrère L, Bareil C, Claustres M. Le test de troncation des protéines (PTT) : un outil pour la détection de mutations dans l'ADN. Med Sci (Paris) 1998. [DOI: 10.4267/10608/1065] [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: 11/30/2022] Open
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Beaufrère L, Tuffery S, Hamel C, Bareil C, Arnaud B, Demaille J, Claustres M. The protein truncation test (PTT) as a method of detection for choroideremia mutations. Exp Eye Res 1997; 65:849-54. [PMID: 9441709 DOI: 10.1006/exer.1997.0392] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The predominance of truncative mutations responsible for choroideremia (CHM) led us to investigate the use of the protein truncation test (PTT) applied to lymphocyte RNA derived from affected males as a scanning method. The entire CHM coding region was reversed-transcribed in three overlapping cDNA segments (RT-PCR) which were amplified and further analysed by PTT after in vitro transcription/ translation. This strategy enabled us to detect the CHM-causative alteration in each of the four unrelated patients from southern France who were investigated. We describe three novel mutations (E177X, 323delT, 1313delTC), and report one recurrent mutation (R267X) in CHM. We believe this to be the first attempt at applying RT-PCR-PTT to CHM mutation detection.
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Affiliation(s)
- L Beaufrère
- Laboratoire de Biochimie Génétique, CNRS ERS 155, Institut de Biologie, Montpellier, France
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40
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Beaufrere L, Tuffery S, Hamel C, Bareil C, Arnaud B, Demaille J, Claustres M. An exonic polymorphism (381A/G) in the choroideremia gene. Genet Couns 1997; 8:223-5. [PMID: 9327266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
By using the single strand conformational analysis (SSCA) to search for point mutations in the choroideremia gene, we have identified a previously undescribed polymorphism within exon 5a (381A/G). We have studied the frequency of this polymorphism in a population from Southern France. The sequence variation creates a new restriction site for HhaI, allowing a convenient DNA-based genetic counseling in families in which the causal disease mutation is unknown.
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Affiliation(s)
- L Beaufrere
- Laboratoire de Biochimie Génétique, CNRS UPR-9008, Institut de Biologie, France
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Marlhens F, Bareil C, Griffoin JM, Zrenner E, Amalric P, Eliaou C, Liu SY, Harris E, Redmond TM, Arnaud B, Claustres M, Hamel CP. Mutations in RPE65 cause Leber's congenital amaurosis. Nat Genet 1997; 17:139-41. [PMID: 9326927 DOI: 10.1038/ng1097-139] [Citation(s) in RCA: 431] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Bareil C, Hamel C, Arnaud B, Demaille J, Claustres M. A complex allele (1064delTC and IVS2 + 22ins7) in the peripherin/RDS gene in retinitis pigmentosa with macular dystrophy. Ophthalmic Genet 1997; 18:129-38. [PMID: 9361310 DOI: 10.3109/13816819709057126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Because mutations in the peripherin/RDS gene have been found in retinal dystrophies involving the macula, we examined various types of macular dystrophies from southern France to characterize sequence variations that may be associated with these conditions. DNA sequence analysis of the full coding and flanking regions of the peripherin/RDS gene was performed in fifteen unrelated patients with different types of macular dystrophy, including nine with retinitis pigmentosa (RP). Of the 15 probands with macular disease, two (13.3%) were found to carry a mutation in the peripherin/RDS gene. The recurrent mutation P216S was identified in a pedigree with autosomal dominant RP. A previously unreported complex allele (1064delTC associated with IVS2 + 22ins7) that is predicted to result in the premature termination of peripherin/RDS synthesis was identified in a sporadic case of macular atrophy with RP. We also report eight novel neutral sequence variations in the peripherin/RDS gene, most of them found in the 3' untranslated part of the gene.
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Affiliation(s)
- C Bareil
- Laboratoire de Biochimie Génétique, University and Hospital of Montpellier, France
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Amtoft HW, Sørensen AB, Bareil C, Schmidt J, Luz A, Pedersen FS. Stability of AML1 (core) site enhancer mutations in T lymphomas induced by attenuated SL3-3 murine leukemia virus mutants. J Virol 1997; 71:5080-7. [PMID: 9188573 PMCID: PMC191741 DOI: 10.1128/jvi.71.7.5080-5087.1997] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Murine retrovirus SL3-3 is highly T lymphomagenic. Its pathogenic properties are determined by the transcriptional enhancer of the U3 repeat region which shows preferential activity in T cells. Within the U3 repeats, the major determinant of T-cell specificity has been mapped to binding sites for the AML1 transcription factor family (also known as the core binding factor [CBF], polyomavirus enhancer binding protein 2 [PEBP2], and SL3-3 enhancer factor 1 [SEF-1]). SL3-3 viruses with AML1 site mutations have lost a major determinant of T-cell-specific enhancer function but have been found to retain a lymphomagenic potential, although disease induction is slower than for the SL3-3 wild type. To compare the specificities and mechanisms of disease induction of wild-type and mutant viruses, we have examined lymphomas induced by mutant viruses harboring transversions of three consecutive base pairs critical to AML1 site function (B. Hallberg, J. Schmidt, A. Luz, F. S. Pedersen, and T. Grundström. J. Virol. 65:4177-4181, 1991). Our results show that the mutated AML1 sites are genetically stable during lymphomagenesis and that ecotropic provirus numbers in DNA of tumors induced by wild-type and mutant viruses fall within the same range. Moreover, proviruses were found to be integrated at the c-myc locus in similar proportions of wild-type and mutant SL3-3-induced tumors, and the mutated AML1 sites of proviruses at c-myc are unaltered. In some cases, however, including one c-myc-integrated provirus, a single-base pair change was detected in a second, weaker AML1 binding site. By DNA rearrangement analysis of the T-cell receptor beta-locus, tumors induced by the AML1 site mutants are found to be of the T-cell type. Thus, although the AML1 site mutants have weakened T-cell-specific enhancers they are T-lymphomagenic, and wild-type- and mutant-virus-induced tumor DNAs are similar with respect to the number of overall ecotropic and c-myc-integrated clonal proviruses. The SL3-3 wild-type and AML1 site mutant viruses may therefore induce disease by similar mechanisms.
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Affiliation(s)
- H W Amtoft
- Department of Molecular and Structural Biology, University of Aarhus, Aarhus C, Denmark
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Tuffery S, Bareil C, Demaille J, Claustres M. Four novel dystrophin point mutations: detection by protein truncation test and transcript analysis in lymphocytes from Duchenne muscular dystrophy patients. Eur J Hum Genet 1996; 4:143-52. [PMID: 8840114 DOI: 10.1159/000472188] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
About 30% of cases of Duchenne muscular dystrophy (DMD) result from point mutations randomly distributed in the immense dystrophin gene. As already observed for the gross rearrangements, most of the DMD point mutations identified so far give rise to truncated proteins. Here, we report results of a comprehensive search for point mutations within the dystrophin gene based on illegitimate transcript analysis by using the RT-PCR technique in combination with a method capable of selectively detecting translation-termination mutations, called the protein truncation test (PTT). The RT-PCR-PTT procedure was successful in detecting mutations in 4 out of the 6 DMD patients who were investigated. These mutations, Q2972X in exon 59, 3474insC in exon 24, delT393-G394+5 in exon/intron 3, and 2436delAG in exon 18, had not been previously described. Moreover, several alternatively spliced forms of ectopic dystrophin mRNA were characterized in normal controls or in DMD patients. Most of these differentially spliced messages consisting of exon skipping or intronic sequence insertion are reported here for the first time.
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Affiliation(s)
- S Tuffery
- Laboratoire de Biochimie Génétique, INSERM U249/CNRS UPR 9008, Institut de Biologie, Montpellier, France
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