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Pacot L, Sabbagh A, Sohier P, Hadjadj D, Ye M, Boland-Auge A, Bacq-Daian D, Laurendeau I, Briand-Suleau A, Deleuze JF, Margueron R, Vidaud M, Ferkal S, Parfait B, Vidaud D, Pasmant E, Wolkenstein P. Identification of potential common genetic modifiers of neurofibromas: a genome-wide association study in 1333 patients with neurofibromatosis type 1. Br J Dermatol 2024; 190:226-243. [PMID: 37831592 DOI: 10.1093/bjd/ljad390] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/23/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is characterized by the highly variable and unpredictable development of benign peripheral nerve sheath tumours: cutaneous (cNFs), subcutaneous (scNFs) and plexiform (pNFs) neurofibromas. OBJECTIVES To identify neurofibroma modifier genes, in order to develop a database of patients with NF1. METHODS All patients were phenotypically evaluated by a medical practitioner using a standardized questionnaire and the causal NF1 variant identified. We enrolled 1333 patients with NF1 who were genotyped for > 7 million common variants. RESULTS A genome-wide association case-only study identified a significant association with 9q21.33 in the pNF phenotype in the discovery cohort. Twelve, three and four regions suggestive of association at the P ≤ 1 × 10-6 threshold were identified for pNFs, cNFs and scNFs, respectively. Evidence of replication was observed for 4, 2 and 6 loci, including 168 candidate modifier protein-coding genes. Among the candidate modifier genes, some were implicated in the RAS-mitogen-activated protein kinase pathway, cell-cycle control and myelination. Using an original CRISPR/Cas9-based functional assay, we confirmed GAS1 and SPRED2 as pNF and scNF candidate modifiers, as their inactivation specifically affected NF1-mutant Schwann cell growth. CONCLUSIONS Our study may shed new light on the pathogenesis of NF1-associated neurofibromas and will, hopefully, contribute to the development of personalized care for patients with this deleterious and life-threatening condition.
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Affiliation(s)
- Laurence Pacot
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Audrey Sabbagh
- UMR 261 MERIT, Institut de Recherche pour le Développement, UFR de Pharmacie de Paris, Université Paris Cité, Paris, France
| | - Pierre Sohier
- Service de Pathologie, Hôpital Cochin, AP-HP, Centre-Université Paris Cité, Paris, France
| | - Djihad Hadjadj
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Manuela Ye
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Anne Boland-Auge
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Delphine Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Ingrid Laurendeau
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Audrey Briand-Suleau
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Raphaël Margueron
- Institut Curie, INSERM U934/CNRS UMR3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Michel Vidaud
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Salah Ferkal
- Department of Dermatology, Hôpital Henri Mondor, Assistance Publique-Hôpital Paris (AP-HP), Créteil, France
- INSERM, Clinical Investigation Center 1430, Referral Center of Neurofibromatosis, Hôpital Henri Mondor, AP-HP, Faculté de Santé Paris Est Créteil, Créteil, France
| | - Béatrice Parfait
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Dominique Vidaud
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Eric Pasmant
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Pierre Wolkenstein
- Department of Dermatology, Hôpital Henri Mondor, Assistance Publique-Hôpital Paris (AP-HP), Créteil, France
- INSERM, Clinical Investigation Center 1430, Referral Center of Neurofibromatosis, Hôpital Henri Mondor, AP-HP, Faculté de Santé Paris Est Créteil, Créteil, France
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Huttin O, Xhaard C, Dandine-Roulland C, Le Floch E, Bacq-Daian D, Lamiral Z, Bozec E, Deleuze JF, Zannad F, Rossignol P, Girerd N. Layer myocardial strain is the most heritable echocardiographic trait. Eur Heart J Cardiovasc Imaging 2023; 24:1394-1403. [PMID: 37352124 DOI: 10.1093/ehjci/jead146] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023] Open
Abstract
AIMS Myocardial deformation assessed by strain analysis represents a significant advancement in our assessment of cardiac mechanics. However, whether this variable is genetically heritable or whether all/most of its variability is related to environmental factors is currently unknown. We sought to determine the heritability of echocardiographically determined cardiac mechanics indices in a population setting. METHODS AND RESULTS A total of 1357 initially healthy subjects (women 51.6%; 48.2 ± 14.1 years) were included in this study from 20-year follow-up after the fourth visit of the longitudinal familial STANISLAS cohort (Lorraine, France). Data were acquired using state-of-the-art cardiac ultrasound equipment, using acquisition and measurement protocols recommended by the EACVI (European Association of Cardiovascular Imaging)/ASE (American Society of Echocardiography)/Industry Task Force. Layer-specific global longitudinal strain (GLS) and global circumferential strain (full-wall, subendocardial, and subepicardial) and conventional structural and functional cardiac parameters and their potential heritability were assessed using restricted maximum likelihood analysis, with genetic relatedness matrix calculated from genome-wide association data. Indices of longitudinal/circumferential myocardial function and left ventricular (LV) ejection fraction had low heritability (ranging from 10% to 20%). Diastolic and standard LV function parameters had moderate heritability (ranging from 20% to 30%) except for end-systolic and end-diastolic volumes (30% and 45%, respectively). In contrast, global longitudinal subendocardial strain (GLSEndo)/global longitudinal subepicardial strain (GLSEpi) ratio had a high level of heritability (65%). Except for GLSEndo/GLSEpi ratio, a large percentage of variance remained unexplained (>50%). CONCLUSIONS In our population cohort, GLSEndo/GLSEpi ratio had a high level of heritability, whereas other classical and mechanical LV function parameters did not. Given the increasing recognition of GLSEndo/GLSEpi ratio as an early/sensitive imaging biomarker of systolic dysfunction, our results suggest the possible existence of individual genetic predispositions to myocardial decline.
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Affiliation(s)
- Olivier Huttin
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
- Service de Cardiologie, Institut Lorrain du Coeur et des Vaisseaux, Centre Hospitalier Universitaire de Nancy, Nancy, France
| | - Constance Xhaard
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
| | - Claire Dandine-Roulland
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Edith Le Floch
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Zohra Lamiral
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
| | - Erwan Bozec
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Faiez Zannad
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
| | - Patrick Rossignol
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
| | - Nicolas Girerd
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
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3
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Luo J, Thomassen JQ, Bellenguez C, Grenier-Boley B, de Rojas I, Castillo A, Parveen K, Küçükali F, Nicolas A, Peters O, Schneider A, Dichgans M, Rujescu D, Scherbaum N, Jürgen D, Riedel-Heller S, Hausner L, Porcel LM, Düzel E, Grimmer T, Wiltfang J, Heilmann-Heimbach S, Moebus S, Tegos T, Scarmeas N, Clarimon J, Moreno F, Pérez-Tur J, Bullido MJ, Pastor P, Sánchez-Valle R, Álvarez V, Boada M, García-González P, Puerta R, Mir P, Real LM, Piñol-Ripoll G, García-Alberca JM, Royo JL, Rodriguez-Rodriguez E, Soininen H, Kuulasmaa T, de Mendonça A, Mehrabian S, Hort J, Vyhnalek M, van der Lee S, Graff C, Papenberg G, Giedraitis V, Boland A, Bacq-Daian D, Deleuze JF, Nicolas G, Dufouil C, Pasquier F, Hanon O, Debette S, Grünblatt E, Popp J, Benussi L, Galimberti D, Arosio B, Mecocci P, Solfrizzi V, Parnetti L, Squassina A, Tremolizzo L, Borroni B, Nacmias B, Sorbi S, Caffarra P, Seripa D, Rainero I, Daniele A, Masullo C, Spalletta G, Williams J, Amouyel P, Jessen F, Kehoe P, Tsolaki M, Rossi G, Sánchez-Juan P, Sleegers K, Ingelsson M, Andreassen OA, Hiltunen M, Van Duijn C, Sims R, van der Flier W, Ruiz A, Ramirez A, Lambert JC, Frikke-Schmidt R. Genetic Associations Between Modifiable Risk Factors and Alzheimer Disease. JAMA Netw Open 2023; 6:e2313734. [PMID: 37195665 PMCID: PMC10193187 DOI: 10.1001/jamanetworkopen.2023.13734] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/18/2023] [Indexed: 05/18/2023] Open
Abstract
Importance An estimated 40% of dementia is potentially preventable by modifying 12 risk factors throughout the life course. However, robust evidence for most of these risk factors is lacking. Effective interventions should target risk factors in the causal pathway to dementia. Objective To comprehensively disentangle potentially causal aspects of modifiable risk factors for Alzheimer disease (AD) to inspire new drug targeting and improved prevention. Design, Setting, and Participants This genetic association study was conducted using 2-sample univariable and multivariable mendelian randomization. Independent genetic variants associated with modifiable risk factors were selected as instrumental variables from genomic consortia. Outcome data for AD were obtained from the European Alzheimer & Dementia Biobank (EADB), generated on August 31, 2021. Main analyses were conducted using the EADB clinically diagnosed end point data. All analyses were performed between April 12 and October 27, 2022. Exposures Genetically determined modifiable risk factors. Main Outcomes and Measures Odds ratios (ORs) and 95% CIs for AD were calculated per 1-unit change of genetically determined risk factors. Results The EADB-diagnosed cohort included 39 106 participants with clinically diagnosed AD and 401 577 control participants without AD. The mean age ranged from 72 to 83 years for participants with AD and 51 to 80 years for control participants. Among participants with AD, 54% to 75% were female, and among control participants, 48% to 60% were female. Genetically determined high-density lipoprotein (HDL) cholesterol concentrations were associated with increased odds of AD (OR per 1-SD increase, 1.10 [95% CI, 1.05-1.16]). Genetically determined high systolic blood pressure was associated with increased risk of AD after adjusting for diastolic blood pressure (OR per 10-mm Hg increase, 1.22 [95% CI, 1.02-1.46]). In a second analysis to minimize bias due to sample overlap, the entire UK Biobank was excluded from the EADB consortium; odds for AD were similar for HDL cholesterol (OR per 1-SD unit increase, 1.08 [95% CI, 1.02-1.15]) and systolic blood pressure after adjusting for diastolic blood pressure (OR per 10-mm Hg increase, 1.23 [95% CI, 1.01-1.50]). Conclusions and Relevance This genetic association study found novel genetic associations between high HDL cholesterol concentrations and high systolic blood pressure with higher risk of AD. These findings may inspire new drug targeting and improved prevention implementation.
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Affiliation(s)
- Jiao Luo
- Department of Clinical Biochemistry, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Jesper Qvist Thomassen
- Department of Clinical Biochemistry, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Céline Bellenguez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Benjamin Grenier-Boley
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Itziar de Rojas
- Research Center and Memory clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Atahualpa Castillo
- Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Wales, United Kingdom
| | - Kayenat Parveen
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Neurodegenerative diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Fahri Küçükali
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Aude Nicolas
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Oliver Peters
- German Center for Neurodegenerative Diseases, Berlin, Germany
- Institute of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Psychiatry and Psychotherapy, Berlin, Germany
| | - Anja Schneider
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Department for Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
- Comprehensive Centre for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Norbert Scherbaum
- LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Deckert Jürgen
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health (ISAP), University of Leipzig, Leipzig, Germany
| | - Lucrezia Hausner
- Department of Geriatric Psychiatry, Central Institute for Mental Health Mannheim, Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Laura Molina Porcel
- Neurological Tissue Bank, Biobanc Hospital Clinic, Instituto de Investigaciones Biomédicas August Pi i Sunyer, Barcelona, Spain
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clinic, Barcelona, Spain
| | - Emrah Düzel
- German Center for Neurodegenerative Diseases, Magdeburg, Germany
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, Magdeburg, Germany
| | - Timo Grimmer
- Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Department of Psychiatry and Psychotherapy, Munich, Germany
| | - Jens Wiltfang
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen, Goettingen, Germany
- German Center for Neurodegenerative Diseases, Goettingen, Germany
- Medical Science Department, Instituto de Biomedicina, Aveiro, Portugal
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Susanne Moebus
- Institute for Urban Public Health, University Hospital of University Duisburg-Essen, Essen, Germany
| | - Thomas Tegos
- First Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Scarmeas
- First Department of Neurology, Aiginition Hospital, National and Kapodistrian University of Athens, Medical School, Athens, Greece
- Taub Institute for Research in Alzheimer's Disease and the Aging Brain, The Gertrude H. Sergievsky Center, Department of Neurology, Columbia University, New York, New York
| | - Jordi Clarimon
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fermin Moreno
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, Hospital Universitario Donostia, San Sebastian, Spain
- Neurosciences Area, Instituto Biodonostia, San Sebastian, Spain
| | - Jordi Pérez-Tur
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Unitat de Genètica Molecular, Institut de Biomedicina de València, Consejo Superior de Investigaciones Científicas, Valencia, Spain
- Unidad Mixta de Neurologia Genètica, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - María J Bullido
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Madrid, Spain
- Instituto de Investigacion Sanitaria Hospital la Paz, Madrid, Spain
| | - Pau Pastor
- Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias i Pujol and The Germans Trias i Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Service of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Victoria Álvarez
- Laboratorio de Genética, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Asturias, Spain
| | - Mercè Boada
- Research Center and Memory clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Pablo García-González
- Research Center and Memory clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Raquel Puerta
- Research Center and Memory clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Pablo Mir
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain
| | - Luis M Real
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
- Depatamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - Gerard Piñol-Ripoll
- Unitat Trastorns Cognitius, Hospital Universitari Santa Maria de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida, Lleida, Spain
| | - Jose María García-Alberca
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Alzheimer Research Center & Memory Clinic, Instituto Andaluz de Neurociencia, Málaga, Spain
| | - Jose Luís Royo
- Depatamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - Eloy Rodriguez-Rodriguez
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Neurology Service, Marqués de Valdecilla University Hospital, University of Cantabria and IDIVAL, Santander, Spain
| | - Hilkka Soininen
- Institute of Clinical Medicine, Neurology, University of Eastern Finland, Kuopio, Finland
| | - Teemu Kuulasmaa
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | | | - Shima Mehrabian
- Clinic of Neurology, UH "Alexandrovska," Medical University-Sofia, Sofia, Bulgaria
| | - Jakub Hort
- Memory Clinic, Department of Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
- International Clinical Research Center, St Anne's University Hospital Brno, Brno, Czech Republic
| | - Martin Vyhnalek
- Memory Clinic, Department of Neurology, Charles University, Second Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
- International Clinical Research Center, St Anne's University Hospital Brno, Brno, Czech Republic
| | - Sven van der Lee
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, locatie VUmc, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC, locatie VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Caroline Graff
- Unit for Hereditary Dementias, Theme Aging, Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Goran Papenberg
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences/ and Geriatrics, Uppsala University, Uppsala, Sweden
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Delphine Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Gael Nicolas
- Normandie Univ, Université de Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Centre national de référence pour les malades Alzheimer jeunes, Rouen, France
| | - Carole Dufouil
- Inserm, Bordeaux Population Health Research Center, UMR 1219, University of Bordeaux, ISPED, CIC 1401-EC, Bordeaux, France
- CHU de Bordeaux, Pole santé publique, Bordeaux, France
| | - Florence Pasquier
- University of Lille, Inserm, CHU Lille, UMR1172, Resources and Research Memory Center of Distalz, Licend, Lille, France
| | - Olivier Hanon
- Université de Paris, EA 4468, Assistance Publique - Hôpitaux de Paris, Hôpital Broca, Paris, France
| | - Stéphanie Debette
- University Bordeaux, Inserm, Bordeaux Population Health Research Center, France
- Department of Neurology, Bordeaux University Hospital, Bordeaux, France
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zürich, Zurich, Switzerland
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Daniela Galimberti
- Neurodegenerative Diseases Unit, Fondazione IRCCS Ca' Granda, Ospedale Policlinico, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Beatrice Arosio
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Geriatric Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Vincenzo Solfrizzi
- Interdisciplinary Department of Medicine, Geriatric Medicine and Memory Unit, University of Bari Aldo Moro, Bari, Italy
| | - Lucilla Parnetti
- Centre for Memory Disturbances, Lab of Clinical Neurochemistry, Section of Neurology, University of Perugia, Perugia, Italy
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Lucio Tremolizzo
- Neurology Unit, Hospital San Gerardo, Monza and University of Milano-Bicocca, Milan, Italy
| | - Barbara Borroni
- Centre for Neurodegenerative Disorders, Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | | | - Davide Seripa
- Laboratory for Advanced Hematological Diagnostics, Department of Hematology and Stem Cell Transplant, Vito Fazzi Hospital, Lecce, Italy
| | - Innocenzo Rainero
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Torino, Italy
| | - Antonio Daniele
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
- Neurology Unit, IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy
| | - Carlo Masullo
- Institute of Neurology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianfranco Spalletta
- Laboratory of Neuropsychiatry, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas
| | - Julie Williams
- UK Dementia Research Institute at Cardiff, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Frank Jessen
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Patrick Kehoe
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Magda Tsolaki
- First Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Giacomina Rossi
- Unit of Neurology V - Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Pascual Sánchez-Juan
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Alzheimer's Centre Reina Sofia-CIEN Foundation-ISCIII, Madrid, Spain
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Martin Ingelsson
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
- Krembil Brain Institute, University Health Network, Toronto, Canada
- Department of Medicine and Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada
| | - Ole A Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Cornelia Van Duijn
- Department of Epidemiology, ErasmusMC, Rotterdam, the Netherlands
- Nuffield Department of Population Health, Oxford University, Oxford, United Kingdom
| | - Rebecca Sims
- Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Wales, United Kingdom
| | - Wiesje van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC, locatie VUmc, Amsterdam, the Netherlands
| | - Agustín Ruiz
- Research Center and Memory clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Neurodegenerative diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department of Psychiatry and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, Texas
| | - Jean-Charles Lambert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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4
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Soilly AL, Robert-Viard C, Besse C, Bruel AL, Gerard B, Boland A, Piton A, Duffourd Y, Muller J, Poë C, Jouan T, El Doueiri S, Faivre L, Bacq-Daian D, Isidor B, Genevieve D, Odent S, Philip N, Doco-Fenzy M, Lacombe D, Asensio ML, Deleuze JF, Binquet C, Thauvin-Robinet C, Lejeune C. Cost of exome analysis in patients with intellectual disability: a micro-costing study in a French setting. BMC Health Serv Res 2023; 23:386. [PMID: 37085862 PMCID: PMC10120135 DOI: 10.1186/s12913-023-09373-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 04/04/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND With the development of next generation sequencing technologies in France, exome sequencing (ES) has recently emerged as an opportunity to improve the diagnosis rate of patients presenting an intellectual disability (ID). To help French policy makers determine an adequate tariff for ES, we aimed to assess the unit cost per ES diagnostic test for ID from the preparation of the pre-analytical step until the report writing step and to identify its main cost drivers. METHODS A micro-costing bottom-up approach was conducted for the year 2018 in a French setting as part of the DISSEQ study, a cost-effectiveness study funded by the Ministry of Health and performed in collaboration with the GAD (Génétique des Anomalies du Développement), a genetic team from the Dijon University Hospital, and a public sequencing platform, the Centre National de Recherche en Génomique Humaine (CNRGH). The analysis was conducted from the point of view of these two ES stakeholders. All of the resources (labor, equipment, disposables and reagents, reusable material) required to analyze blood samples were identified, collected and valued. Several sensitivity analyses were performed. RESULTS The unit nominal cost per ES diagnostic test for ID was estimated to be €2,019.39. Labor represented 50.7% of the total cost. The analytical step (from the preparation of libraries to the analysis of sequences) represented 88% of the total cost. Sensitivity analyses suggested that a simultaneous price decrease of 20% for the capture kit and 50% for the sequencing support kit led to an estimation of €1,769 per ES diagnostic test for ID. CONCLUSION This is the first estimation of ES cost to be done in the French setting of ID diagnosis. The estimation is especially influenced by the price of equipment kits, but more generally by the organization of the centers involved in the different steps of the analysis and the time period in which the study was conducted. This information can now be used to define an adequate tariff and assess the efficiency of ES. TRIAL REGISTRATION ClinicalTrials.gov identifier NCT03287206 on September 19, 2017.
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Affiliation(s)
- A L Soilly
- CHU Dijon Bourgogne, Délégation à la Recherche Clinique et à l'Innovation, USMR, F-21000, Dijon, France
- CHU Dijon Bourgogne, Délégation à la Recherche Clinique et à l'Innovation, Unité Innovation, F-21000, Dijon, France
| | - C Robert-Viard
- CHU Dijon Bourgogne, Délégation à la Recherche Clinique et à l'Innovation, Unité Innovation, F-21000, Dijon, France
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France
| | - C Besse
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - A L Bruel
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - B Gerard
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace (IGMA), 67000, Strasbourg, France
| | - A Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - A Piton
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace (IGMA), 67000, Strasbourg, France
| | - Y Duffourd
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - J Muller
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace (IGMA), 67000, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale appliquée au diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Inserm UMRS_1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, France et CHRU, Strasbourg, France
| | - C Poë
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - T Jouan
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - S El Doueiri
- CHU Dijon Bourgogne, Service financier, 21000, Dijon, France
| | - L Faivre
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
- CHU Dijon-Bourgogne, Centres de Référence Maladies Rares « Anomalies du Développement et syndromes malformatif de l'Est » et « Déficiences intellectuelles de causes rares », Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon, France
| | - D Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - B Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - D Genevieve
- Département de Génétique Médicale, Centre de Référence Maladies Rares, Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - S Odent
- Service de Génétique Clinique, Centre Hospitalier Universitaire Rennes, F-35203, Rennes, France
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 6290, Institut Génétique et Développement de Rennes, Université de Rennes 1, F-35203, Rennes, France
| | - N Philip
- Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| | - M Doco-Fenzy
- Service de Génétique, CHU de Reims, EA3801, Reims, France
- CRMR Anddi-Rares constitutif, CLAD-EST, CHU Reims, Reims, France
| | - D Lacombe
- CHU de Bordeaux, Génétique Médicale, INSERM U1211, Laboratoire MRGM, Université de Bordeaux, Bordeaux, France
| | - M L Asensio
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France
| | - J F Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - C Binquet
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France
| | - C Thauvin-Robinet
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
- CHU Dijon-Bourgogne, Centres de Référence Maladies Rares « Anomalies du Développement et syndromes malformatif de l'Est » et « Déficiences intellectuelles de causes rares », Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon, France
| | - C Lejeune
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France.
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5
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Lokmer A, Alladi CG, Troudet R, Bacq-Daian D, Boland-Auge A, Latapie V, Deleuze JF, RajKumar RP, Shewade DG, Bélivier F, Marie-Claire C, Jamain S. Risperidone response in patients with schizophrenia drives DNA methylation changes in immune and neuronal systems. Epigenomics 2023; 15:21-38. [PMID: 36919681 DOI: 10.2217/epi-2023-0017] [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] [Indexed: 03/16/2023] Open
Abstract
Background: The choice of efficient antipsychotic therapy for schizophrenia relies on a time-consuming trial-and-error approach, whereas the social and economic burdens of the disease call for faster alternatives. Material & methods: In a search for predictive biomarkers of antipsychotic response, blood methylomes of 28 patients were analyzed before and 4 weeks into risperidone therapy. Results: Several CpGs exhibiting response-specific temporal dynamics were identified in otherwise temporally stable methylomes and noticeable global response-related differences were observed between good and bad responders. These were associated with genes involved in immunity, neurotransmission and neuronal development. Polymorphisms in many of these genes were previously linked with schizophrenia etiology and antipsychotic response. Conclusion: Antipsychotic response seems to be shaped by both stable and medication-induced methylation differences.
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Affiliation(s)
- Ana Lokmer
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
| | - Charanraj Goud Alladi
- Université de Paris, INSERM UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie (OTeN), Paris, F-75006, France
| | - Réjane Troudet
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
| | - Delphine Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, F-91057, France
| | - Anne Boland-Auge
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, F-91057, France
| | - Violaine Latapie
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, F-91057, France
| | - Ravi Philip RajKumar
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India
| | - Deepak Gopal Shewade
- Department of Psychiatry, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India.,Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, F-91000, France
| | - Frank Bélivier
- Fondation FondaMental, Créteil, F-94000, France.,Université de Paris, INSERM UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie (OTeN), Paris, F-75006, France.,Hôpitaux Lariboisière-Fernand Widal, GHU APHP Nord, Département de Psychiatrie et de Médecine Addicto-logique, Paris, F-75010, France
| | - Cynthia Marie-Claire
- Université de Paris, INSERM UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie (OTeN), Paris, F-75006, France
| | - Stéphane Jamain
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
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6
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Jiao Y, Truong T, Eon-Marchais S, Mebirouk N, Caputo SM, Dondon MG, Karimi M, Le Gal D, Beauvallet J, Le Floch É, Dandine-Roulland C, Bacq-Daian D, Olaso R, Albuisson J, Audebert-Bellanger S, Berthet P, Bonadona V, Buecher B, Caron O, Cavaillé M, Chiesa J, Colas C, Collonge-Rame MA, Coupier I, Delnatte C, De Pauw A, Dreyfus H, Fert-Ferrer S, Gauthier-Villars M, Gesta P, Giraud S, Gladieff L, Golmard L, Lasset C, Lejeune-Dumoulin S, Léoné M, Limacher JM, Lortholary A, Luporsi É, Mari V, Maugard CM, Mortemousque I, Mouret-Fourme E, Nambot S, Noguès C, Popovici C, Prieur F, Pujol P, Sevenet N, Sobol H, Toulas C, Uhrhammer N, Vaur D, Venat L, Boland-Augé A, Guénel P, Deleuze JF, Stoppa-Lyonnet D, Andrieu N, Lesueur F. Association and performance of polygenic risk scores for breast cancer among French women presenting or not a familial predisposition to the disease. Eur J Cancer 2023; 179:76-86. [PMID: 36509001 DOI: 10.1016/j.ejca.2022.11.007] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Three partially overlapping breast cancer polygenic risk scores (PRS) comprising 77, 179 and 313 SNPs have been proposed for European-ancestry women by the Breast Cancer Association Consortium (BCAC) for improving risk prediction in the general population. However, the effect of these SNPs may vary from one country to another and within a country because of other factors. OBJECTIVE To assess their associated risk and predictive performance in French women from (1) the CECILE population-based case-control study, (2) BRCA1 or BRCA2 (BRCA1/2) pathogenic variant (PV) carriers from the GEMO study, and (3) familial breast cancer cases with no BRCA1/2 PV and unrelated controls from the GENESIS study. RESULTS All three PRS were associated with breast cancer in all studies, with odds ratios per standard deviation varying from 1.7 to 2.0 in CECILE and GENESIS, and hazard ratios varying from 1.1 to 1.4 in GEMO. The predictive performance of PRS313 in CECILE was similar to that reported in BCAC but lower than that in GENESIS (area under the receiver operating characteristic curve (AUC) = 0.67 and 0.75, respectively). PRS were less performant in BRCA2 and BRCA1 PV carriers (AUC = 0.58 and 0.54 respectively). CONCLUSION Our results are in line with previous validation studies in the general population and in BRCA1/2 PV carriers. Additionally, we showed that PRS may be of clinical utility for women with a strong family history of breast cancer and no BRCA1/2 PV, and for those carrying a predicted PV in a moderate-risk gene like ATM, CHEK2 or PALB2.
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Affiliation(s)
- Yue Jiao
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Thérèse Truong
- Université Paris-Saclay, UVSQ, INSERM, U1018, Gustave Roussy, CESP, Team Exposome and Heredity, Villejuif, France
| | - Séverine Eon-Marchais
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Noura Mebirouk
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Sandrine M Caputo
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Marie-Gabrielle Dondon
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Mojgan Karimi
- Université Paris-Saclay, UVSQ, INSERM, U1018, Gustave Roussy, CESP, Team Exposome and Heredity, Villejuif, France
| | - Dorothée Le Gal
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Juana Beauvallet
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Édith Le Floch
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Claire Dandine-Roulland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Juliette Albuisson
- Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France
| | | | - Pascaline Berthet
- Département de Biopathologie, Centre François Baclesse, Caen, France; INSERM, U1245, Rouen, France
| | - Valérie Bonadona
- Université Claude Bernard Lyon 1, Villeurbanne, France; CNRS UMR 5558, Centre Léon Bérard, Unité de Prévention et épidémiologie Génétique, Lyon, France
| | - Bruno Buecher
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Olivier Caron
- Gustave Roussy, Département de Médecine Oncologique, Villejuif, France
| | - Mathias Cavaillé
- Université Clermont Auvergne, UMR INSERM, U1240, Clermont Ferrand, France; Département d'Oncogénétique, Centre Jean Perrin, Clermont Ferrand, France
| | - Jean Chiesa
- UF de Génétique Médicale et Cytogénétique, CHRU Caremeau, Nîmes, France
| | - Chrystelle Colas
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France; INSERM, U830, Paris, France
| | - Marie-Agnès Collonge-Rame
- Service Génétique et Biologie du Développement - Histologie, CHU Hôpital Saint-Jacques, Besançon, France
| | - Isabelle Coupier
- Hôpital Arnaud de Villeneuve, CHU Montpellier, Service de Génétique Médicale et Oncogénétique, Montpellier, France; INSERM, U896, CRCM Val d'Aurelle, Montpellier, France
| | - Capucine Delnatte
- Institut de Cancérologie de l'Ouest, Unité d'Oncogénétique, Saint Herblain, France
| | - Antoine De Pauw
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Hélène Dreyfus
- Clinique Sainte Catherine, Avignon, CHU de Grenoble, Grenoble, France; Hôpital Couple-Enfant, Département de Génétique, Grenoble, France
| | | | - Marion Gauthier-Villars
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Paul Gesta
- CH Georges Renon, Service d'Oncogénétique Régional Poitou-Charentes, Niort, France
| | - Sophie Giraud
- Hospices Civils de Lyon, Service de Génétique, Groupement Hospitalier Est, Bron, France
| | - Laurence Gladieff
- Institut Claudius Regaud - IUCT-Oncopole, Service d'Oncologie Médicale, Toulouse, France
| | - Lisa Golmard
- PSL Research University, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - Christine Lasset
- Université Claude Bernard Lyon 1, Villeurbanne, France; CNRS UMR 5558, Centre Léon Bérard, Unité de Prévention et épidémiologie Génétique, Lyon, France
| | | | - Mélanie Léoné
- Hospices Civils de Lyon, Service de Génétique, Groupement Hospitalier Est, Bron, France
| | | | - Alain Lortholary
- Service d'Oncologie Médicale, Centre Catherine de Sienne, Nantes, France; Hôpital Privé du Confluent, Nantes, France
| | - Élisabeth Luporsi
- Service de Génétique UF4128 CHR Metz-Thionville, Hôpital de Mercy, Metz, France
| | - Véronique Mari
- Unité d'Oncogénétique, Centre Antoine Lacassagne, Nice, France
| | - Christine M Maugard
- Génétique Oncologique Moléculaire, UF1422, Département d'Oncobiologie, LBBM, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; UF6948 Génétique Oncologique Clinique, évaluation Familiale et Suivi, Strasbourg, France
| | | | | | - Sophie Nambot
- Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France; Institut GIMI, CHU de Dijon, Hôpital d'Enfants, France; Oncogénétique, Dijon, France
| | - Catherine Noguès
- Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes, Marseille, France; Aix Marseille Université, INSERM, IRD, SESSTIM, Marseille, France
| | - Cornel Popovici
- Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes, Marseille, France
| | - Fabienne Prieur
- CHU de Saint-Etienne; Hôpital Nord, Service de Génétique, Saint-Etienne, France
| | - Pascal Pujol
- Hôpital Arnaud de Villeneuve, CHU Montpellier, Service de Génétique Médicale et Oncogénétique, Montpellier, France; INSERM, U896, CRCM Val d'Aurelle, Montpellier, France
| | | | - Hagay Sobol
- Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes, Marseille, France
| | - Christine Toulas
- Institut Claudius Regaud - IUCT-Oncopole, Service d'Oncologie Médicale, Toulouse, France
| | - Nancy Uhrhammer
- Centre Jean Perrin, LBM OncoGenAuvergne, Clermont Ferrand, France
| | - Dominique Vaur
- Département de Biopathologie, Centre François Baclesse, Caen, France; INSERM, U1245, Rouen, France
| | - Laurence Venat
- Hôpital Universitaire Dupuytren, Service d'Oncologie Médicale, Limoges, France
| | - Anne Boland-Augé
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Pascal Guénel
- Université Paris-Saclay, UVSQ, INSERM, U1018, Gustave Roussy, CESP, Team Exposome and Heredity, Villejuif, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France; Département d'Oncogénétique, Centre Jean Perrin, Clermont Ferrand, France; Université Paris-Cité, Paris, France
| | - Nadine Andrieu
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France
| | - Fabienne Lesueur
- INSERM, U900, Paris, France; Institut Curie, Paris, France; Mines ParisTech, Fontainebleau, France; PSL Research University, Paris, France.
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7
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Kanbay M, Xhaard C, Le Floch E, Dandine-Roulland C, Girerd N, Ferreira JP, Boivin JM, Wagner S, Bacq-Daian D, Deleuze JF, Zannad F, Rossignol P. Weak Association Between Genetic Markers of Hyperuricemia and Cardiorenal Outcomes: Insights From the STANISLAS Study Cohort With a 20-Year Follow-Up. J Am Heart Assoc 2022; 11:e023301. [PMID: 35470676 PMCID: PMC9238600 DOI: 10.1161/jaha.121.023301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Hyperuricemia is associated with poor cardiovascular outcomes, although it is uncertain whether this relationship is causal in nature. This study aimed to: (1) assess the heritability of serum uric acid (SUA) levels, (2) conduct a genome‐wide association study on SUA levels, and (3) investigate the association between certain single‐nucleotide polymorphisms and target organ damage. Methods and Results The STANISLAS (Suivi Temporaire Annuel Non‐Invasif de la Santé des Lorrains Assurés Sociaux) study cohort is a single‐center longitudinal cohort recruited between 1993 and 1995 (visit 1), with a last visit (visit 4 [V4]) performed ≈20 years apart. Serum lipid profile, SUA, urinary albumin/creatinine ratio, estimated glomerular filtration rate, 24‐hour ambulatory blood pressure monitoring, transthoracic echocardiography, pulse wave velocity, and genotyping for each participant were assessed at V4. A total of 1573 participants were included at V4, among whom 1417 had available SUA data at visit 1. Genome‐wide association study results highlighted multiple single‐nucleotide polymorphisms on the SLC2A9 gene linked to SUA levels. Carriers of the most associated mutated SLC2A9 allele (rs16890979) had significantly lower SUA levels. Although SUA level at V4 was highly associated with diabetes, prediabetes, higher body mass index, CRP (C‐reactive protein) levels, estimated glomerular filtration rate variation (visit 1–V4), carotid intima‐media thickness, and pulse wave velocity, rs16890979 was only associated with higher carotid intima‐media thickness. Conclusions Our findings demonstrate that rs16890979, a genetic determinant of SUA levels located on the SLC2A9 gene, is associated with carotid intima‐media thickness despite significant associations between SUA levels and several clinical outcomes, thereby lending support to the hypothesis of a link between SUA and cardiovascular disease.
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Affiliation(s)
- Mehmet Kanbay
- Division of Nephrology Department of Medicine Koc University School of Medicine Istanbul Turkey
| | - Constance Xhaard
- Université de LorraineINSERM CIC-P 1433CHRU de NancyINSERM U1116F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists) Nancy France
| | - Edith Le Floch
- Centre National de Recherche en Génomique Humaine Institut François JacobCEAUniversité Paris-Saclay Evry France
| | - Claire Dandine-Roulland
- Centre National de Recherche en Génomique Humaine Institut François JacobCEAUniversité Paris-Saclay Evry France
| | - Nicolas Girerd
- Université de LorraineINSERM CIC-P 1433CHRU de NancyINSERM U1116F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists) Nancy France
| | - João Pedro Ferreira
- Université de LorraineINSERM CIC-P 1433CHRU de NancyINSERM U1116F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists) Nancy France
| | - Jean-Marc Boivin
- Université de LorraineINSERM CIC-P 1433CHRU de NancyINSERM U1116F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists) Nancy France
| | - Sandra Wagner
- Université de LorraineINSERM CIC-P 1433CHRU de NancyINSERM U1116F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists) Nancy France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine Institut François JacobCEAUniversité Paris-Saclay Evry France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine Institut François JacobCEAUniversité Paris-Saclay Evry France
| | - Faiez Zannad
- Université de LorraineINSERM CIC-P 1433CHRU de NancyINSERM U1116F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists) Nancy France
| | - Patrick Rossignol
- Université de LorraineINSERM CIC-P 1433CHRU de NancyINSERM U1116F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists) Nancy France
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8
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Bäck M, Xhaard C, Rouget R, Thuillier Q, Plunde O, Larsson SC, Girerd N, Ferreira JP, Boivin JM, Bozec E, Mercklé L, Zannad F, Hoge A, Guillaume M, Dandine-Roulland C, Floch EL, Bacq-Daian D, Deleuze JF, Van den Berghe L, Nazare JA, Laville M, Branlant C, Behm-Ansmant I, Wagner S, Rossignol P. Fatty acid desaturase genetic variations and dietary omega-3 fatty acid intake associate with arterial stiffness. European Heart Journal Open 2022; 2:oeac016. [PMID: 35919123 PMCID: PMC9242081 DOI: 10.1093/ehjopen/oeac016] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 02/11/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Aims
Long-chain polyunsaturated fatty acids (PUFAs) generate diverse bioactive lipid mediators, which tightly regulate vascular inflammation. The effects of omega-3 PUFA supplementation in cardiovascular prevention however remain controversial. In addition to direct dietary intake, fatty acid desaturases (FADS) determine PUFA levels. Increased arterial stiffness represents an independent predictor of mortality and cardiovascular events. The aim of the present study was to determine the association of PUFA intake, FADS1 genotype, and FADS expression with arterial stiffness.
Methods and results
A cross-sectional population-based cohort study of 1464 participants without overt cardiovascular disease was conducted. Dietary intake was assessed using a food frequency questionnaire. Arterial stiffness was assessed by carotid–femoral pulse wave velocity (cfPWV), and the FADS1 locus variant was determined. Blood cell transcriptomics was performed in a subset of 410 individuals. Pulse wave velocity was significantly associated with the FADS1 locus variant. Differential associations between PWV and omega-3 PUFA intake were observed depending on the FADS1 genotype. High omega-3 PUFA intake attenuated the FADS1 genotype-dependent associations. Carriers of the minor FADS1 locus variant exhibited increased expression of FADS2, which is associated with PWV.
Conclusion
Taken together, these findings point to FADS1 genotype-dependent associations of omega-3 PUFA intake on subclinical cardiovascular disease. These findings may have implications for identifying responders and non-responders to omega-3 PUFA supplementation and open up for personalized dietary counselling in cardiovascular prevention.
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Affiliation(s)
- Magnus Bäck
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
- Karolinska Institutet Department of Medicine Solna, , 17176 Stockholm, Sweden
- Karolinska University Hospital Huddinge Department of Cardiology, , 14186 Stockholm, Sweden
| | - Constance Xhaard
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
| | - Raphael Rouget
- Université de Lorraine , CNRS, UMR 7365, IMoPA, F54000 Nancy, France
| | - Quentin Thuillier
- Université de Lorraine , CNRS, UMR 7365, IMoPA, F54000 Nancy, France
| | - Oscar Plunde
- Karolinska Institutet Department of Medicine Solna, , 17176 Stockholm, Sweden
| | - Susanna C. Larsson
- Institute of Environmental Medicine, Karolinska Institutet Unit of Cardiovascular and Nutritional Epidemiology, , 17177 Stockholm, Sweden
- Uppsala University Department of Surgical Sciences, , Uppsala, Sweden
| | - Nicolas Girerd
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
| | - João Pedro Ferreira
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
| | - Jean-Marc Boivin
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
| | - Erwan Bozec
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
| | - Ludovic Mercklé
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
| | - Faiez Zannad
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
| | - Axelle Hoge
- Université de Liège Département des Sciences de la Santé publique, , Liège, Belgium
| | - Michèle Guillaume
- Université de Liège Département des Sciences de la Santé publique, , Liège, Belgium
| | | | - Edith Le Floch
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay , Evry, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay , Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay , Evry, France
| | - Laurie Van den Berghe
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, F-CRIN/FORCE Network, Pierre Bénite , Lyon, France
| | - Julie-Anne Nazare
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, F-CRIN/FORCE Network, Pierre Bénite , Lyon, France
| | - Martine Laville
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, F-CRIN/FORCE Network, Pierre Bénite , Lyon, France
| | | | | | - Sandra Wagner
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
| | - Patrick Rossignol
- University of Lorraine , INSERM U1116, CIC 1433, FCRIN INI-CRCT, Nancy University Hospital, Nancy, France
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9
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Denommé-Pichon AS, Vitobello A, Olaso R, Ziegler A, Jeanne M, Tran Mau-Them F, Couturier V, Racine C, Isidor B, Poë C, Jouan T, Boland A, Fin B, Bacq-Daian D, Besse C, Garde A, Prost A, Garret P, Tisserant É, Delanne J, Nambot S, Juven A, Gorce M, Nizon M, Vincent M, Moutton S, Fradin M, Lavillaureix A, Rollier P, Capri Y, Van-Gils J, Busa T, Sigaudy S, Pasquier L, Barth M, Bruel AL, Flamant C, Prouteau C, Bonneau D, Toutain A, Chantegret C, Callier P, Philippe C, Duffourd Y, Deleuze JF, Sorlin A, Faivre L, Thauvin-Robinet C. Accelerated genome sequencing with controlled costs for infants in intensive care units: a feasibility study in a French hospital network. Eur J Hum Genet 2021; 30:567-576. [PMID: 34782754 PMCID: PMC9091203 DOI: 10.1038/s41431-021-00998-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 10/12/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Obtaining a rapid etiological diagnosis for infants with early-onset rare diseases remains a major challenge. These diseases often have a severe presentation and unknown prognosis, and the genetic causes are very heterogeneous. In a French hospital network, we assessed the feasibility of performing accelerated trio-genome sequencing (GS) with limited additional costs by integrating urgent requests into the routine workflow. In addition to evaluating our capacity for such an approach, this prospective multicentre pilot study was designed to identify pitfalls encountered during its implementation. Over 14 months, we included newborns and infants hospitalized in neonatal or paediatric intensive care units with probable genetic disease and in urgent need for etiological diagnosis to guide medical care. The duration of each step and the pitfalls were recorded. We analysed any deviation from the planned schedule and identified obstacles. Trio-GS was performed for 37 individuals, leading to a molecular diagnosis in 18/37 (49%), and 21/37 (57%) after reanalysis. Corrective measures and protocol adaptations resulted in a median duration of 42 days from blood sampling to report. Accelerated trio-GS is undeniably valuable for individuals in an urgent care context. Such a circuit should coexist with a rapid or ultra-rapid circuit, which, although more expensive, can be used in particularly urgent cases. The drop in GS costs should result in its generalized use for diagnostic purposes and lead to a reduction of the costs of rapid GS.
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Affiliation(s)
- Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France. .,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France. .,Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France.
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Évry, France.,LabEx GENMED, Paris, France
| | - Alban Ziegler
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS 6015-INSERM 1083, Angers, France
| | - Médéric Jeanne
- Service de Génétique, Centre Hospitalier Universitaire de Tours, Tours, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Victor Couturier
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Caroline Racine
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Bertrand Isidor
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU Nantes, Nantes, France
| | - Charlotte Poë
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Thibaud Jouan
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Évry, France
| | - Bertrand Fin
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Évry, France
| | - Delphine Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Évry, France
| | - Céline Besse
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Évry, France
| | - Aurore Garde
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Adeline Prost
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Philippine Garret
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Émilie Tisserant
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Julian Delanne
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sophie Nambot
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Aurélien Juven
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Magali Gorce
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS 6015-INSERM 1083, Angers, France
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU Nantes, Nantes, France
| | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU Nantes, Nantes, France
| | - Sébastien Moutton
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN ITHACA, CHU Rennes, Hôpital Sud, Rennes, France.,Service de Génétique Médicale, CH Saint-Brieuc, Saint-Brieuc, France
| | - Alinoë Lavillaureix
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN ITHACA, CHU Rennes, Hôpital Sud, Rennes, France
| | - Paul Rollier
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN ITHACA, CHU Rennes, Hôpital Sud, Rennes, France
| | - Yline Capri
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Julien Van-Gils
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Tiffany Busa
- Département de génétique médicale, CHU Timone enfants, AP-HM, Marseille, France
| | - Sabine Sigaudy
- Département de génétique médicale, CHU Timone enfants, AP-HM, Marseille, France
| | - Laurent Pasquier
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN ITHACA, CHU Rennes, Hôpital Sud, Rennes, France
| | - Magalie Barth
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS 6015-INSERM 1083, Angers, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Cyril Flamant
- Réanimation Pédiatrique et Médecine Néonatale, CHU de Nantes, Nantes, France
| | - Clément Prouteau
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS 6015-INSERM 1083, Angers, France
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS 6015-INSERM 1083, Angers, France
| | - Annick Toutain
- Service de Génétique, Centre Hospitalier Universitaire de Tours, Tours, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Corinne Chantegret
- Réanimation pédiatrique, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Patrick Callier
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Laboratoire de génétique chromosomique et moléculaire, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Yannis Duffourd
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Évry, France.,Centre de Référence, d'Innovation et d'Expertise (CREFIX) du plan FMG2025, US39, F-91057, Évry, France
| | - Arthur Sorlin
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France. .,UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France. .,Centre de Référence Déficiences Intellectuelles de Causes Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.
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10
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Xhaard C, Rouget R, Vodovar N, Le Floch E, Dandine-Roulland C, Wagner S, Bacq-Daian D, Thuillier Q, Boivin JM, Branlant C, Deleuze JF, Behm-Ansmant I, Zannad F, Rossignol P, Girerd N. Impact of natriuretic peptide polymorphisms on diastolic and metabolic function in a populational cohort: insights from the STANISLAS cohort. ESC Heart Fail 2021; 9:729-739. [PMID: 34734498 PMCID: PMC8788028 DOI: 10.1002/ehf2.13674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022] Open
Abstract
AIMS Elevated brain natriuretic peptide (BNP) and the N-terminal fragment of its pro-hormone (NT-proBNP) have become established biomarkers for heart failure and are associated with cardiovascular morbidity and mortality. Investigating sources of inter-individual heterogeneity, particularly genetic factors, could help better identify patients at risk of future cardiovascular disease. The aim of this study was to estimate the heritability of circulating NT-proBNP levels, to perform a genome-wide association study (GWAS) and gene-candidate analysis focused on NPPB-NPPA genes on these levels, and to examine their association with cardiovascular or metabolic outcomes. METHODS AND RESULTS A total of 1555 individuals from the STANISLAS study were included. The heritability of circulating NT-proBNP levels was estimated at 15%, with seven single nucleotide polymorphisms (SNPs) reaching the significant threshold in the GWAS. All above SNPs were located on the same gene cluster constituted of MTHFR, CLCN6, NPPA, NPPB, and C1orf167. NPPA gene expression was also associated with NT-proBNP levels. Moreover, six other SNPs from NPPA-NPPB genes were associated with diastolic function (lateral e' on echocardiography) and metabolic features (glycated haemoglobin). CONCLUSIONS The heritability of natriuretic peptides appears relatively low (15%) and mainly based on the same gene cluster constituted of MTHFR, CLCN6, NPPA, NPPB, and C1orf167. Natriuretic peptide polymorphisms are associated with natriuretic peptide levels and diastolic function. These results suggest that natriuretic peptide polymorphisms may have an impact in the early stages of cardiovascular and metabolic disease.
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Affiliation(s)
- Constance Xhaard
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
| | - Raphaël Rouget
- Université de Lorraine, CNRS, UMR 7365, IMoPA, Nancy, France
| | | | - Edith Le Floch
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Claire Dandine-Roulland
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Sandra Wagner
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | | | | | | | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | | | - Faiez Zannad
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
| | - Patrick Rossignol
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
| | - Nicolas Girerd
- Université de Lorraine, INSERM, Centre d'Investigations Cliniques Plurithématique 1433, INSERM 1116, CHRU de Nancy, FCRIN INI-CRCT, Nancy, France
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11
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Xhaard C, Dandine-Roulland C, Villemereuil PD, Floch EL, Bacq-Daian D, Machu JL, Ferreira JP, Deleuze JF, Zannad F, Rossignol P, Girerd N. Heritability of a resting heart rate in a 20-year follow-up family cohort with GWAS data: Insights from the STANISLAS cohort. Eur J Prev Cardiol 2021; 28:1334-1341. [PMID: 34647585 DOI: 10.1177/2047487319890763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/05/2019] [Indexed: 11/17/2022]
Abstract
BACKGROUND The association between resting heart rate (HR) and cardiovascular outcomes, especially heart failure, is now well established. However, whether HR is mainly an integrated marker of risk associated with other features, or rather a genetic origin risk marker, is still a matter for debate. Previous studies reported a heritability ranging from 14% to 65%. DESIGN We assessed HR heritability in the STANISLAS family-study, based on the data of four visits performed over a 20-year period, and adjusted for most known confounding effects. METHODS These analyses were conducted using a linear mixed model, adjusted on age, sex, tea or coffee consumption, beta-blocker use, physical activity, tobacco use, and alcohol consumption to estimate the variance captured by additive genetic effects, via average information restricted maximum likelihood analysis, with both self-reported pedigree and genetic relatedness matrix (GRM) calculated from genome-wide association study data. RESULTS Based on the data of all visits, the HR heritability (h2) estimate was 23.2% with GRM and 24.5% with pedigree. However, we found a large heterogeneity of HR heritability estimations when restricting the analysis to each of the four visits (h2 from 19% to 39% using pedigree, and from 14% to 32% using GRM). Moreover, only a little part of variance was explained by the common household effect (<5%), and half of the variance remained unexplained. CONCLUSION Using a comprehensive analysis based on a family cohort, including the data of multiple visits and GRM, we found that HR variability is about 25% from genetic origin, 25% from repeated measures and 50% remains unexplained.
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Affiliation(s)
- Constance Xhaard
- INSERM Centre d'Investigation Clinique CIC-P 1433, CHRU Nancy, INSERM U1116, FCRIN INI-CRCT, Lorraine Université, Nancy, France
| | - Claire Dandine-Roulland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Pierre de Villemereuil
- CEFE, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Edith Le Floch
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-Loup Machu
- INSERM Centre d'Investigation Clinique CIC-P 1433, CHRU Nancy, INSERM U1116, FCRIN INI-CRCT, Lorraine Université, Nancy, France
| | - Joao Pedro Ferreira
- INSERM Centre d'Investigation Clinique CIC-P 1433, CHRU Nancy, INSERM U1116, FCRIN INI-CRCT, Lorraine Université, Nancy, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Faiez Zannad
- INSERM Centre d'Investigation Clinique CIC-P 1433, CHRU Nancy, INSERM U1116, FCRIN INI-CRCT, Lorraine Université, Nancy, France
| | - Patrick Rossignol
- INSERM Centre d'Investigation Clinique CIC-P 1433, CHRU Nancy, INSERM U1116, FCRIN INI-CRCT, Lorraine Université, Nancy, France
| | - Nicolas Girerd
- INSERM Centre d'Investigation Clinique CIC-P 1433, CHRU Nancy, INSERM U1116, FCRIN INI-CRCT, Lorraine Université, Nancy, France
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12
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Truong T, Lesueur F, Sugier PE, Guibon J, Xhaard C, Karimi M, Kulkarni O, Lucotte EA, Bacq-Daian D, Boland-Auge A, Mulot C, Laurent-Puig P, Schvartz C, Guizard AV, Ren Y, Adjadj E, Rachédi F, Borson-Chazot F, Ortiz RM, Lence-Anta JJ, Pereda CM, Comiskey DF, He H, Liyanarachchi S, de la Chapelle A, Elisei R, Gemignani F, Thomsen H, Forsti A, Herzig AF, Leutenegger AL, Rubino C, Ostroumova E, Kesminiene A, Boutron-Ruault MC, Deleuze JF, Guénel P, de Vathaire F. Multiethnic genome-wide association study of differentiated thyroid cancer in the EPITHYR consortium. Int J Cancer 2021; 148:2935-2946. [PMID: 33527407 DOI: 10.1002/ijc.33488] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/17/2020] [Accepted: 01/11/2021] [Indexed: 02/05/2023]
Abstract
Incidence of differentiated thyroid carcinoma (DTC) varies considerably between ethnic groups, with particularly high incidence rates in Pacific Islanders. DTC is one of the cancers with the highest familial risk suggesting a major role of genetic risk factors, but only few susceptibility loci were identified so far. In order to assess the contribution of known DTC susceptibility loci and to identify new ones, we conducted a multiethnic genome-wide association study (GWAS) in individuals of European ancestry and of Oceanian ancestry from Pacific Islands. Our study included 1554 cases/1973 controls of European ancestry and 301 cases/348 controls of Oceanian ancestry from seven population-based case-control studies participating to the EPITHYR consortium. All participants were genotyped using the OncoArray-500K Beadchip (Illumina). We confirmed the association with the known DTC susceptibility loci at 2q35, 8p12, 9q22.33 and 14q13.3 in the European ancestry population and suggested two novel signals at 1p31.3 and 16q23.2, which were associated with thyroid-stimulating hormone levels in previous GWAS. We additionally replicated an association with 5p15.33 reported previously in Chinese and European populations. Except at 1p31.3, all associations were in the same direction in the population of Oceanian ancestry. We also observed that the frequencies of risk alleles at 2q35, 5p15.33 and 16q23.2 were significantly higher in Oceanians than in Europeans. However, additional GWAS and epidemiological studies in Oceanian populations are needed to fully understand the highest incidence observed in these populations.
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Affiliation(s)
- Thérèse Truong
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif, France
| | - Fabienne Lesueur
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Pierre-Emmanuel Sugier
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif, France
| | - Julie Guibon
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif, France
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Constance Xhaard
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Epidemiology of radiations", Villejuif, France
- University of Lorraine, INSERM CIC 1433, Nancy CHRU, Inserm U1116, FCRIN, INI-CRCT, Nancy, France
| | - Mojgan Karimi
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif, France
| | - Om Kulkarni
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Elise A Lucotte
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif, France
| | - Delphine Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Anne Boland-Auge
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Claire Mulot
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, Paris, France
| | - Claire Schvartz
- Registre des Cancers Thyroïdiens, Institut GODINOT, Reims, France
| | - Anne-Valérie Guizard
- Registre Général des tumeurs du Calvados, Centre François Baclesse, Caen, France
- Inserm U1086 -UCN "ANTICIPE", Caen, France
| | - Yan Ren
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Epidemiology of radiations", Villejuif, France
| | - Elisabeth Adjadj
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Epidemiology of radiations", Villejuif, France
| | - Frédérique Rachédi
- Endocrinology Unit, Territorial Hospital Taaone, Papeete, Tahiti, French Polynesia
| | - Francoise Borson-Chazot
- Fédération d'endocrinologie, Hôpital Louis Pradel, Hospices Civils de Lyon, EA 7425, Université Lyon 1, Lyon, France
| | | | | | | | - Daniel F Comiskey
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Huiling He
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Sandya Liyanarachchi
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Albert de la Chapelle
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | | | | | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- GeneWerk GmbH, Heidelberg, Germany
| | - Asta Forsti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Anthony F Herzig
- Inserm, U1078, GGB, Université de Bretagne Occidentale, EFS, Brest, France
| | | | - Carole Rubino
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Epidemiology of radiations", Villejuif, France
| | | | | | | | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Pascal Guénel
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif, France
| | - Florent de Vathaire
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Epidemiology of radiations", Villejuif, France
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13
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Garnier S, Harakalova M, Weiss S, Mokry M, Regitz-Zagrosek V, Hengstenberg C, Cappola TP, Isnard R, Arbustini E, Cook SA, van Setten J, Calis JJA, Hakonarson H, Morley MP, Stark K, Prasad SK, Li J, O'Regan DP, Grasso M, Müller-Nurasyid M, Meitinger T, Empana JP, Strauch K, Waldenberger M, Marguiles KB, Seidman CE, Kararigas G, Meder B, Haas J, Boutouyrie P, Lacolley P, Jouven X, Erdmann J, Blankenberg S, Wichter T, Ruppert V, Tavazzi L, Dubourg O, Roizes G, Dorent R, de Groote P, Fauchier L, Trochu JN, Aupetit JF, Bilinska ZT, Germain M, Völker U, Hemerich D, Raji I, Bacq-Daian D, Proust C, Remior P, Gomez-Bueno M, Lehnert K, Maas R, Olaso R, Saripella GV, Felix SB, McGinn S, Duboscq-Bidot L, van Mil A, Besse C, Fontaine V, Blanché H, Ader F, Keating B, Curjol A, Boland A, Komajda M, Cambien F, Deleuze JF, Dörr M, Asselbergs FW, Villard E, Trégouët DA, Charron P. Genome-wide association analysis in dilated cardiomyopathy reveals two new players in systolic heart failure on chromosomes 3p25.1 and 22q11.23. Eur Heart J 2021; 42:2000-2011. [PMID: 33677556 PMCID: PMC8139853 DOI: 10.1093/eurheartj/ehab030] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/13/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022] Open
Abstract
AIMS Our objective was to better understand the genetic bases of dilated cardiomyopathy (DCM), a leading cause of systolic heart failure. METHODS AND RESULTS We conducted the largest genome-wide association study performed so far in DCM, with 2719 cases and 4440 controls in the discovery population. We identified and replicated two new DCM-associated loci on chromosome 3p25.1 [lead single-nucleotide polymorphism (SNP) rs62232870, P = 8.7 × 10-11 and 7.7 × 10-4 in the discovery and replication steps, respectively] and chromosome 22q11.23 (lead SNP rs7284877, P = 3.3 × 10-8 and 1.4 × 10-3 in the discovery and replication steps, respectively), while confirming two previously identified DCM loci on chromosomes 10 and 1, BAG3 and HSPB7. A genetic risk score constructed from the number of risk alleles at these four DCM loci revealed a 3-fold increased risk of DCM for individuals with 8 risk alleles compared to individuals with 5 risk alleles (median of the referral population). In silico annotation and functional 4C-sequencing analyses on iPSC-derived cardiomyocytes identify SLC6A6 as the most likely DCM gene at the 3p25.1 locus. This gene encodes a taurine transporter whose involvement in myocardial dysfunction and DCM is supported by numerous observations in humans and animals. At the 22q11.23 locus, in silico and data mining annotations, and to a lesser extent functional analysis, strongly suggest SMARCB1 as the candidate culprit gene. CONCLUSION This study provides a better understanding of the genetic architecture of DCM and sheds light on novel biological pathways underlying heart failure.
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Affiliation(s)
- Sophie Garnier
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Michal Mokry
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Laboratory of Clinical Chemistry and Haematology, University Medical Center, Heidelberglaan 100, Utrecht, the Netherlands
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, the Netherlands
| | - Vera Regitz-Zagrosek
- Institute of Gender in Medicine and Center for Cardiovascular Research, Charite University Hospital, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Berlin, Germany
| | - Christian Hengstenberg
- Department of Internal Medicine, Division of Cardiology, Medical University of Vienna, Austria
- Department of Internal Medicine, Medical University of Regensburg, Germany
| | - Thomas P Cappola
- Penn Cardiovascular Institute and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard Isnard
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
- Cardiology Department, APHP, Pitié-Salpêtrière Hospital, Paris, France
| | | | - Stuart A Cook
- National Heart and Lung Institute, Imperial College London, London, UK
- National Heart Centre Singapore, Singapore
- Duke-NUS, Singapore
| | - Jessica van Setten
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jorg J A Calis
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael P Morley
- Penn Cardiovascular Institute and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Klaus Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Sanjay K Prasad
- National Heart Centre Singapore, Singapore
- Royal Brompton Hospital, London, UK
| | - Jin Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Declan P O'Regan
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Maurizia Grasso
- Centre for Inherited Cardiovascular Diseases—IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, Germany
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Thomas Meitinger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jean-Philippe Empana
- Université de Paris, INSERM, UMR-S970, Integrative Epidemiology of cardiovascular disease, Paris, France
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz 55101, Germany
| | - Melanie Waldenberger
- Research unit of Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Kenneth B Marguiles
- Penn Cardiovascular Institute and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christine E Seidman
- Department of Medicine and Genetics Harvard Medical School, Boston, MA, USA
- Brigham & Women's Cardiovascular Genetics Center, Boston, MA, USA
| | - Georgios Kararigas
- Department of Physiology, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavík, Iceland
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg, Heidelberg University, Germany
- Stanford Genome Technology Center, Department of Genetics, Stanford Medical School, CA, USA
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg, Heidelberg University, Germany
| | - Pierre Boutouyrie
- Université de Paris, INSERM, UMR-S970, Integrative Epidemiology of cardiovascular disease, Paris, France
- Cardiology Department, APHP, Georges Pompidou European Hospital, Paris, France
| | | | - Xavier Jouven
- Université de Paris, INSERM, UMR-S970, Integrative Epidemiology of cardiovascular disease, Paris, France
- Cardiology Department, APHP, Georges Pompidou European Hospital, Paris, France
| | - Jeanette Erdmann
- Medizinische Klinik und Poliklinik, Universitätsmedizin der Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | | | - Thomas Wichter
- Dept. of Cardiology and Angiology, Niels-Stensen-Kliniken Marienhospital Osnabrück, Heart Centre Osnabrück/Bad Rothenfelde, Osnabrück 49074, Germany
| | - Volker Ruppert
- Klinik für Innere Medizin-Kardiologie UKGM GmbH Standort Marburg Baldingerstrasse, Marburg, Germany
| | - Luigi Tavazzi
- Maria Cecilia Hospital, GVM Care and Research, Cotignola, Italy
| | - Olivier Dubourg
- Université de Versailles-Saint Quentin, Hôpital Ambroise Paré, AP-HP, Boulogne, France
| | - Gérard Roizes
- Institut de Génétique Humaine, UPR 1142, CNRS, Montpellier, France
| | | | | | - Laurent Fauchier
- Service de Cardiologie, Centre Hospitalier Universitaire Trousseau, Tours, France
| | - Jean-Noël Trochu
- Université de Nantes, CHU Nantes, CNRS, INSERM, l’institut du thorax, Nantes 44000, France
| | - Jean-François Aupetit
- Département de pathologie cardiovasculaire, Hôpital Saint-Joseph-Saint-Luc, Lyon, France
| | - Zofia T Bilinska
- Unit for Screening Studies in Inherited Cardiovascular Diseases, National Institute of Cardiology, Warsaw, Poland
| | - Marine Germain
- Univ. Bordeaux, INSERM, BPH, U1219, Bordeaux 33000, France
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Daiane Hemerich
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ibticem Raji
- AP-HP, Département de Génétique, Centre de Référence Maladies Cardiaques Héréditaires, Hôpital Pitié-Salpêtrière, Paris, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Carole Proust
- Univ. Bordeaux, INSERM, BPH, U1219, Bordeaux 33000, France
| | - Paloma Remior
- Department of Cardiology, Hospital Universitario Puerta de Hierro, CIBERCV, Madrid, Spain
| | - Manuel Gomez-Bueno
- Department of Cardiology, Hospital Universitario Puerta de Hierro, CIBERCV, Madrid, Spain
| | - Kristin Lehnert
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Renee Maas
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Ganapathi Varma Saripella
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- SLU Bioinformatics Infrastructure (SLUBI), PlantLink, Department of Plant Breeding, Swedish University of Agricultural Sciences, Almas Allé 8, 750 07 Uppsala, Sweden
| | - Stephan B Felix
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Steven McGinn
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Laëtitia Duboscq-Bidot
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
| | - Alain van Mil
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Céline Besse
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Vincent Fontaine
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
| | - Hélène Blanché
- Laboratory of Excellence GENMED (Medical Genomics)
- Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Flavie Ader
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- APHP, UF Cardiogénétique et Myogénétique, service de Biochimie métabolique, Hôpital universitaire Pitié-Salpêtrière Paris, France
- Faculté de Pharmacie Paris Descartes, Département 3, Paris 75006, France
| | - Brendan Keating
- Division of Transplantation, Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Angélique Curjol
- AP-HP, Département de Génétique, Centre de Référence Maladies Cardiaques Héréditaires, Hôpital Pitié-Salpêtrière, Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Michel Komajda
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
- Cardiology Department, Groupe Hospitalier Paris Saint Joseph, Paris, France
| | | | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry 91057, France
- Laboratory of Excellence GENMED (Medical Genomics)
- Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Marcus Dörr
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Eric Villard
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
| | - David-Alexandre Trégouët
- Univ. Bordeaux, INSERM, BPH, U1219, Bordeaux 33000, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Philippe Charron
- Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France
- Cardiology Department, APHP, Pitié-Salpêtrière Hospital, Paris, France
- AP-HP, Département de Génétique, Centre de Référence Maladies Cardiaques Héréditaires, Hôpital Pitié-Salpêtrière, Paris, France
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14
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Kulkarni O, Sugier PE, Guibon J, Boland-Augé A, Lonjou C, Bacq-Daian D, Olaso R, Rubino C, Souchard V, Rachedi F, Lence-Anta JJ, Ortiz RM, Xhaard C, Laurent-Puig P, Mulot C, Guizard AV, Schvartz C, Boutron-Ruault MC, Ostroumova E, Kesminiene A, Deleuze JF, Guénel P, De Vathaire F, Truong T, Lesueur F. Gene network and biological pathways associated with susceptibility to differentiated thyroid carcinoma. Sci Rep 2021; 11:8932. [PMID: 33903625 PMCID: PMC8076215 DOI: 10.1038/s41598-021-88253-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/09/2021] [Indexed: 12/11/2022] Open
Abstract
Variants identified in earlier genome-wide association studies (GWAS) on differentiated thyroid carcinoma (DTC) explain about 10% of the overall estimated genetic contribution and could not provide complete insights into biological mechanisms involved in DTC susceptibility. Integrating systems biology information from model organisms, genome-wide expression data from tumor and matched normal tissue and GWAS data could help identifying DTC-associated genes, and pathways or functional networks in which they are involved. We performed data mining of GWAS data of the EPITHYR consortium (1551 cases and 1957 controls) using various pathways and protein-protein interaction (PPI) annotation databases and gene expression data from The Cancer Genome Atlas. We identified eight DTC-associated genes at known loci 2q35 (DIRC3), 8p12 (NRG1), 9q22 (FOXE1, TRMO, HEMGN, ANP32B, NANS) and 14q13 (MBIP). Using the EW_dmGWAS approach we found that gene networks related to glycogenolysis, glycogen metabolism, insulin metabolism and signal transduction pathways associated with muscle contraction were overrepresented with association signals (false discovery rate adjusted p-value < 0.05). Additionally, suggestive association of 21 KEGG and 75 REACTOME pathways with DTC indicate a link between DTC susceptibility and functions related to metabolism of cholesterol, amino sugar and nucleotide sugar metabolism, steroid biosynthesis, and downregulation of ERBB2 signaling pathways. Together, our results provide novel insights into biological mechanisms contributing to DTC risk.
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Affiliation(s)
- Om Kulkarni
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, 75248, Paris, France
| | | | - Julie Guibon
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, 75248, Paris, France
- Université Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, 94807, Villejuif, France
| | - Anne Boland-Augé
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Evry, France
| | - Christine Lonjou
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, 75248, Paris, France
| | - Delphine Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Evry, France
| | - Carole Rubino
- Université Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, 94807, Villejuif, France
| | - Vincent Souchard
- Université Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, 94807, Villejuif, France
| | - Frédérique Rachedi
- Centre Hospitalier Territorial de Polynésie Française, CHTPF, Pirae, Tahiti, 98713, Papeete, French Polynesia
| | | | - Rosa Maria Ortiz
- Instituto Nacional de Oncologia y de Radiobiologia, INOR, La Havana, Cuba
| | - Constance Xhaard
- Université Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, 94807, Villejuif, France
- University of Lorraine, INSERM CIC 1433, Nancy CHRU, Inserm U1116, FCRIN, INI-CRCT, 54000, Nancy, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, 75006, Paris, France
| | - Claire Mulot
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, 75006, Paris, France
| | - Anne-Valérie Guizard
- Registre Général des Tumeurs du Calvados, Centre François Baclesse, 14000, Caen, France
- Inserm U1086-UCNB, Cancers and Prevention, 14000, Caen, France
| | - Claire Schvartz
- Registre des Cancers Thyroïdiens, Institut Jean Godinot, 51100, Reims, France
| | | | - Evgenia Ostroumova
- Environment and Radiation Section, International Agency for Research on Cancer, 69008, Lyon, France
| | - Ausrele Kesminiene
- Environment and Radiation Section, International Agency for Research on Cancer, 69008, Lyon, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057, Evry, France
| | - Pascal Guénel
- Université Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, 94807, Villejuif, France
| | - Florent De Vathaire
- Université Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, 94807, Villejuif, France
| | - Thérèse Truong
- Université Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, 94807, Villejuif, France
| | - Fabienne Lesueur
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, 75248, Paris, France.
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15
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Guibon J, Sugier PE, Kulkarni O, Karimi M, Bacq-Daian D, Besse C, Boland A, Adjadj E, Rachédi F, Rubino C, Xhaard C, Mulot C, Laurent-Puig P, Guizard AV, Schvartz C, Ortiz RM, Ren Y, Ostroumova E, Deleuze JF, Boutron-Ruault MC, Kesminiene A, De Vathaire F, Guénel P, Lesueur F, Truong T. Fine-mapping of two differentiated thyroid carcinoma susceptibility loci at 2q35 and 8p12 in Europeans, Melanesians and Polynesians. Oncotarget 2021; 12:493-506. [PMID: 33747362 PMCID: PMC7939525 DOI: 10.18632/oncotarget.27888] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/26/2021] [Indexed: 01/06/2023] Open
Abstract
Differentiated thyroid carcinoma (DTC) incidence is characterized by wide ethnic and geographic variations, with high incidence rates observed in Oceanian populations. Genome-wide association studies (GWAS) identified mainly four DTC susceptibility loci at 9q22.33, 14q13.3, 2q35 and 8p12. Here we performed fine-mapping of the 2q35 and 8p12 loci in the population of the EPITHYR consortium that includes Europeans, Melanesians and Polynesians to identify likely causal variants for DTC risk. We conducted a colocalization analysis using eQTLs data to determine the SNPs with the highest probability of causality. At 2q35, we highlighted rs16857609 located in DIRC3. This SNP has a high probability of causality in the three populations, and a significant association in Europeans (OR = 1.4, p = 1.9 x 10-10). It is also associated with expression of DIRC3 and of the nearby gene IGFBP5 in thyroid tumour cells. At 8p12, we identified rs7844425 which was significantly associated with DTC in Europeans (OR = 1.32, p = 7.6 x 10-8) and rs2439304, which was highlighted by the colocalization analysis but only moderately associated with DTC in our dataset (OR = 1.2, p = 0.001). These SNPs are linked to the expression of NRG1 in thyroid tissue. Hence, our study identified novel variants at 2q35 and 8p12 to be prioritized for further functional studies.
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Affiliation(s)
- Julie Guibon
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Exposome and Heredity Team, Villejuif, France
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Pierre-Emmanuel Sugier
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Exposome and Heredity Team, Villejuif, France
| | - Om Kulkarni
- University Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Mojgan Karimi
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Exposome and Heredity Team, Villejuif, France
| | - Delphine Bacq-Daian
- University Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Céline Besse
- University Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Anne Boland
- University Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Elisabeth Adjadj
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Epidemiology of Radiations Team, Villejuif, France
| | - Frédérique Rachédi
- Endocrinology Unit, Territorial Hospital Taaone, Papeete, French Polynesia
| | - Carole Rubino
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Epidemiology of Radiations Team, Villejuif, France
| | - Constance Xhaard
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Epidemiology of Radiations Team, Villejuif, France
- University of Lorraine, INSERM CIC 1433, Nancy CHRU, Inserm U1116, FCRIN, INI-CRCT, Nancy, France
| | - Claire Mulot
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, Paris, France
| | - Anne-Valérie Guizard
- Registre Général des Tumeurs du Calvados, Centre François Baclesse, Caen, France
- Inserm U1086 -UCN "ANTICIPE", Caen, France
| | - Claire Schvartz
- Registre des Cancers Thyroïdiens, Institut Godinot, Reims, France
| | | | - Yan Ren
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Epidemiology of Radiations Team, Villejuif, France
| | | | - Jean-François Deleuze
- University Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | | | | | - Florent De Vathaire
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Epidemiology of Radiations Team, Villejuif, France
| | - Pascal Guénel
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Exposome and Heredity Team, Villejuif, France
| | - Fabienne Lesueur
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
- These authors contributed equally to this work
| | - Thérèse Truong
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Exposome and Heredity Team, Villejuif, France
- These authors contributed equally to this work
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16
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Sabbagh A, Pacot L, Parfait B, Boland-Auge A, Bacq-Daian D, Laurendeau I, Ferkal S, Briand A, Allanore L, Deleuze J, Vidaud M, Vidaud D, Pasmant E, Wolkenstein P. La première étude d’association génome entier dans la neurofibromatose de type 1 : vers l’identification des modificateurs génétiques de l’expression clinique de la maladie. Ann Dermatol Venereol 2019. [DOI: 10.1016/j.annder.2019.09.121] [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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17
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Laskar RS, Muller DC, Li P, Machiela MJ, Ye Y, Gaborieau V, Foll M, Hofmann JN, Colli L, Sampson JN, Wang Z, Bacq-Daian D, Boland A, Abedi-Ardekani B, Durand G, Le Calvez-Kelm F, Robinot N, Blanche H, Prokhortchouk E, Skryabin KG, Burdett L, Yeager M, Radojevic-Skodric S, Savic S, Foretova L, Holcatova I, Janout V, Mates D, Rascu S, Mukeria A, Zaridze D, Bencko V, Cybulski C, Fabianova E, Jinga V, Lissowska J, Lubinski J, Navratilova M, Rudnai P, Świątkowska B, Benhamou S, Cancel-Tassin G, Cussenot O, Trichopoulou A, Riboli E, Overvad K, Panico S, Ljungberg B, Sitaram RT, Giles GG, Milne RL, Severi G, Bruinsma F, Fletcher T, Koppova K, Larsson SC, Wolk A, Banks RE, Selby PJ, Easton DF, Pharoah P, Andreotti G, Beane Freeman LE, Koutros S, Albanes D, Männistö S, Weinstein S, Clark PE, Edwards TL, Lipworth L, Carol H, Freedman ML, Pomerantz MM, Cho E, Kraft P, Preston MA, Wilson KM, Michael Gaziano J, Sesso HD, Black A, Freedman ND, Huang WY, Anema JG, Kahnoski RJ, Lane BR, Noyes SL, Petillo D, Teh BT, Peters U, White E, Anderson GL, Johnson L, Luo J, Chow WH, Moore LE, Choueiri TK, Wood C, Johansson M, McKay JD, Brown KM, Rothman N, Lathrop MG, Deleuze JF, Wu X, Brennan P, Chanock SJ, Purdue MP, Scelo G. Sex specific associations in genome wide association analysis of renal cell carcinoma. Eur J Hum Genet 2019; 27:1589-1598. [PMID: 31231134 PMCID: PMC6777615 DOI: 10.1038/s41431-019-0455-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 12/15/2022] Open
Abstract
Renal cell carcinoma (RCC) has an undisputed genetic component and a stable 2:1 male to female sex ratio in its incidence across populations, suggesting possible sexual dimorphism in its genetic susceptibility. We conducted the first sex-specific genome-wide association analysis of RCC for men (3227 cases, 4916 controls) and women (1992 cases, 3095 controls) of European ancestry from two RCC genome-wide scans and replicated the top findings using an additional series of men (2261 cases, 5852 controls) and women (1399 cases, 1575 controls) from two independent cohorts of European origin. Our study confirmed sex-specific associations for two known RCC risk loci at 14q24.2 (DPF3) and 2p21(EPAS1). We also identified two additional suggestive male-specific loci at 6q24.3 (SAMD5, male odds ratio (ORmale) = 0.83 [95% CI = 0.78-0.89], Pmale = 1.71 × 10-8 compared with female odds ratio (ORfemale) = 0.98 [95% CI = 0.90-1.07], Pfemale = 0.68) and 12q23.3 (intergenic, ORmale = 0.75 [95% CI = 0.68-0.83], Pmale = 1.59 × 10-8 compared with ORfemale = 0.93 [95% CI = 0.82-1.06], Pfemale = 0.21) that attained genome-wide significance in the joint meta-analysis. Herein, we provide evidence of sex-specific associations in RCC genetic susceptibility and advocate the necessity of larger genetic and genomic studies to unravel the endogenous causes of sex bias in sexually dimorphic traits and diseases like RCC.
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Affiliation(s)
- Ruhina S Laskar
- International Agency for Research on Cancer (IARC), Lyon, France
| | - David C Muller
- Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Peng Li
- Max Planck Institute for Demographic Research, Rostock, Germany
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Yuanqing Ye
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Matthieu Foll
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Leandro Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine, , Institut de biologie François Jacob, CEA, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, , Institut de biologie François Jacob, CEA, Evry, France
| | | | - Geoffroy Durand
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | | | - Helene Blanche
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Egor Prokhortchouk
- Center 'Bioengineering' of the Russian Academy of Sciences, Moscow, Russian Federation
- Kurchatov Scientific Center, Moscow, Russian Federation
| | - Konstantin G Skryabin
- Center 'Bioengineering' of the Russian Academy of Sciences, Moscow, Russian Federation
- Kurchatov Scientific Center, Moscow, Russian Federation
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | | | - Slavisa Savic
- Department of Urology, University Hospital "Dr D. Misovic" Clinical Center, Belgrade, Serbia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ivana Holcatova
- 2nd Faculty of Medicine, Institute of Public Health and Preventive Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Janout
- Department of Preventive Medicine, Faculty of Medicine, Palacky University, Olomouc, Czech Republic
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Stefan Rascu
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - Anush Mukeria
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Vladimir Bencko
- First Faculty of Medicine, Institute of Hygiene and Epidemiology, Charles University, Prague, Czech Republic
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Eleonora Fabianova
- Regional Authority of Public Health in BanskaBystrica, BanskaBystrica, Slovakia
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Th. Burghele Hospital, Bucharest, Romania
| | - Jolanta Lissowska
- The M Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Peter Rudnai
- National Public Health Institute, Budapest, Hungary
| | - Beata Świątkowska
- Department of Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Simone Benhamou
- INSERM U946, Paris, France
- CNRS UMR8200, Institute Gustave Roussy, Villejuif, France
| | - Geraldine Cancel-Tassin
- Sorbonne Université, GRC no. 5, ONCOTYPE-URO, AP-HP, Tenon Hospital, Paris, France
- CeRePP, Paris, France
| | - Olivier Cussenot
- Sorbonne Université, GRC no. 5, ONCOTYPE-URO, AP-HP, Tenon Hospital, Paris, France
- CeRePP, Paris, France
| | | | - Elio Riboli
- Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Kim Overvad
- Department of Public Health, Section for Epidemiology, Aarhus University, Aarhus C, Denmark
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | - Borje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Raviprakash T Sitaram
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council of Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville Victoria, 3010, Australia
| | - Roger L Milne
- Cancer Epidemiology & Intelligence Division, Cancer Council of Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville Victoria, 3010, Australia
| | - Gianluca Severi
- Cancer Epidemiology & Intelligence Division, Cancer Council of Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
- Inserm U1018, Center for Research in Epidemiology and Population Health (CESP), Facultés de Medicine, Université Paris-Saclay, Université Paris-Sud, UVSQ, Gustave Roussy, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
| | - Fiona Bruinsma
- Cancer Epidemiology & Intelligence Division, Cancer Council of Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
| | - Tony Fletcher
- London School of Hygiene and Tropical Medicine, University of London, London, UK
| | - Kvetoslava Koppova
- Regional Authority of Public Health in BanskaBystrica, BanskaBystrica, Slovakia
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rosamonde E Banks
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, UK
| | - Peter J Selby
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, UK
| | - Douglas F Easton
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Satu Männistö
- National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | | | | | | | | | | | | | | | - Peter Kraft
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark A Preston
- Brigham and Women's Hospital and VA Boston, Boston, MA, USA
| | | | | | - Howard D Sesso
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - John G Anema
- Division of Urology, Spectrum Health, Grand Rapids, MI, USA
| | | | - Brian R Lane
- Division of Urology, Spectrum Health, Grand Rapids, MI, USA
- College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Sabrina L Noyes
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - David Petillo
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - Bin Tean Teh
- Van Andel Research Institute, Center for Cancer Genomics and Quantitative Biology, Grand Rapids, MI, USA
| | - Ulrike Peters
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily White
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Lisa Johnson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Juhua Luo
- Department of Epidemiology and Biostatistics, School of Public Health Indiana University Bloomington, Bloomington, IN, USA
| | - Wong-Ho Chow
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lee E Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | | | - Christopher Wood
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - James D McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Mark G Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine, , Institut de biologie François Jacob, CEA, Evry, France
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France.
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18
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Bonnet E, Moutet ML, Baulard C, Bacq-Daian D, Sandron F, Mesrob L, Fin B, Delépine M, Palomares MA, Jubin C, Blanché H, Meyer V, Boland A, Olaso R, Deleuze JF. Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples. PLoS One 2018; 13:e0195471. [PMID: 29621323 PMCID: PMC5886566 DOI: 10.1371/journal.pone.0195471] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/25/2018] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling. Here, we generated 42 human whole-exome sequencing data sets from fresh-frozen (FF) and FFPE samples. These samples include normal and tumor tissues from two different organs (liver and colon), that we extracted with three different FFPE extraction kits (QIAamp DNA FFPE Tissue kit and GeneRead DNA FFPE kit from Qiagen, Maxwell™ RSC DNA FFPE Kit from Promega). We determined the rate of concordance of called variants between matched FF and FFPE samples on all common variants (representing at least 86% of the total number of variants for SNVs). The concordance rate is very high between all matched FF / FFPE pairs, with equivalent values for the three kits we analyzed. On the other hand, when looking at the difference between the total number of variants in FF and FFPE, we find a significant variation for the three different FFPE DNA extraction kits. Coverage analysis shows that FFPE samples have less good indicators than FF samples, yet the coverage quality remains above accepted thresholds. We detect limited but statistically significant variations in coverage indicator values between the three FFPE extraction kits. Globally, the GeneRead and QIAamp kits have better variant calling and coverage indicators than the Maxwell kit on the samples used in this study, although this kit performs better on some indicators and has advantages in terms of practical usage. Taken together, our results confirm the potential of FFPE samples analysis for clinical genomic studies, but also indicate that the choice of a FFPE DNA extraction kit should be done with careful testing and analysis beforehand in order to maximize the accuracy of the results.
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Affiliation(s)
- Eric Bonnet
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Marie-Laure Moutet
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Céline Baulard
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Florian Sandron
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Lilia Mesrob
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Bertrand Fin
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Marc Delépine
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Marie-Ange Palomares
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Claire Jubin
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Hélène Blanché
- Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
- LabEx GenMed, Evry, France
- Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
- Centre de REFérence, d’Innovation, d’eXpertise et de transfert (CREFIX), Evry, France
- * E-mail:
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19
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Sabbagh A, Parfait B, Boland-Auge A, Bacq-Daian D, Ferkal S, Allanore L, Pasmant E, Deleuze JF, Vidaud M, Vidaud D, Wolkenstein P. La première étude d’association génome entier dans la neurofibromatose de type 1 : vers l’identification de gènes modificateurs. Ann Dermatol Venereol 2017. [DOI: 10.1016/j.annder.2017.09.101] [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: 10/18/2022]
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20
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Rufflé F, Audoux J, Boureux A, Beaumeunier S, Gaillard JB, Bou Samra E, Megarbane A, Cassinat B, Chomienne C, Alves R, Riquier S, Gilbert N, Lemaitre JM, Bacq-Daian D, Bougé AL, Philippe N, Commes T. New chimeric RNAs in acute myeloid leukemia. F1000Res 2017; 6. [PMID: 29623188 PMCID: PMC5861515 DOI: 10.12688/f1000research.11352.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/05/2017] [Indexed: 12/24/2022] Open
Abstract
Background: High-throughput next generation sequencing (NGS) technologies enable the detection of biomarkers used for tumor classification, disease monitoring and cancer therapy. Whole-transcriptome analysis using RNA-seq is important, not only as a means of understanding the mechanisms responsible for complex diseases but also to efficiently identify novel genes/exons, splice isoforms, RNA editing, allele-specific mutations, differential gene expression and fusion-transcripts or chimeric RNA (chRNA). Methods: We used
Crac, a tool that uses genomic locations and local coverage to classify biological events and directly infer splice and chimeric junctions within a single read. Crac’s algorithm extracts transcriptional chimeric events irrespective of annotation with a high sensitivity, and
CracTools was used to aggregate, annotate and filter the chRNA reads. The selected chRNA candidates were validated by real time PCR and sequencing. In order to check the tumor specific expression of chRNA, we analyzed a publicly available dataset using a new tag search approach. Results: We present data related to acute myeloid leukemia (AML) RNA-seq analysis. We highlight novel biological cases of chRNA, in addition to previously well characterized leukemia chRNA. We have identified and validated 17 chRNAs among 3 AML patients: 10 from an AML patient with a translocation between chromosomes 15 and 17 (AML-t(15;17), 4 from patient with normal karyotype (AML-NK) 3 from a patient with chromosomal 16 inversion (AML-inv16). The new fusion transcripts can be classified into four groups according to the exon organization. Conclusions: All groups suggest complex but distinct synthesis mechanisms involving either collinear exons of different genes, non-collinear exons, or exons of different chromosomes. Finally, we check tumor-specific expression in a larger RNA-seq AML cohort and identify new AML biomarkers that could improve diagnosis and prognosis of AML.
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Affiliation(s)
- Florence Rufflé
- Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.,Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | - Jerome Audoux
- Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.,Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | - Anthony Boureux
- Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.,Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | - Sacha Beaumeunier
- Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.,Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | | | - Elias Bou Samra
- Université Paris Sud, Université Paris-Saclay, Orsay, France.,Institut Curie, PSL Research University, Paris, France
| | | | - Bruno Cassinat
- Laboratoire de Biologie Cellulaire, Hôpital Saint-Louis, Assistance publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Christine Chomienne
- Laboratoire de Biologie Cellulaire, Hôpital Saint-Louis, Assistance publique - Hôpitaux de Paris (AP-HP), Paris, France.,Hôpital Saint-Louis, Université Paris Diderot, INSERM UMRS 1131, Paris, France
| | - Ronnie Alves
- Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.,Instituto Tecnológico Vale, Nazaré, Belém, PA, Brazil
| | - Sebastien Riquier
- Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.,Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | - Nicolas Gilbert
- Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | - Jean-Marc Lemaitre
- Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | | | - Anne Laure Bougé
- Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.,Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | - Nicolas Philippe
- Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.,Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | - Therese Commes
- Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.,Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
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21
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Pedergnana V, Gessain A, Tortevoye P, Byun M, Bacq-Daian D, Boland A, Casanova JL, Abel L, Plancoulaine S. A major locus on chromosome 3p22 conferring predisposition to human herpesvirus 8 infection. Eur J Hum Genet 2012; 20:690-5. [PMID: 22258534 DOI: 10.1038/ejhg.2011.260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Infection with human herpesvirus 8 (HHV-8), the etiological agent of Kaposi's sarcoma, has been shown to display strong familial aggregation, in countries in which HHV-8 infection is endemic. We investigated 40 large families (608 subjects aged one to 88 years) living in an isolated area of Cameroon in which HHV-8 is highly endemic. We performed a two-step genetic analysis for HHV-8 infection status (HHV-8+/HHV-8- determined by immunofluorescence) consisting of an initial segregation analysis followed by a model-based genome-wide linkage analysis. Overall HHV-8 seroprevalence was 60%, increasing with age. Segregation analysis provided strong evidence for a recessive major gene conferring predisposition to HHV-8 infection. This gene is predicted to have a major effect during childhood, with almost all homozygous predisposed subjects (∼7% of the population) becoming infected by the age of 10. Linkage analysis was carried out on the 15 most informative families, corresponding to 205 genotyped subjects. A single region on chromosome 3p22 was significantly linked to HHV-8 infection (LOD score=3.83, P=2.0 × 10(-5)). This study provides the first evidence that HHV-8 infection in children in endemic areas has a strong genetic basis involving at least one recessive major locus on chromosome 3p22.
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Affiliation(s)
- Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
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22
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Stanescu HC, Arcos-Burgos M, Medlar A, Bockenhauer D, Kottgen A, Dragomirescu L, Voinescu C, Patel N, Pearce K, Hubank M, Stephens HAF, Laundy V, Padmanabhan S, Zawadzka A, Hofstra JM, Coenen MJH, den Heijer M, Kiemeney LALM, Bacq-Daian D, Stengel B, Powis SH, Brenchley P, Feehally J, Rees AJ, Debiec H, Wetzels JFM, Ronco P, Mathieson PW, Kleta R. Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy. N Engl J Med 2011; 364:616-26. [PMID: 21323541 DOI: 10.1056/nejmoa1009742] [Citation(s) in RCA: 348] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Idiopathic membranous nephropathy is a major cause of the nephrotic syndrome in adults, but its etiologic basis is not fully understood. We investigated the genetic basis of biopsy-proven cases of idiopathic membranous nephropathy in a white population. METHODS We performed independent genomewide association studies of single-nucleotide polymorphisms (SNPs) in patients with idiopathic membranous nephropathy from three populations of white ancestry (75 French, 146 Dutch, and 335 British patients). The patients were compared with racially matched control subjects; population stratification and quality controls were carried out according to standard criteria. Associations were calculated by means of a chi-square basic allele test; the threshold for significance was adjusted for multiple comparisons (with the Bonferroni method). RESULTS In a joint analysis of data from the 556 patients studied (398 men), we identified significant alleles at two genomic loci associated with idiopathic membranous nephropathy. Chromosome 2q24 contains the gene encoding M-type phospholipase A(2) receptor (PLA(2)R1) (SNP rs4664308, P=8.6×10(-29)), previously shown to be the target of an autoimmune response. Chromosome 6p21 contains the gene encoding HLA complex class II HLA-DQ alpha chain 1 (HLA-DQA1) (SNP rs2187668, P=8.0×10(-93)). The association with HLA-DQA1 was significant in all three populations (P=1.8×10(-9), P=5.6×10(-27), and P=5.2×10(-36) in the French, Dutch, and British groups, respectively). The odds ratio for idiopathic membranous nephropathy with homozygosity for both risk alleles was 78.5 (95% confidence interval, 34.6 to 178.2). CONCLUSIONS An HLA-DQA1 allele on chromosome 6p21 is most closely associated with idiopathic membranous nephropathy in persons of white ancestry. This allele may facilitate an autoimmune response against targets such as variants of PLA2R1. Our findings suggest a basis for understanding this disease and illuminate how adaptive immunity is regulated by HLA.
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Affiliation(s)
- Horia C Stanescu
- Centre for Nephrology, Royal Free Hospital, University College London, London, United Kingdom
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