1
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Collobert M, Bocher O, Le Nabec A, Génin E, Férec C, Moisan. S. WS03.1 New cis-regulatory elements modulate CFTR expression. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)00927-9] [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: 10/21/2022]
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2
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Guilloux CA, Marenne G, Mondot S, Lamoureux C, Billard L, Gouriou S, Vallet S, Le Berre R, Férec C, Génin E, Héry-Arnaud G. EPS4.02 Porphyromonas, a candidate biomarker for detection of Pseudomonas aeruginosa pulmonary infection in cystic fibrosis. J Cyst Fibros 2018. [DOI: 10.1016/s1569-1993(18)30254-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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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3
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Abadie MA, Trivelli X, Medina F, Duhal N, Kouach M, Linden B, Génin E, Vandewalle M, Capet F, Roussel P, Del Rosal I, Maron L, Agbossou-Niedercorn F, Michon C. Frontispiece: Gold(I)-Catalysed Asymmetric Hydroamination of Alkenes: A Silver- and Solvent-Dependent Enantiodivergent Reaction. Chemistry 2017. [DOI: 10.1002/chem.201784564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marc-Antoine Abadie
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
- ENSCL; UCCS-CCM-MOCAH (Chimie-C7) CS 90108; 59652 Villeneuve d'Ascq Cedex France
| | - Xavier Trivelli
- UGSF CNRS, UMR 8576; Université Lille Nord de France; 59655 Villeneuve d'Ascq Cedex France
| | - Florian Medina
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
- ENSCL; UCCS-CCM-MOCAH (Chimie-C7) CS 90108; 59652 Villeneuve d'Ascq Cedex France
| | - Nathalie Duhal
- Service commun de physico-chimie CUMA; Faculté de Pharmacie-Univ. Lille; 3 rue du Professeur Laguesse BP 83-59006 Lille Cedex France
| | - Mostafa Kouach
- Service commun de physico-chimie CUMA; Faculté de Pharmacie-Univ. Lille; 3 rue du Professeur Laguesse BP 83-59006 Lille Cedex France
| | - Bernhard Linden
- Linden ChroMasSpec GmbH; Auf dem Berge 25 28844 Weyhe Germany
| | - Eric Génin
- ThermoFisher Scientific; 16 avenue du Québec-silic 765 Villebon-sur-Yvette 91963 Courtaboeuf Cedex France
| | - Maxence Vandewalle
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
| | - Frédéric Capet
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
| | - Pascal Roussel
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
| | - Iker Del Rosal
- Université de Toulouse et CNRS INSA; UPS, CNRS, UMR 5215, LPCNO; 135 avenue de Rangueil 31077 Toulouse France
| | - Laurent Maron
- Université de Toulouse et CNRS INSA; UPS, CNRS, UMR 5215, LPCNO; 135 avenue de Rangueil 31077 Toulouse France
| | - Francine Agbossou-Niedercorn
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
- ENSCL; UCCS-CCM-MOCAH (Chimie-C7) CS 90108; 59652 Villeneuve d'Ascq Cedex France
| | - Christophe Michon
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
- ENSCL; UCCS-CCM-MOCAH (Chimie-C7) CS 90108; 59652 Villeneuve d'Ascq Cedex France
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4
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Le Guennec K, Quenez O, Nicolas G, Wallon D, Rousseau S, Richard AC, Alexander J, Paschou P, Charbonnier C, Bellenguez C, Grenier-Boley B, Lechner D, Bihoreau MT, Olaso R, Boland A, Meyer V, Deleuze JF, Amouyel P, Munter HM, Bourque G, Lathrop M, Frebourg T, Redon R, Letenneur L, Dartigues JF, Martinaud O, Kalev O, Mehrabian S, Traykov L, Ströbel T, Le Ber I, Caroppo P, Epelbaum S, Jonveaux T, Pasquier F, Rollin-Sillaire A, Génin E, Guyant-Maréchal L, Kovacs GG, Lambert JC, Hannequin D, Campion D, Rovelet-Lecrux A, Rovelet-Lecrux A. 17q21.31 duplication causes prominent tau-related dementia with increased MAPT expression. Mol Psychiatry 2017; 22:1119-1125. [PMID: 27956742 DOI: 10.1038/mp.2016.226] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/26/2016] [Accepted: 10/27/2016] [Indexed: 01/07/2023]
Abstract
To assess the role of rare copy number variations in Alzheimer's disease (AD), we conducted a case-control study using whole-exome sequencing data from 522 early-onset cases and 584 controls. The most recurrent rearrangement was a 17q21.31 microduplication, overlapping the CRHR1, MAPT, STH and KANSL1 genes that was found in four cases, including one de novo rearrangement, and was absent in controls. The increased MAPT gene dosage led to a 1.6-1.9-fold expression of the MAPT messenger RNA. Clinical signs, neuroimaging and cerebrospinal fluid biomarker profiles were consistent with an AD diagnosis in MAPT duplication carriers. However, amyloid positon emission tomography (PET) imaging, performed in three patients, was negative. Analysis of an additional case with neuropathological examination confirmed that the MAPT duplication causes a complex tauopathy, including prominent neurofibrillary tangle pathology in the medial temporal lobe without amyloid-β deposits. 17q21.31 duplication is the genetic basis of a novel entity marked by prominent tauopathy, leading to early-onset dementia with an AD clinical phenotype. This entity could account for a proportion of probable AD cases with negative amyloid PET imaging recently identified in large clinical series.
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Affiliation(s)
- K Le Guennec
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France
| | - O Quenez
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - G Nicolas
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - D Wallon
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - S Rousseau
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - A-C Richard
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - J Alexander
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
| | - P Paschou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
| | - C Charbonnier
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - C Bellenguez
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - B Grenier-Boley
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - D Lechner
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - M-T Bihoreau
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - R Olaso
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - A Boland
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - V Meyer
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - J-F Deleuze
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France.,Fondation Jean Dausset, Centre d'études du Polymorphisme Humain, Paris, France
| | - P Amouyel
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - H M Munter
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - G Bourque
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - M Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - T Frebourg
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - R Redon
- Inserm, UMR 1087, l'institut du thorax, CHU Nantes, Nantes, France.,CNRS, UMR 6291, Université de Nantes, Nantes, France
| | - L Letenneur
- INSERM, U1219, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - J-F Dartigues
- INSERM, U1219, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - O Martinaud
- CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - O Kalev
- Institute of Pathology and Neuropathology, Kepler University Hospital, Linz, Austria
| | - S Mehrabian
- Department of Neurology, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
| | - L Traykov
- Department of Neurology, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
| | - T Ströbel
- Institute of Neurology, Medical University Vienna, Vienna, Austria
| | - I Le Ber
- Sorbonne Universités, Inserm, CNRS, UPMC Univ Paris 06, UMR S 1127, Paris, France.,CNR-MAJ, IMMA, département des maladies du système nerveux, Hôpital Pitié-Salpêtrière, Paris, France
| | - P Caroppo
- Sorbonne Universités, Inserm, CNRS, UPMC Univ Paris 06, UMR S 1127, Paris, France.,CNR-MAJ, IMMA, département des maladies du système nerveux, Hôpital Pitié-Salpêtrière, Paris, France
| | - S Epelbaum
- Sorbonne Universités, Inserm, CNRS, UPMC Univ Paris 06, UMR S 1127, Paris, France.,CNR-MAJ, IMMA, département des maladies du système nerveux, Hôpital Pitié-Salpêtrière, Paris, France
| | - T Jonveaux
- Centre Mémoire de Ressources et de Recherche de Lorraine, CHRU Nancy Service de Gériatrie, Hôpital de Brabois, Vandoeuvre les Nancy, France.,Laboratoire INTERPSY, EA 4432, Groupe de recherche sur les Communications (GRC), Université de Lorraine, Psychologie, Nancy, France
| | - F Pasquier
- CNR-MAJ Inserm U1171, Univ Lille, CHU, Lille, France
| | | | - E Génin
- Inserm, UMR1078, CHU Brest, Université Bretagne Occidentale, Brest, France
| | - L Guyant-Maréchal
- Department of Neurology, Rouen University Hospital, Rouen, France.,Department of Neurophysiology, Rouen University Hospital, Rouen, France
| | - G G Kovacs
- Institute of Neurology, Medical University Vienna, Vienna, Austria
| | - J-C Lambert
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - D Hannequin
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - D Campion
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Research, Rouvray Psychiatric Hospital, Sotteville-lès-Rouen, France
| | - A Rovelet-Lecrux
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
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5
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Abadie MA, Trivelli X, Medina F, Duhal N, Kouach M, Linden B, Génin E, Vandewalle M, Capet F, Roussel P, Del Rosal I, Maron L, Agbossou-Niedercorn F, Michon C. Gold(I)-Catalysed Asymmetric Hydroamination of Alkenes: A Silver- and Solvent-Dependent Enantiodivergent Reaction. Chemistry 2017; 23:10777-10788. [DOI: 10.1002/chem.201701301] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Marc-Antoine Abadie
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
- ENSCL; UCCS-CCM-MOCAH (Chimie-C7) CS 90108; 59652 Villeneuve d'Ascq Cedex France
| | - Xavier Trivelli
- UGSF CNRS, UMR 8576; Université Lille Nord de France; 59655 Villeneuve d'Ascq Cedex France
| | - Florian Medina
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
- ENSCL; UCCS-CCM-MOCAH (Chimie-C7) CS 90108; 59652 Villeneuve d'Ascq Cedex France
| | - Nathalie Duhal
- Service commun de physico-chimie CUMA; Faculté de Pharmacie-Univ. Lille; 3 rue du Professeur Laguesse BP 83-59006 Lille Cedex France
| | - Mostafa Kouach
- Service commun de physico-chimie CUMA; Faculté de Pharmacie-Univ. Lille; 3 rue du Professeur Laguesse BP 83-59006 Lille Cedex France
| | - Bernhard Linden
- Linden ChroMasSpec GmbH; Auf dem Berge 25 28844 Weyhe Germany
| | - Eric Génin
- ThermoFisher Scientific; 16 avenue du Québec-silic 765 Villebon-sur-Yvette 91963 Courtaboeuf Cedex France
| | - Maxence Vandewalle
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
| | - Frédéric Capet
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
| | - Pascal Roussel
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
| | - Iker Del Rosal
- Université de Toulouse et CNRS INSA; UPS, CNRS, UMR 5215, LPCNO; 135 avenue de Rangueil 31077 Toulouse France
| | - Laurent Maron
- Université de Toulouse et CNRS INSA; UPS, CNRS, UMR 5215, LPCNO; 135 avenue de Rangueil 31077 Toulouse France
| | - Francine Agbossou-Niedercorn
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
- ENSCL; UCCS-CCM-MOCAH (Chimie-C7) CS 90108; 59652 Villeneuve d'Ascq Cedex France
| | - Christophe Michon
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois; UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide; 59000 Lille France
- ENSCL; UCCS-CCM-MOCAH (Chimie-C7) CS 90108; 59652 Villeneuve d'Ascq Cedex France
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6
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Nicolas G, Charbonnier C, Wallon D, Quenez O, Bellenguez C, Grenier-Boley B, Rousseau S, Richard AC, Rovelet-Lecrux A, Le Guennec K, Bacq D, Garnier JG, Olaso R, Boland A, Meyer V, Deleuze JF, Amouyel P, Munter HM, Bourque G, Lathrop M, Frebourg T, Redon R, Letenneur L, Dartigues JF, Génin E, Lambert JC, Hannequin D, Campion D. SORL1 rare variants: a major risk factor for familial early-onset Alzheimer's disease. Mol Psychiatry 2016; 21:831-6. [PMID: 26303663 DOI: 10.1038/mp.2015.121] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 01/22/2023]
Abstract
The SORL1 protein plays a protective role against the secretion of the amyloid β peptide, a key event in the pathogeny of Alzheimer's disease. We assessed the impact of SORL1 rare variants in early-onset Alzheimer's disease (EOAD) in a case-control setting. We conducted a whole exome analysis among 484 French EOAD patients and 498 ethnically matched controls. After collapsing rare variants (minor allele frequency ≤1%), we detected an enrichment of disruptive and predicted damaging missense SORL1 variants in cases (odds radio (OR)=5.03, 95% confidence interval (CI)=(2.02-14.99), P=7.49.10(-5)). This enrichment was even stronger when restricting the analysis to the 205 cases with a positive family history (OR=8.86, 95% CI=(3.35-27.31), P=3.82.10(-7)). We conclude that predicted damaging rare SORL1 variants are a strong risk factor for EOAD and that the association signal is mainly driven by cases with positive family history.
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Affiliation(s)
- G Nicolas
- Department of Genetics, Rouen University Hospital, Rouen, France.,Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - C Charbonnier
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - D Wallon
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - O Quenez
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - C Bellenguez
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - B Grenier-Boley
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - S Rousseau
- CNR-MAJ, Rouen University Hospital, Rouen, France
| | - A-C Richard
- CNR-MAJ, Rouen University Hospital, Rouen, France
| | - A Rovelet-Lecrux
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France
| | - K Le Guennec
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France
| | - D Bacq
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - J-G Garnier
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - R Olaso
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - A Boland
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - V Meyer
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - J-F Deleuze
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France.,Fondation Jean Dausset, Centre d'études du Polymorphisme Humain, Paris, France
| | - P Amouyel
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - H M Munter
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - G Bourque
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - M Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - T Frebourg
- Department of Genetics, Rouen University Hospital, Rouen, France.,Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France
| | - R Redon
- Inserm UMR 1087, l'institut du Thorax, CHU Nantes, Nantes, France.,CNRS, UMR 6291, Université de Nantes, Nantes, France
| | - L Letenneur
- Inserm U897, Univ Bordeaux, Bordeaux, France
| | | | - E Génin
- Inserm UMR1078, CHU Brest, Univ Bretagne Occidentale, Brest, France
| | - J-C Lambert
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - D Hannequin
- Department of Genetics, Rouen University Hospital, Rouen, France.,Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - D Campion
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Research, Rouvray Psychiatric Hospital, Sotteville-lès-Rouen, France
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7
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Scotet V, L'Hostis C, Duguépéroux I, Rault G, Frachon I, Bernard R, Parent P, Blayau M, Schmitt S, Génin E, Audrézet MP, Férec C. ePS01.3 Cascade carrier testing within CF-affected families: who makes the test and when? J Cyst Fibros 2016. [DOI: 10.1016/s1569-1993(16)30190-4] [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: 11/16/2022]
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8
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Marchal A, Génin E, Waffo-Téguo P, Bibès A, Da Costa G, Mérillon JM, Dubourdieu D. Development of an analytical methodology using Fourier transform mass spectrometry to discover new structural analogs of wine natural sweeteners. Anal Chim Acta 2015; 853:425-434. [DOI: 10.1016/j.aca.2014.10.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 10/23/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
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9
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Gómez-Pérez ML, Romero-González R, Plaza-Bolaños P, Génin E, Martínez Vidal JL, Garrido Frenich A. Wide-scope analysis of pesticide and veterinary drug residues in meat matrices by high resolution MS: detection and identification using Exactive-Orbitrap. J Mass Spectrom 2014; 49:27-36. [PMID: 24446260 DOI: 10.1002/jms.3309] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 10/31/2013] [Accepted: 11/04/2013] [Indexed: 06/03/2023]
Abstract
A multiresidue and multiclass method for the simultaneous determination of more than 350 compounds including pesticides, biopesticides and veterinary drugs in different meat matrices (beef, pork and chicken) by ultra-high performance liquid chromatography coupled to Orbitrap MS has been developed. In the present study, the determination of fragments was accomplished as an essential tool for a reliable identification of compounds using high resolution MS. To obtain these fragments, different strategies have been carried out in order to ensure an appropriate fragment assignment and identification. The analytical method is suitable for qualitative analysis, and it was also evaluated for quantitative analysis. Generic extraction conditions were optimized, obtaining adequate recovery and precision values for most of the studied analytes (>290). The limits of detection ranged from 2 to 16 µg kg(-1). Limits of quantification were 10 µg kg(-1) with the exception of few compounds with a higher value (50 or 100 µg kg(-1)). Limits of identification were also established, and they ranged from 2 to 150 µg kg(-1). This method was applied to the analysis of 18 meat samples and some veterinary drugs as enrofloxacin and sulfadiazine were detected and further identified/quantified (with triple quadrupole) in two different samples at 33 µg kg(-1) and trace levels, respectively. No pesticides were detected in the analyzed samples.
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Affiliation(s)
- María Luz Gómez-Pérez
- Research Group 'Analytical Chemistry of Contaminants', Department of Chemistry and Physics, Research Centre for Agricultural and Food Biotechnology (BITAL), University of Almeria, Agrifood Campus of International Excellence, ceiA3, E-04120, Almeria, Spain
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10
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Rifflet A, Gavalda S, Téné N, Orivel J, Leprince J, Guilhaudis L, Génin E, Vétillard A, Treilhou M. Identification and characterization of a novel antimicrobial peptide from the venom of the ant Tetramorium bicarinatum. Peptides 2012; 38:363-70. [PMID: 22960382 DOI: 10.1016/j.peptides.2012.08.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 08/29/2012] [Accepted: 08/30/2012] [Indexed: 11/21/2022]
Abstract
A novel antimicrobial peptide, named Bicarinalin, has been isolated from the venom of the ant Tetramorium bicarinatum. Its amino acid sequence has been determined by de novo sequencing using mass spectrometry and by Edman degradation. Bicarinalin contained 20 amino acid residues and was C-terminally amidated as the majority of antimicrobial peptides isolated to date from insect venoms. Interestingly, this peptide had a linear structure and exhibited no meaningful similarity with any known peptides. Antibacterial activities against Staphylococcus aureus and S. xylosus strains were evaluated using a synthetic replicate. Bicarinalin had a potent and broad antibacterial activity of the same magnitude as Melittin and other hymenopteran antimicrobial peptides such as Pilosulin or Defensin. Moreover, this antimicrobial peptide has a weak hemolytic activity compared to Melittin on erythrocytes, suggesting potential for development into an anti-infective agent for use against emerging antibiotic-resistant pathogens.
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Affiliation(s)
- Aline Rifflet
- Equipe VacBio EA 4357, PRES Université Toulouse, CUFR JF Champollion, Place de Verdun, 81012 Albi, France
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11
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Marchal A, Waffo-Téguo P, Génin E, Mérillon JM, Dubourdieu D. Identification of new natural sweet compounds in wine using centrifugal partition chromatography-gustatometry and Fourier transform mass spectrometry. Anal Chem 2011; 83:9629-37. [PMID: 22044220 DOI: 10.1021/ac202499a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sweetness contributes notably to the taste-balance of dry wines and increases during oak-barrel aging owing to the release of natural sweeteners from wood. The search for such taste-active molecules, which are sometimes present at very low concentrations in wine or other complex matrixes, requires both reliable purification tools and powerful identification techniques. Here, we report the development of an original inductive method using centrifugal partition chromatography (CPC) and sensorial analysis. This method, called CPC-gustatometry, was implemented to isolate a sweet fraction with only four compounds from a complex oak wood extract. The recently developed Fourier transform mass spectrometry (FT-MS, Orbitrap analyzer) was used jointly with two-dimensional nuclear magnetic resonance (2D (1)H and (13)C NMR) to obtain the structural elucidation of the purified compounds. The tandem mass spectrometry (MS/MS) spectra obtained with resonant and nonresonant fragmentation modes were compared, thus providing complementary information about the molecular structure. Two oleanane-type triterpenoids substituted with galloyl and glucosyl moieties were identified, one of which exhibits sweet properties. We term these compounds which have never been reported, Quercotriterpenoside I and II.
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Affiliation(s)
- Axel Marchal
- Université de Bordeaux, ISVV, EA 4577, Unité de Recherche OENOLOGIE, Villenave d'Ornon, France.
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12
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Fichou Y, Génin E, LeMaréchal C, Audrézet M, Scotet V, Férec C. 403 Estimating the age of common CFTR mutations in Brittany (western France). J Cyst Fibros 2007. [DOI: 10.1016/s1569-1993(07)60370-1] [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: 11/26/2022]
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13
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Cournu-Rebeix I, Génin E, Lesca G, Azoulay-Cayla A, Tubridy N, Noé E, Clanet M, Edan G, Clerget-Darpoux F, Sémana G, Fontaine B. Intercellular adhesion molecule-1: a protective haplotype against multiple sclerosis. Genes Immun 2003; 4:518-23. [PMID: 14551606 DOI: 10.1038/sj.gene.6364009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [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: 11/08/2022]
Abstract
Intercellular adhesion molecule-1 (ICAM-1) and its receptors are adhesion molecules that play a key role in the transmigration of inflammatory cells through the blood-brain barrier, one of the earliest events in multiple sclerosis (MS), which leads to demyelination in the central nervous system. To investigate the role of genes encoding ICAM-1 and its receptors, we used a strategy of genetic linkage and association in 439 case-parent MS families of French origin, well characterized according to HLA status and severity. We demonstrate that the genes encoding ICAM-1 receptors do not influence MS susceptibility or severity. ICAM-1 had a modest, but significant effect on MS genetic susceptibility, independent of HLA and disease severity. We observed a rare, and an as yet unreported, ICAM-1 gene haplotype defined by amino acids K469 and R241 that was never transmitted to patients suggesting a protective effect against MS in our population.
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Affiliation(s)
- I Cournu-Rebeix
- Laboratoire des affections de la myéline et des canaux ioniques musculaires-INSERM U546, Faculté de Médecine Pitié-Salpêtrière, Paris, France
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14
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Bourgain C, Génin E, Margaritte-Jeannin P, Clerget-Darpoux F. Maximum identity length contrast: a powerful method for susceptibility gene detection in isolated populations. Genet Epidemiol 2002; 21 Suppl 1:S560-4. [PMID: 11793738 DOI: 10.1002/gepi.2001.21.s1.s560] [Citation(s) in RCA: 13] [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: 11/12/2022]
Abstract
We report the results of our analysis of the Genetic Analysis Workshop 12 simulated data set. Focusing on the isolated populations, we compare the efficiency of a new method, the maximum identity length contrast statistic (MILC) with the maximum likelihood score (MLS) in a genome screen strategy. MILC is a method based on the contrast of haplotype identity between transmitted and nontransmitted haplotypes in trios. It uses information on linkage and association. We found that MILC allows the detection of a risk factor corresponding to candidate gene 1 where the MLS fails, though the same population replicates were used. Interestingly, the association between this risk factor and the disease could not have been detected with the TDT at a genome-wide level.
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Affiliation(s)
- C Bourgain
- Genetic Epidemiology Unit, INSERM U535, Bâtiment Gregory Pincus, 80 Avenue du Général Leclerc 94276 Le Kremlin-Bicêtre, France
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15
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Abstract
Comparison of polymorphic sites such as single nucleotide polymorphisms (SNPs) within a gene between cases and controls may be useful for establishing a role of this gene in disease susceptibility. The approach includes two steps: the first step is the discovery of the different SNPs within the candidate gene and the second step is the association testing per se that can be done on the entire set of sites discovered or on a subset of these sites only. Selecting a subset of sites may increase the power to detect the association with the candidate gene since a smaller number of tests would then be performed. We proposed a strategy to select sites within a candidate gene and applied it on the Genetic Analysis Workshop 12 candidate gene data. Using these selected sites, we detected an association with candidate genes 1 and 6.
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Affiliation(s)
- E Génin
- INSERM U535, Bâtiment Gregory Pincus, 80 rue du General Leclerc, 94 276 Le Kremlin-Bicêtre
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16
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Norris JM, Selinger-Leneman H, Génin E. Investigation of a candidate gene, environment, and G x E interaction using case-control and case-parent study designs. Genet Epidemiol 2002; 21 Suppl 1:S843-8. [PMID: 11793790 DOI: 10.1002/gepi.2001.21.s1.s843] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We investigated the independent contributions of a candidate gene and an environmental factor, and the presence of gene x environment (G x E) interaction, in the etiology of a disease in the Genetic Analysis Workshop (GAW) 12 problem 2 simulated data using a two-stage approach utilizing both case-control and case-parent study designs. Using the case-control design, several SNPs within candidate gene 1 (CG1) and environmental factor 1 (dichotomized using the 75th percentile as a cut-off) (EXP) were independently associated with disease status, in models adjusted for age and sex. We found evidence of gene x environment (G x E) interaction between EXP and two single-nucleotide polymorphisms (SNPs) within CG1 using the case-control design. Using the case-parent study design in the same population, we detected association between SNPs within CG1 and disease, but no G x E interaction was detected.
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Affiliation(s)
- J M Norris
- Univ. of Colorado Health Sci. Center, Department of Preventive Medicine and Biometrics, 4200 East Ninth Ave., Box C245, Denver, CO 80262, USA
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17
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Abstract
We report the results of our analyses of the Genetic Analysis Workshop 12 simulated data set, using phylogenetic methods to reconstruct the history of haplotypes. We selected candidate gene 1 and 6, drawn from the isolate population. In a first step, haplotypes were inferred using family data. In a second step, cladistic approaches were performed to select the most parsimonious trees under various conditions of character state transformation and ancestral hypotheses, in order to check whether the affected status is more frequent in some clades than in others. Sites which are synapormophies of such clades can be viewed as candidate sites for the disease susceptibility. The method seems to be efficient for the candidate gene 1, but not for the candidate gene 6. Effects of the genetic model underlying the affection status are discussed, particularly dominance, penetrance, and, in the context of this simulated data, procedure followed to generate haplotypes. These preliminary results deserve further investigations.
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Affiliation(s)
- P Darlu
- INSERM U535, Bâtiment Gregory Pincus, 80 rue du General Leclerc, 94 276 Le Kremlin-Biêctre
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18
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Valdes AM, Noble JA, Génin E, Clerget-Darpoux F, Erlich HA, Thomson G. Modeling of HLA class II susceptibility to Type I diabetes reveals an effect associated with DPB1. Genet Epidemiol 2001; 21:212-23. [PMID: 11668578 DOI: 10.1002/gepi.1030] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this report, we present evidence that the HLA class II DPB1 locus (or a locus with alleles in linkage disequilibrium with DPB1) contributes to Type I diabetes (IDDM) susceptibility in addition to the contribution of the HLA DR and DQ loci. The marker association segregation chi-square (MASC) method, which fits both genotype frequency and affected sib-pair identity-by-descent (IBD) distributions, was applied to 257 sib pairs affected with IDDM. Fitting DR-DQ as the sole HLA susceptibility loci was strongly rejected. Next, we considered the DPB1 contribution to disease susceptibility. Published reports indicate a predisposing role for alleles DPB1*0301 and DPB1*0202, including our previous stratification analyses of association data on this sample. IDDM probands were stratified into those not carrying the alleles DPB1*0301 and DPB1*0202 (group DPB1-A), and those carrying at least one copy of either allele (group DPB1-B). Both groups of probands have almost identical frequencies of DR and DQ haplotypes but significantly different IBD distributions in the subset of families with probands who do not carry the highly predisposing DR3/DR4 genotype. In these data, DPB1 (or a locus in linkage disequilibrium), in addition to DR-DQ, is involved in IDDM susceptibility and affects IBD in the HLA region. Addition of DPB1 in a genetic model of IDDM gives a better fit to the data than consideration of DR-DQ alone. Our results are consistent with previous reports implicating DPB1 in IDDM susceptibility.
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Affiliation(s)
- A M Valdes
- Department of Integrative Biology, University of California, 3060 Valley Life Sciences Building MC #3140, Berkeley, CA 94720-3140, USA
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19
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Bourgain C, Génin E, Holopainen P, Mustalahti K, Mäki M, Partanen J, Clerget-Darpoux F. Use of closely related affected individuals for the genetic study of complex diseases in founder populations. Am J Hum Genet 2001; 68:154-159. [PMID: 11102286 PMCID: PMC1234909 DOI: 10.1086/316933] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [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: 09/14/2000] [Accepted: 11/06/2000] [Indexed: 11/04/2022] Open
Abstract
We propose a method, the maximum identity length contrast (MILC) statistic, to locate genetic risk factors for complex diseases in founder populations. The MILC approach compares the identity length of parental haplotypes that are transmitted to affected offspring with the identity length of those that are not transmitted to affected offspring. Initially, the statistical properties of the method were assessed using randomly selected affected individuals with unknown relationship. Because both nuclear families with multiple affected sibs and large pedigrees are often available in founder populations, we performed simulations to investigate the properties of the MILC statistic in the presence of closely related affected individuals. The simulation showed that the use of closely related affected individuals greatly enhances the power of the statistic. For a given sample size and type I error, the use of affected sib pairs, instead of affected individuals randomly selected from the population, could increase the power by a factor of two. This increase was related to an increase of kinship-coefficient contrast between haplotype groups when closely related individuals were considered. The MILC approach allows the simultaneous use of affected individuals from a founder population and affected individuals with any kind of relationship, close or remote. We used the MILC approach to analyze the role of HLA in celiac disease and showed that the effect of HLA may be detected with the MILC approach by typing only 11 affected individuals, who were part of a single large Finnish pedigree.
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Affiliation(s)
- C Bourgain
- Unité de Recherche d'Epidémiologie Génétique, INSERM U535, 94276 Le Kremlin-Bicêtre Cedex France.
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20
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Margaritte-Jeannin P, Babron MC, Génin E, Eichenbaum-Voline S, Clerget-Darpoux F. Heterogeneity of marker allele frequencies hinders interpretation of linkage analysis: illustration on chromosome 18 markers. Genet Epidemiol 2000; 14:669-74. [PMID: 9433561 DOI: 10.1002/(sici)1098-2272(1997)14:6<669::aid-gepi20>3.0.co;2-n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [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
In the first part of our study we tested linkage with chromosome 18 markers in a sample of bipolar I sib pairs. We did not obtain evidence for linkage but showed that we could not exclude the presence of a disease locus (having even a non-negligible effect). The limitation of the sib-pair sample size, and consequently of the conclusions, was a result of our care in assuring that the linkage analysis was free of possible errors in the marker allele frequencies. In the second part, we illustrated the possible impact of such heterogeneity in a single data set when applying the multipoint (APM) method. An Amish pedigree included in the study of Berrettini et al. was analyzed under two sets of marker allele frequencies. One set corresponds to estimates from the entire data set and the second to estimates from the Amish pedigree only. Very different values for the APM statistics were obtained. Although the real frequencies are unknown for this family belonging to an isolated population, this example illustrates that heterogeneity in the populations from which familial data are collected may artificially increase evidence for linkage and hinder interpretation of the analysis.
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21
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Abstract
We study the statistical properties of the maximum likelihood score (MLS) test. We show that the criteria for reaching conclusions about linkage are not the same for single point analysis as for multipoint, where the maximization is performed over an additional parameter, the position in the marker interval where the MLS is computed. In addition, this test is shown to be very sensitive to errors in allele frequencies and recombination fraction.
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Affiliation(s)
- S Eichenbaum-Voline
- Laboratory of Medical Statistics, URA CNRS 1323, University of Paris V, France
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22
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Génin E, Babron MC, McDermott MF, Mulcahy B, Waldron-Lynch F, Adams C, Clegg DO, Ward RH, Shanahan F, Molloy MG, O'Gara F, Clerget-Darpoux F. Modelling the major histocompatibility complex susceptibility to RA using the MASC method. Genet Epidemiol 2000; 15:419-30. [PMID: 9671990 DOI: 10.1002/(sici)1098-2272(1998)15:4<419::aid-gepi7>3.0.co;2-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
To explain the association between HLA-DRB1 gene and rheumatoid arthritis (RA), two main hypotheses have been proposed. The first, the shared epitope hypothesis, assumes a direct role of DRB1 in RA susceptibility. The second hypothesis assumes a recessive disease susceptibility gene in linkage disequilibrium with DRB1. To investigate these two hypotheses, we analysed data on the HLA-DRB1 and TNF-LT loci in 49 affected sib-pairs. We used the Marker Association Segregation Chi-square (MASC) method in which the genotype distribution of markers among index cases and the haplotype sharing in affected sib-pairs are jointly taken into account. With DRB1 data alone, both hypotheses were shown to fit but with analysis of TNF data, both hypotheses were strongly rejected. Thus the TNF data provided additional information for a better understanding of genetic susceptibility to RA than was previously possible using only HLA-DR data. A theoretical standpoint is addressed here on the advisability of using different linked markers in a candidate region for modelling the contribution of this region in disease susceptibility.
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23
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Abstract
Testing for random mating in human populations is difficult due to confounding factors such as ethnic preference and population stratification. With HLA, the high level of polymorphism is an additional problem since it is rare for couples to share the same haplotype. Focus on an ethnically homogeneous population, where levels of polymorphism at HLA loci are more limited, may provide the best situation in which to detect non-random mating. However, such populations are often genetic isolates where there may be inbreeding to an extent that is difficult to quantify and account for. We have developed a test for random mating at a multiallelic locus that is robust to stratification and inbreeding. This test relies on the availability of genotypic information from the parents of both spouses. The focus of the test is on families where there is allele sharing between the parents of both spouses, so that potential spouses could share an allele. Denoting the shared allele at the locus of interest by A, then under the assumption of random mating, heterozygous parents AX should transmit allele A equally as frequently as allele X to their offspring. When there is positive (negative) assortative mating, A will be transmitted more (less) often than X. The power of the test has been computed in a number of situations. Data on high resolution HLA haplotypes from the Hutterite population were reinvestigated by the proposed test. The test detects significant negative assortative mating when the parental origin of the shared haplotype is taken into account.
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Affiliation(s)
- E Génin
- Department of Integrative Biology, University of California, Berkeley, USA.
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24
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Génin E, Guyon F, Margaritte-Jeannin P, Quesneville H, Clerget-Darpoux F. Detection and modeling of disease susceptibility locus effects: how much can be learned from contrast of populations? Genet Epidemiol 1999; 17 Suppl 1:S569-74. [PMID: 10597494 DOI: 10.1002/gepi.1370170792] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report the results of our analyses of the GAW11 Problem 2 data set, using information from three different populations. In the first part of the paper, we used classical population genetic tests to compare affected individuals from the different populations, stratifying on the environmental factors. Thanks to existing linkage disequilibrium in one population, we found one of the disease susceptibility loci. In the second part of the paper, we used the marker association segregation chi 2 method to model the role of this disease susceptibility locus in the different populations and draw some inferences regarding the model used at that locus to generate the data.
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25
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Abstract
We describe the use of a high-throughput, fluorescent, polymorphism-detection system, based on single-strand conformation polymorphism to screen for polymorphism in the RING3 gene. This is the first extensive mutation screen of this major histocompatibility complex-linked gene, and the entire coding region and intron-exon junctions were examined by multiplexing over 3000 polymerase chain reaction products. These techniques should be applicable for analysis of variation in other human genes. Investigation of DNA from acute lymphoblastic leukemia (ALL) and chronic myeloid leukemia (CML) patients, as well as healthy individuals revealed low levels of polymorphism across the RING3 gene. Comparison of the distribution of genotypes at each polymorphic site between patients and healthy individuals revealed a single site which significantly deviates from Hardy-Weinberg proportions.
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Affiliation(s)
- K L Thorpe
- The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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26
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Génin E, Todorov AA, Clerget-Darpoux F. Optimization of genome search strategies for homozygosity mapping: influence of marker spacing on power and threshold criteria for identification of candidate regions. Ann Hum Genet 1998; 62:419-29. [PMID: 10088039 DOI: 10.1046/j.1469-1809.1998.6250419.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mapping of genes involved in rare recessive diseases is usually difficult because of the lack of families with more than one affected progeny. The problem may be avoided by using inbred affected individuals and the strategy of homozygosity mapping. In practice, the use of homozygosity mapping in a genome-wide scan requires that a set of markers regularly spaced and spanning the whole genome are tested. Investigators are then faced to the problem of choosing the spacing of markers. To help solve this problem, we give some useful clues by computing (1) the expected length of the region of identity by descent around the disease locus, (2) the distribution, given the spacing of markers, of the number of affected individuals expected not to be homozygous at the marker closest to the disease locus and, (3) the expected type-one error. We show that even if the markers are very closely spaced, it is not unlikely that some affected individuals in the sample will not be homozygous at the marker closest to the disease locus. Excluding a region by the criterion that all affected individuals in the sample are not homozygous may then dramatically increase the rate of false negatives. We thus propose to relax the criterion to declare a region candidate, based on the sample size and the spacing of markers.
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Affiliation(s)
- E Génin
- Unité de recherche d'Epidémiologie Génétique, INSERM U155, Paris, France.
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27
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Leprêtre F, Vionnet N, Budhan S, Dina C, Powell KL, Génin E, Das AK, Nallam V, Passa P, Froguel P. Genetic studies of polymorphisms in ten non-insulin-dependent diabetes mellitus candidate genes in Tamil Indians from Pondichery. Diabetes Metab 1998; 24:244-50. [PMID: 9690058] [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: 02/08/2023]
Abstract
We report a study of 10 candidate genes presumably involved in diabetes or insulin resistance or obesity among Pondicherian Tamil Indians, an isolated population with a high prevalence of diabetes. Forty-nine families with at least two affected patients in the sibship (567 individuals) were selected and tested by PCR-RFLP techniques for reported mutations in 10 diabetes or obesity candidate genes: glucagon receptor, insulin receptor substrate 1, insulin receptor, human beta 3 adrenergic receptor, fatty acid binding protein 2, mitochondrial tRNA(Leu(UUR)), sulphonylurea receptor, human uncoupling protein and the glycogen-associated regulatory subunit of protein phosphatase-1. Glucokinase gene was also screened for mutations. No mutations were found in glucokinase, glucagon receptor and mitochondrial genes in any of the 49 probands. Frequencies of polymorphisms at other loci were similar to those reported in Caucasian populations, except for 4 of the loci at which a higher frequency of variants was observed: human beta 3 adrenergic receptor, human uncoupling type 1 protein, fatty acid binding protein 2 and the glycogen-associated regulatory subunit of protein phosphatase-1. However, no evidence of association between any of these gene variants and non-insulin-dependent diabetes mellitus (NIDDM) or quantitative traits related to NIDDM (including body mass index, waist/hip ratio, insulinaemia, glycaemia, triglycerides and total cholesterol) was found in our sample. These results suggest that none of these gene variants commonly found in the Pondicherian Tamil population of South India is a major NIDDM predisposing locus, although it cannot be excluded that they may contribute to the polygenic background of the metabolic syndrome in Pondichery.
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Affiliation(s)
- F Leprêtre
- CNRS EP10, Pasteur Institute of Lille, France
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28
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Génin E, Quesneville H, Clerget-Darpoux F. On the probability of identity states in permutable populations: reply to Cannings. Am J Hum Genet 1998; 62:726-7. [PMID: 9497268 PMCID: PMC1376965 DOI: 10.1086/301771] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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29
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Génin E, Bellis G, Clerget-Darpoux F. Information provided by pairs of distantly affected relatives to search for genes involved in rare autosomal dominant diseases. Ann Hum Genet 1997; 61:25-36. [PMID: 9066925 DOI: 10.1046/j.1469-1809.1997.6110025.x] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
When dominant mutations of different genes may lead to the same disease, it is often difficult to detect in a particular patient which gene is involved. A strategy is to make genealogical extensions to find affected relatives that should have inherited the same mutation. In particular, for diseases with late age of onset or short survival time, only poor information may be obtained from close relatives of probands and it can be particularly efficient to make genealogical extensions to detect pairs of distantly related affected individuals. Such a pair of affecteds may provide information concerning the region of the genome where the mutated gene should map. Two situations may be encountered depending on whether or not prior information on the location of mutated genes involved in the disease are available. If we already know, from previous linkage studies, that a gene located in a given region R of the genome may be involved in the disease, the problem is then to confirm that it is indeed a mutation of this gene that is involved in the affected pair. Once the implication of a gene in region R has been confirmed the affected pair of relatives may give information to restrict the length of this region R. In this paper we discuss these two points by deriving analytically first the lod score expected and second the expected reduction of the length of the region where the mutation is suspected to map as a function of the number of meioses between the two affected individuals and of the polymorphism of the markers available in the region.
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Affiliation(s)
- E Génin
- Institut National d'Etudes Démographiques, Paris.
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Génin E, Clerget-Darpoux F. Consanguinity and the sib-pair method: an approach using identity by descent between and within individuals. Am J Hum Genet 1996; 59:1149-62. [PMID: 8900245 PMCID: PMC1914848] [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: 02/02/2023] Open
Abstract
To test for linkage between a trait and a marker, one can consider identical marker alleles in related individuals, for instance, sibs. For recessive diseases, it has been shown that some information may be gained from the identity by descent (IBD) of the two alleles of an affected inbred individual at the marker locus. The aim of this paper is to extend the sib-pair method of linkage analysis to the situation of sib pairs sampled from consanguineous populations. This extension takes maximum advantage of the information provided by both the IBD pattern between sibs and allelic identity within each sib of the pair. This is possible through the use of the condensed identity coefficients. Here, we propose a new test of linkage based on a chi2. We compare the performance of this test with that of the classical chi2 test based on the distribution of sib pairs sharing 0, 1, or 2 alleles IBD. For sib pairs from first-cousin matings, the proposed test can better detect the role of a disease-susceptibility (DS) locus. Its power is shown to be greater than that of the classical test, especially for models where the DS allele may be common and incompletely penetrant; that is to say for situations that may be encountered in multifactorial diseases. A study of the impact of inbreeding on the expected proportions of sib pairs sharing 0, 1, or 2 alleles IBD is also performed here. Ignoring inbreeding, when in fact inbreeding exists, increases the rate of type I errors in tests of linkage.
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Affiliation(s)
- E Génin
- Unité de recherche d'Epidémiologie Génétique, INSERM U155, Paris
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Génin E, Clerget-Darpoux F. Association studies in consanguineous populations. Am J Hum Genet 1996; 58:861-6. [PMID: 8644750 PMCID: PMC1914684] [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: 02/01/2023] Open
Abstract
To study the genetic determinism of multifactorial diseases in large panmictic populations, a strategy consists in looking for an association with markers closely linked to candidate genes. A distribution of marker genotypes different in patients and controls may indicate that the candidate gene is involved in the disease. In panmictic populations, the power to detect the role of a candidate gene depends on the gametic disequilibrium with the marker locus. In consanguineous populations, we show that it depends on the inbreeding coefficient F as well. Inbreeding increases the power to detect the role of a recessive or quasi-recessive disease-susceptibility factor. The gain in power turns out to be greater for small values of the gametic disequilibrium. Moreover, even in the absence of gametic disequilibrium, the presence of inbreeding may allow to detect the role of a recessive factor. Ignoring inbreeding when it exists may lead to reject falsely a recessive model if the mode of inheritance is inferred on the distribution of genotypes among patients.
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Affiliation(s)
- E Génin
- INSERM U 155 and Insitut National d'Etudes Démographiques, Paris, France
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Abstract
To detect linkage between a trait and a marker, Morton (1955) proposed to calculate the lod score z(theta 1) at a given value theta 1 of the recombination fraction. If z(theta 1) reaches +3 then linkage is concluded. However, in practice, lod scores are calculated for different values of the recombination fraction between 0 and 0.5 and the test is based on the maximum value of the lod score Zmax. The impact of this deviation of the test on the probability that in fact linkage does not exist, when linkage was concluded, is documented here. This posterior probability of no linkage can be derived by using Bayes' theorem. It is less than 5% when the lod score at a predetermined theta 1 is used for the test. But, for a Zmax of +3, we showed that it can reach 16.4%. Thus, considering a composite alternative hypothesis instead of a single one decreases the reliability of the test. The reliability decreases rapidly when Zmax is less than +3. Given a Zmax of +2.5, there is a 33% chance that linkage does not exist. Moreover, the posterior probability depends not only on the value of Zmax but also jointly on the family structures and on the genetic model. For a given Zmax, the chance that linkage exists may then vary.
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Affiliation(s)
- E Génin
- Unité de recherche d'Epidémiologie Génétique, INSERM U155, Paris, France
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