25 results on '"Amélie Pinard"'
Search Results
2. Preventing Acute Aortic Dissections: The Power of Familial Screening and Risk Assessment
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Alana C. Cecchi, Maura L. Boerio, Isabella Marin, Amélie Pinard, and Dianna M. Milewicz
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Editorials ,familial thoracic aortic aneurysm and dissection ,genetic screening ,whole exome sequencing ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Published
- 2022
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3. A novel USP51 variant in a patient with autism spectrum disorder and epilepsy
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Ria Garg, Amelie Pinard, and Robert Wallerstein
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Autism spectrum disorder ,Epilepsy ,Genetics ,USP51 ,Deubiquitinating enzyme ,DNA damage response ,Medicine (General) ,R5-920 ,QH426-470 - Abstract
Abstract Background Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder characterized by impaired social communication and repetitive behaviours. The genetic basis of ASD is complex and involves both rare variants with large effect sizes and common variants with small effect sizes. Case presentation This case report describes a 19-year-old male with ASD, intellectual disability, absent speech, and epilepsy. Molecular testing revealed a novel maternally inherited variant in the USP51 gene, which encodes Ubiquitin Specific Peptidase 51, a deubiquitinating enzyme involved in the DNA damage response. Conclusions Based on current knowledge, the variant is predicted to result in a truncated protein and is considered a variant of uncertain significance (VUS). The USP51 gene has been implicated in neurodevelopment, and its role in the developing brain suggests its potential relevance to ASD. Further studies are needed to establish the association of USP51 variants with ASD and elucidate the full phenotypic spectrum associated with these variants.
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- 2024
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4. Further Evidence That ARIH1 Rare Variants Predispose to Thoracic Aortic Disease
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Maura L. Boerio, Nicole M. Engelhardt, Sanmati Cuddapah, Jessica I. Gold, Isabella C. Marin, Amélie Pinard, Dongchuan Guo, Siddharth K. Prakash, and Dianna M. Milewicz
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General Medicine - Published
- 2022
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5. Further Evidence That
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Maura L, Boerio, Nicole, Engelhardt, Sanmati, Cuddapah, Jessica I, Gold, Isabella C, Marin, Amélie, Pinard, Dongchuan, Guo, Siddharth K, Prakash, and Dianna M, Milewicz
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- 2022
6. The pleiotropy associated with de novo variants in CHD4, CNOT3, and SETD5 extends to moyamoya angiopathy
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Dongchuan Guo, Natasha Kharas, Michael J. Bamshad, Ellen M. Hostetler, Stephanie E. Wallace, Stéphanie Guey, Markus Kraemer, Anjail Sharrief, Ellen S. Regalado, Deborah A. Nickerson, Alana C. Cecchi, Manoelle Kossorotoff, Elisabeth Tournier-Lasserve, Amélie Pinard, Françoise Bergametti, Dianna M. Milewicz, Edward R. Smith, and Dominique Hervé
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Adult ,Male ,Proband ,Heart disease ,Developmental Disabilities ,Cell Cycle Proteins ,Disease ,Article ,Chromatin remodeling ,Angiopathy ,Pleiotropy ,Intellectual Disability ,Exome Sequencing ,medicine ,Humans ,Exome ,Genetic Predisposition to Disease ,Child ,Genetics (clinical) ,Exome sequencing ,Genetics ,business.industry ,DNA Helicases ,Nuclear Proteins ,food and beverages ,Methyltransferases ,Middle Aged ,medicine.disease ,Human genetics ,Cerebrovascular Disorders ,Child, Preschool ,Mutation ,Female ,Moyamoya Disease ,business ,Mi-2 Nucleosome Remodeling and Deacetylase Complex ,Transcription Factors - Abstract
PURPOSE: Moyamoya angiopathy (MMA) is a cerebrovascular disease characterized by occlusion of large arteries, which leads to strokes starting in childhood. Twelve altered genes predispose to MMA but the majority of cases of European descent do not have an identified genetic trigger. METHODS: Exome sequencing from 39 trios were analyzed. RESULTS: We identified four de novo variants in three genes not previously associated with MMA: CHD4, CNOT3, and SETD5. Identification of additional rare variants in these genes in 158 unrelated MMA probands provided further support that rare pathogenic variants in CHD4 and CNOT3 predispose to MMA. Previous studies identified de novo variants in these genes in children with developmental disorders (DD), intellectual disability, and congenital heart disease. CONCLUSION: These genes encode proteins involved in chromatin remodeling, and taken together with previously reported genes leading to MMA-like cerebrovascular occlusive disease (YY1AP1, SMARCAL1), implicate disrupted chromatin remodeling as a molecular pathway predisposing to early onset, large artery occlusive cerebrovascular disease. Furthermore, these data expand the spectrum of phenotypic pleiotropy due to alterations of CHD4, CNOT3, and SETD5 beyond DD to later onset disease in the cerebrovascular arteries and emphasize the need to assess clinical complications into adulthood for genes associated with DD.
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- 2020
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7. Genetics of Thoracic and Abdominal Aortic Diseases
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Amélie Pinard, Dianna M. Milewicz, and Gregory T. Jones
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medicine.medical_specialty ,Aorta ,education.field_of_study ,Physiology ,business.industry ,Vascular disease ,Population ,Disease ,medicine.disease ,Thoracic aortic aneurysm ,Abdominal aortic aneurysm ,Aortic aneurysm ,Internal medicine ,medicine.artery ,cardiovascular system ,medicine ,Cardiology ,Cardiology and Cardiovascular Medicine ,business ,education ,Cause of death - Abstract
Dissections or ruptures of aortic aneurysms remain a leading cause of death in the developed world, with the majority of deaths being preventable if individuals at risk are identified and properly managed. Genetic variants predispose individuals to these aortic diseases. In the case of thoracic aortic aneurysm and dissections (thoracic aortic disease), genetic data can be used to identify some at-risk individuals and dictate management of the associated vascular disease. For abdominal aortic aneurysms, genetic associations have been identified, which provide insight on the molecular pathogenesis but cannot be used clinically yet to identify individuals at risk for abdominal aortic aneurysms. This compendium will discuss our current understanding of the genetic basis of thoracic aortic disease and abdominal aortic aneurysm disease. Although both diseases share several pathogenic similarities, including proteolytic elastic tissue degeneration and smooth muscle dysfunction, they also have several distinct differences, including population prevalence and modes of inheritance.
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- 2019
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8. DIAPH1 Variants in Non–East Asian Patients With Sporadic Moyamoya Disease
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Carol Nelson-Williams, Nicholas S. Diab, Qiongshi Lu, Danielle F Miyagishima, Phan Q. Duy, Daniel H. Geschwind, Shih Shan Lang Chen, Dean Thumkeo, James R. Knight, Bo Zhang, Shozeb Haider, Adam J. Kundishora, Francesc López-Giráldez, Darren B. Orbach, Boyang Li, Samuel T. Peters, Sheng Chih Jin, Tanyeri Barak, Arnaud Marlier, Charles C. Matouk, Seth L. Alper, Richard P. Lifton, Michael J. Bamshad, Shrikant Mane, Shujuan Zhao, Jack Ocken, Weilai Dong, Hannah Smith, Ashley Dunbar, Amber N. Stratman, Daniel Duran, Kristopher T. Kahle, Shreyas Panchagnula, Christopher Castaldi, Dianna M. Milewicz, Benjamin C. Reeves, Rebecca L. Walker, Michael L. DiLuna, Phillip B. Storm, Isabelle Roszko, Nanthiya Sujijantarat, Yi Hsien Chen, Amélie Pinard, Murat Gunel, Stephanie M. Robert, Deborah A. Nickerson, Hongyu Zhao, and Edward R. Smith
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Proband ,Oncology ,Adult ,Male ,medicine.medical_specialty ,Candidate gene ,Formins ,Genome-wide association study ,Compound heterozygosity ,White People ,Cohort Studies ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Exome Sequencing ,medicine ,Humans ,Computer Simulation ,Exome ,030212 general & internal medicine ,Age of Onset ,Child ,Exome sequencing ,Genetic association ,Original Investigation ,business.industry ,Sequence Analysis, RNA ,Genetic Variation ,Infant ,Middle Aged ,Actin cytoskeleton ,Magnetic Resonance Imaging ,Phenotype ,Child, Preschool ,Cohort ,Female ,Neurology (clinical) ,Moyamoya Disease ,business ,Cell Adhesion Molecules ,030217 neurology & neurosurgery - Abstract
Importance Moyamoya disease (MMD), a progressive vasculopathy leading to narrowing and ultimate occlusion of the intracranial internal carotid arteries, is a cause of childhood stroke. The cause of MMD is poorly understood, but genetic factors play a role. Several familial forms of MMD have been identified, but the cause of most cases remains elusive, especially among non-East Asian individuals. Objective To assess whether ultrarare de novo and rare, damaging transmitted variants with large effect sizes are associated with MMD risk. Design, setting, and participants A genetic association study was conducted using whole-exome sequencing case-parent MMD trios in a small discovery cohort collected over 3.5 years (2016-2019); data were analyzed in 2020. Medical records from US hospitals spanning a range of 1 month to 1.5 years were reviewed for phenotyping. Exomes from a larger validation cohort were analyzed to identify additional rare, large-effect variants in the top candidate gene. Participants included patients with MMD and, when available, their parents. All participants who met criteria and were presented with the option to join the study agreed to do so; none were excluded. Twenty-four probands (22 trios and 2 singletons) composed the discovery cohort, and 84 probands (29 trios and 55 singletons) composed the validation cohort. Main outcomes and measures Gene variants were identified and filtered using stringent criteria. Enrichment and case-control tests assessed gene-level variant burden. In silico modeling estimated the probability of variant association with protein structure. Integrative genomics assessed expression patterns of MMD risk genes derived from single-cell RNA sequencing data of human and mouse brain tissue. Results Of the 24 patients in the discovery cohort, 14 (58.3%) were men and 18 (75.0%) were of European ancestry. Three of 24 discovery cohort probands contained 2 do novo (1-tailed Poisson P = 1.1 × 10-6) and 1 rare, transmitted damaging variant (12.5% of cases) in DIAPH1 (mammalian diaphanous-1), a key regulator of actin remodeling in vascular cells and platelets. Four additional ultrarare damaging heterozygous DIAPH1 variants (3 unphased) were identified in 3 other patients in an 84-proband validation cohort (73.8% female, 77.4% European). All 6 patients were non-East Asian. Compound heterozygous variants were identified in ena/vasodilator-stimulated phosphoproteinlike protein EVL, a mammalian diaphanous-1 interactor that regulates actin polymerization. DIAPH1 and EVL mutant probands had severe, bilateral MMD associated with transfusion-dependent thrombocytopenia. DIAPH1 and other MMD risk genes are enriched in mural cells of midgestational human brain. The DIAPH1 coexpression network converges in vascular cell actin cytoskeleton regulatory pathways. Conclusions and relevance These findings provide the largest collection to date of non-East Asian individuals with sporadic MMD harboring pathogenic variants in the same gene. The results suggest that DIAPH1 is a novel MMD risk gene and impaired vascular cell actin remodeling in MMD pathogenesis, with diagnostic and therapeutic ramifications.
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- 2021
9. Update on the genetic risk for thoracic aortic aneurysms and acute aortic dissections: implications for clinical care
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Isabella Marin, Amélie Pinard, Alana C. Cecchi, Dianna M. Milewicz, Dongchuan Guo, and Ellen M. Hostetler
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medicine.medical_specialty ,Genomic research ,030204 cardiovascular system & hematology ,Article ,03 medical and health sciences ,0302 clinical medicine ,Risk Factors ,Genetic variation ,medicine ,Clinical genetic ,Humans ,Genetic Predisposition to Disease ,Genetic risk ,Clinical care ,Intensive care medicine ,Genetic testing ,Aortic Aneurysm, Thoracic ,medicine.diagnostic_test ,Acute aortic dissections ,business.industry ,General Medicine ,Tailored treatment ,Aortic Dissection ,030228 respiratory system ,Acute Disease ,cardiovascular system ,Surgery ,Cardiology and Cardiovascular Medicine ,business - Abstract
Genetic variation plays a significant role in predisposing individuals to thoracic aortic aneurysms and dissections. Advances in genomic research have led to the discovery of 11 genes validated to cause heritable thoracic aortic disease (HTAD). Identifying the pathogenic variants responsible for aortic disease in affected patients confers substantial clinical utility by establishing a definitive diagnosis to inform tailored treatment and management, and enables identification of at-risk relatives to prevent downstream morbidity and mortality. The availability and access to clinical genetic testing has improved dramatically such that genetic testing is considered an integral part of the clinical evaluation for patients with thoracic aortic disease. This review provides an update on our current understanding of the genetic basis of thoracic aortic disease, practical recommendations for genetic testing, and clinical implications.
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- 2021
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10. Association of De Novo RNF213 Variants With Childhood Onset Moyamoya Disease and Diffuse Occlusive Vasculopathy
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Maximillian D.J. Fiander, Michael J. Bamshad, Dongchuan Guo, Anna C.E. Hurst, Deborah A. Nickerson, Sarah C. Novara, Alana C. Cecchi, Andrea L. Rideout, Dianna M. Milewicz, Amélie Pinard, Anthony Vandersteen, Mohamed Azouz, P. Daniel McNeely, Simon Walling, Sandhya Parkash, and Stuart M. Fraser
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0301 basic medicine ,Adult ,Male ,Pathology ,medicine.medical_specialty ,Ubiquitin-Protein Ligases ,Aortic Diseases ,Arterial Occlusive Diseases ,Renal artery stenosis ,Renal Artery Obstruction ,Iliac Artery ,Article ,03 medical and health sciences ,0302 clinical medicine ,medicine.artery ,Occlusion ,medicine ,Humans ,Ring domain ,Moyamoya disease ,Age of Onset ,Exome sequencing ,Adenosine Triphosphatases ,business.industry ,Abdominal aorta ,Occlusive ,medicine.disease ,Femoral Artery ,Young age ,030104 developmental biology ,Child, Preschool ,Mutation ,Female ,Neurology (clinical) ,Moyamoya Disease ,business ,030217 neurology & neurosurgery - Abstract
ObjectiveTo test the hypothesis that de novo genetic variants are responsible for moyamoya disease (MMD) in children with unaffected relatives, we performed exome sequencing of 28 affected children and their unaffected parents.MethodsExome sequencing was performed on 28 trios of affected patients with MMD and unaffected parents.ResultsWe identified 3 novel rare de novo RNF213 variants, 1 in the RING domain and 2 in a highly conserved region distal to the RING domain (4,114–4,120). These de novo cases of MMD present at a young age with aggressive MMD and uniquely have additional occlusive vascular lesions, including renal artery stenosis. Two previously reported cases had de novo variants in the same limited region and presented young with aggressive MMD, and 1 case had narrowing of the inferior abdominal aorta.ConclusionsThese results indicate a novel syndrome associated with RNF213 rare variants defined by de novo mutations disrupting highly conserved amino acids in the RING domain and a discrete region distal to the RING domain delimited by amino acids 4,114 to 4,120 leading to onset of severe MMD before 3 years of age and occlusion of other arteries, including the abdominal aorta, renal, iliac, and femoral arteries.
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- 2021
11. Rare deleterious variants of NOTCH1 , GATA4 , SMAD6 , and ROBO4 are enriched in BAV with early onset complications but not in BAV with heritable thoracic aortic disease
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Dongchuan Guo, Siddharth K. Prakash, Deborah A. Nickerson, Amélie Pinard, Fadi I Musfee, Elizabeth E. Blue, Ellen M. Hostetler, Dianna M. Milewicz, and Michael J. Bamshad
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0301 basic medicine ,Proband ,medicine.medical_specialty ,medicine.diagnostic_test ,GATA4 ,business.industry ,Disease ,030105 genetics & heredity ,medicine.disease ,Thoracic aortic aneurysm ,03 medical and health sciences ,030104 developmental biology ,Bicuspid aortic valve ,Internal medicine ,Cohort ,cardiovascular system ,Genetics ,medicine ,Cardiology ,business ,Molecular Biology ,Genetics (clinical) ,Exome sequencing ,Genetic testing - Abstract
BACKGROUND Bicuspid aortic valve (BAV) is the most common cardiovascular malformation in adults, with a prevalence of 0.5%-2%. The prevalence of BAV in cohorts who were ascertained due to thoracic aortic aneurysms or acute aortic dissections (TAD) is as high as 20%. However, the contribution of causal BAV genes to TAD is not known. Therefore, we evaluated rare deleterious variants of GATA4, NOTCH1, SMAD6, or ROBO4 in patients with BAV who presented with TAD. METHODS Our cohort consisted of 487 probands with Heritable Thoracic Aortic Aneurysms or Dissections (HTAD, 12% BAV, 29% female) and 63 probands with Early onset complications of Bicuspid Aortic Valve disease (EBAV, 63% TAD, 34% female). After whole exome sequencing, we functionally annotated GATA4, NOTCH1, SMAD6, and ROBO4 variants and compared the prevalence of rare variants in these genes to controls without HTAD. RESULTS We identified 11 rare deleterious variants of GATA4, SMAD6, or ROBO4 in 12 (18%) EBAV cases. The burden of rare SMAD6 and GATA4 variants was significantly enriched in EBAV but not in HTAD cases, even among HTAD cases with BAV (p
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- 2020
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12. Abstract 53: Missense Pathogenic Variants in ANO1 Predispose to Moyamoya Disease
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Stéphanie Guey, Mu He, Jill A. Rosenfeld, Wenlei Ye, Andrea M. Lewis, Dongchuan Guo, Deborah A. Nickerson, Alana C. Cecchi, Michael J. Bamshad, Scott E. Hickey, Elisabeth Tournier-Lasserve, Amélie Pinard, Dianna M. Milewicz, and Chaker Aloui
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Advanced and Specialized Nursing ,medicine.medical_specialty ,business.industry ,Pediatric onset ,Carotid arteries ,medicine.disease ,Internal medicine ,Occlusion ,medicine ,Cardiology ,Missense mutation ,Pediatric stroke ,Neurology (clinical) ,Moyamoya disease ,Cardiology and Cardiovascular Medicine ,business - Abstract
Introduction: Moyamoya disease (MMD) is a cerebrovascular disease often causing pediatric onset strokes and characterized by progressive bilateral occlusion of the distal internal carotid arteries and formation of a compensatory network of collateral vessels. Several genes harbor variants that increase the risk for MMD, but the majority of cases of European descent does not have an identified genetic cause. Hypothesis: MMD is associated with significant genetic heterogeneity, i.e., many genes in the human genome can be altered to predispose to this condition. Methods: To identify novel genes for MMD, exome sequencing was performed on DNA from 145 individuals from 80 families with one or more affected members. Bioinformatics filtering included a CADD (GRCh37-v1.4) score > 20 and a minor allele frequency < 0.0001 in gnomAD (v2.1.1 controls). For a subset of ANO1 mutant alleles, we characterized the channel activities via patch recording and assessed protein localization in heterologous cell cultures. Results: We identified 6 rare variants in ANO1 ( TMEM16A ), which encodes an evolutionarily conserved calcium-activated chloride channel. One rare heterozygous variant, p.Met658Val (CADD: 22.9, absent in gnomAD), was found in two very distantly related MMD families and segregated with disease in multiple affected members; p.Glu459Lys and p.Arg890Gln were identified in two unrelated affected probands. Through Matchmaker Exchange (MyGene2) collaboration, we identified 3 additional rare variants: homozygous p.Glu170Lys in a consanguineous MMD family, heterozygous p.Thr740Ile in a MMD case and p.Ala333Ser in a case with ischemic stroke. Functional analyses determined that p.Glu170Lys affects channel gating and calcium sensitivity, producing much smaller chloride current, but the channel itself is more sensitive to calcium, which means it is more likely to open. Ano1 knock out (KO) in mice is lethal by 1 week of age with pathology in multiple organ systems. Smooth muscle cells-specific KO is not lethal, and phenotyping of these mice is ongoing. Conclusions: ANO1 is a novel gene predisposing to MMD and future studies will focus on defining the role of ANO1 protein to connect the altered gene to the occlusive lesions observed in MMD patients.
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- 2020
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13. Analysis of HOXB1 gene in a cohort of patients with sporadic ventricular septal defect
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Gwenaëlle Collod-Béroud, Joséphine Okoronkwo, Damien Bonnet, Julia Mitchell, Nathalie Eudes, Amélie Pinard, Stéphane Zaffran, Fanny Bajolle, Maude Grelet, Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and ANR-13-BSV2-0003,TransCARDIAC,Réseau transcriptionnel controllant la différenciation des progéniteurs cardiaques du second champ cardiaque.(2013)
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Heart Defects, Congenital ,Heart Septal Defects, Ventricular ,Male ,0301 basic medicine ,congenital, hereditary, and neonatal diseases and abnormalities ,medicine.medical_specialty ,animal structures ,Ventricular septal defect ,Cohort Studies ,03 medical and health sciences ,Double outlet right ventricle ,Internal medicine ,Genetics ,Humans ,Medicine ,Variant ,Child ,Molecular Biology ,Gene ,Congenital heart disease ,Homeodomain Proteins ,business.industry ,General Medicine ,medicine.disease ,Double Outlet Right Ventricle ,3. Good health ,030104 developmental biology ,[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics ,Child, Preschool ,embryonic structures ,Cohort ,Etiology ,Cardiology ,Female ,business ,HOXB1 ,Transcription Factors - Abstract
International audience; Ventricular septal defect (VSD) including outlet VSD of double outlet right ventricle (DORV) and perimembranous VSD are among the most common congenital heart diseases found at birth. HOXB1 encodes a homeodomain transcription factor essential for normal cardiac outflow tract development. The aim of the present study was to investigate the possible genetic effect of sequence variations in HOXB1 on VSD. The coding regions and splice junctions of the HOXB1 gene were sequenced in 57 unrelated VSD patients. As a result, a homozygous c.74\₈2dup (p.Pro28delinsHisSerAlaPro) variant was identified in one individual with DORV. We also identified five previously reported polymorphisms (rs35114525, rs12946855, rs14534040, rs12939811, and rs7207109) in 18 patients (12 DORV and 6 perimembranous VSD). Our study did not show any pathogenic alterations in the coding region of HOXB1 among patients with VSD. To our knowledge this is the first study investigating the role of HOXB1 in nonsyndromic VSD, which provide more insight on the etiology of this disease.
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- 2018
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14. Piezo1 is required for outflow tract and aortic valve development
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David Salgado, Guillaume Lebon, Amélie Pinard, Jean-Pierre Desvignes, Gaëlle Odelin, Adèle Faucherre, Jean François Avierinos, Hamid Moha Ou Maati, Alexis Theron, Stéphane Zaffran, Gwenaëlle Collod-Béroud, Nathalie Nasr, Chris Jopling, Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique Médicale et Génomique Fonctionnelle (GMGF), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de cardiologie, Université de la Méditerranée - Aix-Marseille 2-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), ANR-17-CE18-0001,AT2R-TRAAK-BIOANALGESICS,Caractérisations moléculaires et cellulaires de voies de signalisation de la douleur: contrôle de la douleur dans l'ulcère de buruli comme source d'inspiration pour la conception rationnelle de nouveaux analgésiques puissants(2017), and Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)
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Models, Molecular ,0301 basic medicine ,Aortic valve ,medicine.medical_specialty ,Endothelium ,Protein Conformation ,Organogenesis ,[SDV]Life Sciences [q-bio] ,Fluorescent Antibody Technique ,Gene Expression ,030204 cardiovascular system & hematology ,Ion Channels ,03 medical and health sciences ,0302 clinical medicine ,Mechanosensitive ion channel ,Bicuspid aortic valve ,Genes, Reporter ,Internal medicine ,Animals ,Humans ,Ventricular outflow tract ,Medicine ,Amino Acid Sequence ,Molecular Biology ,Zebrafish ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,Alleles ,030304 developmental biology ,0303 health sciences ,Cardiac cycle ,biology ,Heart development ,business.industry ,PIEZO1 ,Hemodynamics ,Zebrafish Proteins ,medicine.disease ,biology.organism_classification ,030104 developmental biology ,medicine.anatomical_structure ,Aortic Valve ,Gene Knockdown Techniques ,Mutation ,Circulatory system ,Cardiology ,cardiovascular system ,Cardiology and Cardiovascular Medicine ,business - Abstract
Aims-During embryogenesis, the onset of circulatory blood flow generates a variety of hemodynamic forces which reciprocally induce changes in cardiovascular development and performance. It has been known for some time that these forces can be detected by as yet unknown mechanosensory systems which in turn promote cardiogenic events such as outflow tract and aortic valve development. PIEZO1 is a mechanosensitive ion channel present in endothelial cells where it serves to detect hemodynamic forces making it an ideal candidate to play a role during cardiac development. We sought to determine whether PIEZO1 is required for outflow tract and aortic valve development.Methods and results-By analysing heart development in zebrafish we have determined thatpiezo1is expressed in the developing outflow tract where it serves to detect hemodynamic forces. In particular, we have found that mechanical forces generated during the cardiac cycle activate Piezo1 which triggers nitric oxide to be released in the outflow tract. Consequently, disrupting Piezo1 signalling leads to defective outflow tract and aortic valve development and indicates this gene may be involved in the etiology of congenital heart diseases. Based on these findings, we analysed genomic data generated from a cohort of bicuspid aortic valve patients and identified 3 probands who each harboured a novel variant inPIEZO1. Subsequentin vitroandin vivoassays indicates that these variants behave as dominant negatives leading to an inhibition of normal PIEZO1 mechanosensory activity and defective aortic valve development.Conclusion-These data indicate that the mechanosensitive ion channelpiezo1is required for OFT and aortic valve development and, furthermore, dominant negative variants ofPIEZO1appear to be associated with BAV in humans.
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- 2019
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15. A genome-wide search for new imprinted genes in the human placenta identifies DSCAM as the first imprinted gene on chromosome 21
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Luisa Dandolo, Laila El Khattabi, Hélène Jammes, Amélie Pinard, Daniel Vaiman, Marie-Noëlle Dieudonné, Sandrine Barbaux, Vassilis Tsatsaris, Stéphanie Backer, Evelyne Bloch-Gallego, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5), AP-HP - Hôpital Cochin Broca Hôtel Dieu [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), McGoven Medical School at the University of Texas Science Center, Partenaires INRAE, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Maternité Cochin-Port Royal, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), ProdInra, Migration, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), and École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)
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Chromosomes, Human, Pair 21 ,Placenta ,[SDV]Life Sciences [q-bio] ,Biology ,[INFO] Computer Science [cs] ,Article ,03 medical and health sciences ,DSCAM ,Genomic Imprinting ,Mice ,Pregnancy ,Chlorocebus aethiops ,Genetics ,medicine ,Human Umbilical Vein Endothelial Cells ,Animals ,Humans ,[INFO]Computer Science [cs] ,Imprinting (psychology) ,Gene ,Genetics (clinical) ,reproductive and urinary physiology ,Cells, Cultured ,0303 health sciences ,030305 genetics & heredity ,Intron ,DNA Methylation ,Cell biology ,Mice, Inbred C57BL ,[SDV] Life Sciences [q-bio] ,medicine.anatomical_structure ,DNA methylation ,COS Cells ,embryonic structures ,Female ,Chromosome 21 ,Genomic imprinting ,Cell Adhesion Molecules - Abstract
Notice à reprendre en chantier qualité avec la version finale de l’Editeur; International audience; We identified, through a genome-wide search for new imprinted genes in the human placenta, DSCAM (Down Syndrome Cellular Adhesion Molecule) as a paternally expressed imprinted gene. Our work revealed the presence of a Differentially Methylated Region (DMR), located within intron 1 that might regulate the imprinting in the region. This DMR showed a maternal allele methylation, compatible with its paternal expression. We showed that DSCAM is present in endothelial cells and the syncytiotrophoblast layer of the human placenta. In mouse, Dscam expression is biallelic in foetal brain and placenta excluding any possible imprinting in these tissues. This gene encodes a cellular adhesion molecule mainly known for its role in neurone development but its function in the placenta remains unclear. We report here the first imprinted gene located on human chromosome 21 with potential clinical implications.
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- 2019
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16. LTBP3 Pathogenic Variants Predispose Individuals to Thoracic Aortic Aneurysms and Dissections
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Daniel B. Rifkin, Suzanne M. Leal, Dianna M. Milewicz, Marvin R. Natowicz, Siddharth K. Prakash, Kwanghyuk Lee, Ellen S. Regalado, Dongchuan Guo, Christina Rigelsky, Amélie Pinard, Micheala A. Aldred, Michael J. Bamshad, Jiyuan Chen, Deborah A. Nickerson, Lior Zilberberg, Ellen M. Hostetler, and Stephanie E. Wallace
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0301 basic medicine ,Adult ,Male ,Pathology ,medicine.medical_specialty ,Blood Pressure ,Compound heterozygosity ,Short stature ,03 medical and health sciences ,Mice ,medicine.artery ,Report ,Genetics ,medicine ,Thoracic aorta ,Animals ,Humans ,Amelogenesis imperfecta ,Genetic Predisposition to Disease ,Gene ,Genetics (clinical) ,Exome sequencing ,Aged, 80 and over ,Aorta ,Aortic Aneurysm, Thoracic ,business.industry ,Abdominal aorta ,Homozygote ,Middle Aged ,medicine.disease ,Pedigree ,Aortic Dissection ,030104 developmental biology ,Latent TGF-beta Binding Proteins ,Mutation ,cardiovascular system ,Female ,medicine.symptom ,business - Abstract
The major diseases affecting the thoracic aorta are aneurysms and acute dissections, and pathogenic variants in 11 genes are confirmed to lead to heritable thoracic aortic disease. However, many families in which multiple members have thoracic aortic disease do not have alterations in the known aortopathy genes. Genes highly expressed in the aorta were assessed for rare variants in exome sequencing data from such families, and compound rare heterozygous variants (p.Pro45Argfs∗25 and p.Glu750∗) in LTBP3 were identified in affected members of one family. A homozygous variant (p.Asn678_Gly681delinsThrCys) that introduces an additional cysteine into an epidermal growth factor (EGF)-like domain in the corresponding protein, latent TGF-β binding protein (LTBP-3), was identified in a second family. Individuals with compound heterozygous or homozygous variants in these families have aneurysms and dissections of the thoracic aorta, as well as aneurysms of the abdominal aorta and other arteries, along with dental abnormalities and short stature. Heterozygous carriers of the p.Asn678_Gly681delinsThrCys variant have later onset of thoracic aortic disease, as well as dental abnormalities. In these families, LTBP3 variants segregated with thoracic aortic disease with a combined LOD score of 3.9. Additionally, heterozygous rare LTBP3 variants were found in individuals with early onset of acute aortic dissections, and some of these variants disrupted LTBP-3 levels or EGF-like domains. When compared to wild-type mice, Ltbp3−/− mice have enlarged aortic roots and ascending aortas. In summary, homozygous LTBP3 pathogenic variants predispose individuals to thoracic aortic aneurysms and dissections, along with the previously described skeletal and dental abnormalities.
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- 2018
17. The revised ghent nosology; reclassifying isolated ectopia lentis
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D. Patel, Laurence Faivre, David G. Charteris, P. Comeglio, Catherine Boileau, Anne H. Child, Gavin Arno, Gwenaëlle Collod-Béroud, Aman Chandra, Jose Antonio Aragon-Martin, and Amélie Pinard
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musculoskeletal diseases ,Proband ,Marfan syndrome ,Nosology ,congenital, hereditary, and neonatal diseases and abnormalities ,Pediatrics ,medicine.medical_specialty ,business.industry ,medicine.disease ,3. Good health ,Dissection ,Genetics ,Medicine ,In patient ,Chinese family ,Aortic dilation ,business ,Ectopia lentis ,Genetics (clinical) - Abstract
Inherited ectopia lentis (EL) is most commonly caused by Marfan syndrome (MFS), a multisystemic disorder caused by mutations in FBN1. Historically the diagnosis for patients with EL who have no systemic features of MFS is isolated EL (IEL). However, the Ghent nosology for MFS was updated in 2010 and made some important alterations. In particular, patients with EL and a FBN1 mutation are now categorically diagnosed with MFS, if their mutation has previously been described with aortic dilation/dissection. This carries significant systemic implications, as many patients previously diagnosed with IEL are now reclassified. We provide a review of all published cases of IEL caused by FBN1 mutations over the last 20 years to assess what impact the new Ghent nosology has on these. Indeed, 57/123 probands (46.3%) are now classified as MFS according to the revised Ghent nosology and 37/96 mutations (38.5%) reported to cause isolated EL have also been found in patients with aortic dilation/dissection. These findings suggest that EL caused by mutations in FBN1 is actually part of a spectrum of fibrillinopathies with MFS, and the term 'IEL' should be avoided in such cases.
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- 2014
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18. Actionable Genes, Core Databases, and Locus-Specific Databases
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Arnaud Blanchard, Sylviane Olschwang, Christophe Béroud, Catherine Boileau, Martin Krahn, Aurélie Fabre, Jean-Pierre Desvignes, Morgane Miltgen, Pauline Arnaud, Amélie Pinard, David Salgado, Philippe Grandval, Stéphane Zaffran, Gwenaëlle Collod-Béroud, Laura Barre, Hélène Mathieu, Génétique Médicale et Génomique Fonctionnelle (GMGF), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de reference national pour le syndrome de Marfan et apparentés, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Département d'Oncologie [Hôpital Clairval - Marseille], Hôpital Privé Clairval [Marseille], Hôpital Européen [Fondation Ambroise Paré - Marseille], Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), APHP Service de Génétique, Hôpital Bichat, Université Paris Diderot - Paris 7 (UPD7), and Gall, Valérie
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0301 basic medicine ,databases ,secondary variant ,Locus (genetics) ,030105 genetics & heredity ,Biology ,Gene mutation ,computer.software_genre ,03 medical and health sciences ,Neoplasms ,Databases, Genetic ,Genetics ,Humans ,Genetic Predisposition to Disease ,Gene ,Genetics (clinical) ,[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Database ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Cancer susceptibility ,Molecular Sequence Annotation ,Atherosclerosis ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,3. Good health ,030104 developmental biology ,NGS ,Mutation ,actionable genes ,LSDB ,computer ,Software - Abstract
International audience; Adoption of next-generation sequencing (NGS) in a diagnostic context raises numerous questions with regard to identification and reports of secondary variants (SVs) in actionable genes. To better understand the whys and wherefores of these questioning, it is necessary to understand how they are selected during the filtering process and how their proportion can be estimated. It is likely that SVs are underestimated and that our capacity to label all true SVs can be improved. In this context, Locus-specific databases (LSDBs) can be key by providing a wealth of information and enabling classifying variants. We illustrate this issue by analyzing 318 SVs in 23 actionable genes involved in cancer susceptibility syndromes identified through sequencing of 572 participants selected for a range of atherosclerosis phenotypes. Among these 318 SVs, only 43.4% are reported in Human Gene Mutation Database (HGMD) Professional versus 71.4% in LSDB. In addition, 23.9% of HGMD Professional variants are reported as pathogenic versus 4.8% for LSDB. These data underline the benefits of LSDBs to annotate SVs and minimize overinterpretation of mutations thanks to their efficient curation process and collection of unpublished data. (C) 2016 Wiley Periodicals, Inc.
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- 2016
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19. UMD-Predictor: A High-Throughput Sequencing Compliant System for Pathogenicity Prediction of any Human cDNA Substitution
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Arnaud Blanchard, Ghadi Rai, Amélie Pinard, Jean-Pierre Desvignes, Christophe Béroud, Morgane Miltgen, Nicolas Lévy, Gwenaëlle Collod-Béroud, David Salgado, Génétique Médicale et Génomique Fonctionnelle (GMGF), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique Moléculaire [Hôpital de la Timone - APHM], Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), European Project: 305444,EC:FP7:HEALTH,FP7-HEALTH-2012-INNOVATION-1,RD-CONNECT(2012), European Project: 200754,EC:FP7:HEALTH,FP7-HEALTH-2007-A,GEN2PHEN(2008), COLLOD-BEROUD, Gwenaëlle, INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID, RD-CONNECT: An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research - RD-CONNECT - - EC:FP7:HEALTH2012-11-01 - 2018-10-31 - 305444 - VALID, Genotype-To-Phenotype Databases: A Holistic Solution - GEN2PHEN - - EC:FP7:HEALTH2008-01-01 - 2013-06-30 - 200754 - VALID, Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Centre National de la Recherche Scientifique (CNRS)
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0301 basic medicine ,Nonsynonymous substitution ,Informatics ,pathogenicity prediction ,synonymous ,nonsynonymous ,Biology ,[SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics ,medicine.disease_cause ,[SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,Substitution matrix ,03 medical and health sciences ,0302 clinical medicine ,Complementary DNA ,Genetic variation ,Databases, Genetic ,substitution ,Genetics ,medicine ,Humans ,Point Mutation ,Exome ,Genetic Predisposition to Disease ,Genetics (clinical) ,[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM] ,Mutation ,Point mutation ,Computational Biology ,High-Throughput Nucleotide Sequencing ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,Sequence Analysis, DNA ,bioinformatics ,Matthews correlation coefficient ,030104 developmental biology ,Amino Acid Substitution ,[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics ,030220 oncology & carcinogenesis ,NGS ,nonsense ,mutation ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,Algorithms - Abstract
International audience; Whole-exome sequencing (WES) is increasingly applied to research and clinical diagnosis of human diseases. It typically results in large amounts of genetic variations. Depending on the mode of inheritance, only one or two correspond to pathogenic mutations responsible for the disease and present in affected individuals. Therefore , it is crucial to filter out nonpathogenic variants and limit downstream analysis to a handful of candidate mutations. We have developed a new computational combi-natorial system UMD-Predictor (http://umd-predictor.eu) to efficiently annotate cDNA substitutions of all human transcripts for their potential pathogenicity. It combines biochemical properties, impact on splicing signals, localiza-tion in protein domains, variation frequency in the global population, and conservation through the BLOSUM62 global substitution matrix and a protein-specific conservation among 100 species. We compared its accuracy with the seven most used and reliable prediction tools, using the largest reference variation datasets including more than 140,000 annotated variations. This system consistently demonstrated a better accuracy, specificity, Matthews correlation coefficient, diagnostic odds ratio, speed, and provided the shortest list of candidate mutations for WES. Webservices allow its implementation in any bioinfor-matics pipeline for next-generation sequencing analysis. It could benefit to a wide range of users and applications varying from gene discovery to clinical diagnosis.
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- 2016
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20. An uncommon cause of tricuspid regurgitation: three-dimensional echocardiographic incremental value, surgical and genetic insights
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Amélie Pinard, Alexis Theron, Alberto Riberi, Stéphane Zaffran, Génétique Médicale et Génomique Fonctionnelle (GMGF), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Service de cardiologie, and Université de la Méditerranée - Aix-Marseille 2-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)
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0301 basic medicine ,Pulmonary and Respiratory Medicine ,Tricuspid Valve Disorder ,Male ,medicine.medical_specialty ,congenital, hereditary, and neonatal diseases and abnormalities ,Perforation (oil well) ,Echocardiography, Three-Dimensional ,Regurgitation (circulation) ,030204 cardiovascular system & hematology ,030105 genetics & heredity ,03 medical and health sciences ,0302 clinical medicine ,Tricuspid Valve Insufficiency ,[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system ,Internal medicine ,Mitral valve ,Tricuspid valve ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,medicine ,Endocarditis ,Humans ,cardiovascular diseases ,business.industry ,valvular heart disease ,General Medicine ,Middle Aged ,medicine.disease ,Valvular heart disease ,3. Good health ,medicine.anatomical_structure ,Echocardiography ,Cardiology ,cardiovascular system ,Surgery ,Radiology ,Cardiology and Cardiovascular Medicine ,business - Abstract
International audience; Congenital tricuspid valve disease is a rare defect that includes regurgitation, stenosis and Ebstein's anomaly. We report a case of severe tricuspid regurgitation associated with functional mitral regurgitation in a 47-year-old man with congestive heart failure. Transthoracic echocardiography (TTE) ruled out any Ebstein's anomaly. Three-dimensional TTE revealed a `tricuspid hole' into the anterior leaflet that was only attached to the tricuspid annulus next to both anteroseptal and anteroposterior commissures. There was no sign of leaflet tear or perforation. The surgical repair of the tricuspid and mitral valves was performed with an optimal result. No sign of endocarditis or rheumatic disease was observed during the intervention. Sequence analysis of GATA4, HEY2 and ZFPM2 genes was performed, but no causative mutation was identified.
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- 2016
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21. WES/WGS Reporting of Mutations from Cardiovascular 'Actionable' Genes in Clinical Practice: A Key Role for UMD Knowledgebases in the Era of Big Databases
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Celine Guien, Christophe Béroud, Guillaume Jondeau, Stéphane Zaffran, Gwenaëlle Collod-Béroud, Catherine Boileau, Laurence Faivre, David Salgado, Maria Martinez, Amélie Pinard, Nadine Hanna, Pauline Arnaud, Jean-Pierre Desvignes, Ghadi Rai, Génétique Médicale et Génomique Fonctionnelle (GMGF), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Recherche Vasculaire Translationnelle (LVTS (UMR_S_1148 / U1148)), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut de Recherche en Santé Digestive (IRSD ), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique des Anomalies du Développement (GAD), Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, Aix-Marseille Universite INSERM European Union 305444, European Project: 305444,EC:FP7:HEALTH,FP7-HEALTH-2012-INNOVATION-1,RD-CONNECT(2012), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), IFR100 - Structure fédérative de recherche Santé-STIC-Université de Bourgogne (UB), université de Bourgogne, GAD, and RD-CONNECT: An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research - RD-CONNECT - - EC:FP7:HEALTH2012-11-01 - 2018-10-31 - 305444 - VALID
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0301 basic medicine ,medicine.medical_specialty ,Knowledge Bases ,Genomics ,marfan-syndrome ,[SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics ,030105 genetics & heredity ,Biology ,computer.software_genre ,Genome ,ExAC ,03 medical and health sciences ,Annotation ,incidental findings ,Genetics ,medicine ,Humans ,pathogenicity ,Genetic Predisposition to Disease ,tgfbr2 ,Exome ,genome ,ESP ,Genetics (clinical) ,Exome sequencing ,[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM] ,variants ,Database ,thoracic aortic-aneurysms ,Genome, Human ,High-Throughput Nucleotide Sequencing ,MYLK ,prediction ,mutations ,3. Good health ,Marfan syndrome ,030104 developmental biology ,dissection ,[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics ,Cardiovascular Diseases ,Mutation ,Medical genetics ,Identification (biology) ,LSDB ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,computer ,exome - Abstract
International audience; High-throughput next-generation sequencing such as whole-exome and whole-genome sequencing are being rapidly integrated into clinical practice. The use of these techniques leads to the identification of secondary variants for which decisions about the reporting or not to the patient need to be made. The American College of Medical Genetics and Genomics recently published recommendations for the reporting of these variants in clinical practice for 56 "actionable" genes. Among these, seven are involved in Marfan Syndrome And Related Disorders (MSARD) resulting from mutations of the FBN1, TGFBR1 and 2, ACTA2, SMAD3, MYH11 and MYLK genes. Here, we show that mutations collected in UMD databases for MSARD genes (UMD-MSARD) are rarely reported, including the most frequent ones, in global scale initiatives for variant annotation such as the NHLBI GO Exome Sequencing Project (ESP), the Exome Aggregation Consortium (ExAC), and ClinVar. The predicted pathogenic mutations reported in global scale initiatives but absent in locus-specific databases (LSDBs) mainly correspond to rare events. UMD-MSARD databases are therefore the only resources providing access to the full spectrum of known pathogenic mutations. They are the most comprehensive resources for clinicians and geneticists to interpret MSARD-related variations not only primary variants but also secondary variants.
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- 2016
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22. P535: Validation and real-life experience of a comprehensive, targeted next-generation sequencing panel for hereditary cancer predisposition
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Amelie Pinard, Anthony Chua, Ugur Hodoglugil, Pierre-Marie Martin, Julie Mak, Amie Blanco, Marta Sabbadini, Aleksandar Rajkovic, W. Patrick Devine, and Jessica Van Ziffle
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Genetics ,QH426-470 ,Medicine - Published
- 2023
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23. Comparative genomics of emerging pathogens in the Candida glabrata clade
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Christiane Bouchier, Christian Marck, Ralitsa Atanasova, Gabriela Aguileta, Adela Enache-Angoulvant, Toni Gabaldón, Eric Westhof, Cécile Fairhead, Bernard Dujon, Cécile Neuvéglise, Patrick Wincker, Marina Marcet-Houben, Tiphaine Martin, Arnaud Couloux, Laurence Ma, Julien Recoquillay, Eric Pelletier, Olivier Lespinet, Juliette Guitard, Julie Poulain, Sophie Creno, Hugo Devillers, Sylvie Arnaise, Stéphanie Boisnard, Amélie Pinard, José Almeida Cruz, Laure Jaouen, Monique Bolotin-Fukuhara, Christophe Hennequin, Pascal Durrens, Bioinformatics and Genomics Programme, Universitat Pompeu Fabra [Barcelona] (UPF)-Centre for Genomic Regulation (CRG), Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Immunité et Infection, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Comparative Genomics Group, CRG-Centre for Genomic Regulation, Service de Microbiologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, Institut de Biologie et de Technologies de Saclay (IBITECS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007- 2013)/ERC Grant Agreement n.310325, a Grant from the Qatar National Research Fund grant (NPRP 5-298-3-086), and by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161). CF's research is funded in part by an 'Attractivité' grant from the University Paris Sud. GA is a recipient of a Marie Curie grant (FP7-PEOPLE-2010-IEF-No.274223). SB, HD and RA are recipients of, respectively, a shared post-doctoral grant and a Ph. D. grant, from the Région Ile-de-France's DIM Malinf program. JAC was supported by the Ph.D. Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia, SFRH/ BD/33528/2008)., European Project: 310325,NONCODEVOL - FP7-IDEAS-ERC, European Project: 274223,EC:FP7:PEOPLE,FP7-PEOPLE-2010-IEF,FUNGI-PATHNCODE(2012), Guitard, Juliette, Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hôpital Bicêtre, Mucoviscidose: physiopathologie et phénogénomique [CRSA], Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Service de Parasitologie - Mycologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut Pasteur [Paris], Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Universitat Pompeu Fabra [Barcelona]-Centre for Genomic Regulation (CRG), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR113-Université Pierre et Marie Curie - Paris 6 (UPMC), Génomique (Plate-Forme), Centre National de la Recherche Scientifique (CNRS)-Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Bicêtre, Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), BMC, Ed., Evolutionary genomics of long, non-coding RNAs - NONCODEVOL - FP7-IDEAS-ERC - 310325 - INCOMING, and The genomic basis of emerging fungal pathogenicity - FUNGI-PATHNCODE - - EC:FP7:PEOPLE2012-01-01 - 2013-12-31 - 274223 - VALID
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Nakaseomyces ,Yeast evolution ,[SDV]Life Sciences [q-bio] ,Yeast genomes ,Virulence ,Genomics ,Candida glabrata ,Genome ,Evolution, Molecular ,03 medical and health sciences ,Phylogenetics ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Genetics ,Gene family ,Selection, Genetic ,Clade ,DNA, Fungal ,Phylogeny ,Fungal pathogens ,030304 developmental biology ,Comparative genomics ,0303 health sciences ,biology ,030306 microbiology ,Càndida ,Llevats -- Genètica ,Sequence Analysis, DNA ,biology.organism_classification ,3. Good health ,[SDV] Life Sciences [q-bio] ,Genòmica ,Saccharomycetales ,[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Genome, Fungal ,Biotechnology ,Research Article - Abstract
BACKGROUND: Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens have recently been described within this group: C. nivariensis and C. bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts. RESULTS: Our results indicate that the two new pathogens are more closely related to the non-pathogenic N. delphensis than to C. glabrata. We uncover duplications and accelerated evolution that specifically affected genes in the lineage preceding the group containing N. delphensis and the three pathogens, which may provide clues to the higher propensity of this group to infect humans. Finally, the number of Epa-like adhesins is specifically enriched in the pathogens, particularly in C. glabrata. CONCLUSIONS: Remarkably, some features thought to be the result of adaptation of C. glabrata to a pathogenic lifestyle, are present throughout the Nakaseomyces, indicating these are rather ancient adaptations to other environments. Phylogeny suggests that human pathogenesis evolved several times, independently within the clade. The expansion of the EPA gene family in pathogens establishes an evolutionary link between adhesion and virulence phenotypes. Our analyses thus shed light onto the relationships between virulence and the recent genomic changes that occurred within the Nakaseomyces. This work was supported by funding from the European Research Council/nunder the European Union’s Seventh Framework Programme (FP/2007- 2013)/ERC Grant Agreement n.310325, a Grant from the Qatar National Research Fund grant (NPRP 5-298-3-086), and by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161). CF’s research is/nfunded in part by an “Attractivité” grant from the University Paris Sud. GA is/na recipient of a Marie Curie grant (FP7-PEOPLE-2010-IEF-No.274223). SB, HD and RA are recipients of, respectively, a shared post-doctoral grant and a Ph. D. grant, from the Région Ile-de-France’s DIM Malinf program. JAC was supported by the Ph.D. Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia; SFRH/BD/33528/2008)
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- 2013
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24. A genome-wide approach reveals novel imprinted genes expressed in the human placenta
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Umberto Simeoni, Bettina Bessières, Christophe Buffat, Paul Monnier, Anne Barlier, Géraldine Gascoin-Lachambre, Françoise Mondon, Sandrine Barbaux, Sébastien Jacques, Franck Letourneur, Jana Auer, Hélène Jammes, Luisa Dandolo, Amélie Pinard, Marie-Béatrice Tonanny, Daniel Vaiman, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Maternité Port-Royal [CHU Cochin], Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Moléculaire, Assistance Publique - Hôpitaux de Marseille (APHM), Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Vascular research center of Marseille (VRCM), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Médecine Néonatale, Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), CHU Cochin [AP-HP]-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Cochin [AP-HP], Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)
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Cancer Research ,Candidate gene ,placenta ,Single-nucleotide polymorphism ,Biology ,Polymorphism, Single Nucleotide ,Genome ,Genomic Imprinting ,Mice ,Pregnancy ,Complementary DNA ,Animals ,Humans ,RNA, Messenger ,gene ,Molecular Biology ,Gene ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,Oligonucleotide Array Sequence Analysis ,Genetics ,monoallelic expression ,zinc finger ,Genome, Human ,Gene Expression Profiling ,[SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology ,parental imprinting ,Mice, Inbred C57BL ,genomic DNA ,Genetic Loci ,Cattle ,Female ,DNA microarray ,Genomic imprinting ,Transcription Factors ,Research Paper - Abstract
Supplemental materials : www.landesbioscience.com/journals/epigenetics/article/21495; Genomic imprinting characterizes genes with a monoallelic expression, which is dependent on the parental origin of each allele. Approximately 150 imprinted genes are known to date, in humans and mice but, though computational searches have tried to extract intrinsic characteristics of these genes to identify new ones, the existing list is probably far from being comprehensive. We used a high-throughput strategy by diverting the classical use of genotyping microarrays to compare the genotypes of mRNA/cDNA vs. genomic DNA to identify new genes presenting monoallelic expression, starting from human placental material. After filtering of data, we obtained a list of 1,082 putative candidate monoallelic SNPs located in more than one hundred candidate genes. Among these, we found known imprinted genes, such as IPW, GRB10, INPP5F and ZNF597, which contribute to validate the approach. We also explored some likely candidates of our list and identified seven new imprinted genes, including ZFAT, ZFAT-AS1, GLIS3, NTM, MAGI2, ZC3H12Cand LIN28B, four of which encode zinc finger transcription factors. They are, however, not imprinted in the mouse placenta, except for Magi2. We analyzed in more details the ZFAT gene, which is paternally expressed in the placenta (as ZFAT-AS1, a non-coding antisense RNA) but biallelic in other tissues. The ZFAT protein is expressed in endothelial cells, as well as in syncytiotrophoblasts. The expression of this gene is, moreover, downregulated in placentas from complicated pregnancies. With this work we increase by about 10% the number of known imprinted genes in humans.
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- 2012
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25. DSCAM, un nouveau gène soumis à empreinte parentale
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Laila El Khattabi, Amélie Pinard, Stéphanie Backer, Daniel Vaiman, Hélène Jammes, Evelyne Bloch-Gallego, and Sandrine Barbaux
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Anatomy - Abstract
L’empreinte parentale est un phenomene epigenetique complexe qui regule l’expression monoallelique de certains genes en fonction de l’origine parentale de l’allele. Les genes soumis a empreinte (GSE) participent au developpement placentaire et fœtal. Des defauts d’empreinte de certains GSE entrainent des syndromes cliniques associant une pathologie placentaire a l’origine notamment d’un defaut de croissance fœtale, et des manifestations neuro-developpementales. Environ 70 GSE ont ete identifies a ce jour chez l’homme. Nous avons developpe une strategie de criblage haut debit pour identifier de nouveaux GSE dans le placenta humain. Une premiere serie de validation a permis de confirmer le statut d’empreinte d’une dizaine de nouveaux genes [1] . Recemment, nous avons revele le statut de GSE pour le gene DSCAM (Down Syndrome Cellular Adhesion Molecule). Ce gene, qui se trouve dans la region critique du syndrome de Down, est ainsi le premier GSE identifie sur le chromosome 21. Notre etude montre que c’est l’allele paternel qui est exprime dans le placenta. Des resultats preliminaires nous laissent penser que l’empreinte de ce gene pourrait etre regulee par une region differentiellement methylee en amont du gene. L’etude par immunohistochimie de coupes placentaires montre une expression dans les cellules endotheliales et le syncytiotrophoblaste pouvant suggerer un role dans l’angiogenese placentaire via son ligand Netrin. Une etude est en cours a partir d’un modele cellulaire de trophoblaste avant et apres syncytialisation pour analyser son role dans ce type cellulaire. Par ailleurs, DSCAM est connu pour son role dans la mise en place des connections inter-neurones [2] . Une etude est en cours sur des modeles murins afin d’analyser le statut d’empreinte de ce gene dans le tissu nerveux et les consequences d’un defaut d’expression de son ligand Netrin sur le developpement placentaire.
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- 2015
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