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Oliveira‐Mendes B, Feliciangeli S, Ménard M, Chatelain F, Alameh M, Montnach J, Nicolas S, Ollivier B, Barc J, Baró I, Schott J, Probst V, Kyndt F, Denjoy I, Lesage F, Loussouarn G, De Waard M. A standardised hERG phenotyping pipeline to evaluate KCNH2 genetic variant pathogenicity. Clin Transl Med 2021; 11:e609. [PMID: 34841674 PMCID: PMC8609418 DOI: 10.1002/ctm2.609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND AND AIMS Mutations in KCNH2 cause long or short QT syndromes (LQTS or SQTS) predisposing to life-threatening arrhythmias. Over 1000 hERG variants have been described by clinicians, but most remain to be characterised. The objective is to standardise and accelerate the phenotyping process to contribute to clinician diagnosis and patient counselling. In silico evaluation was also included to characterise the structural impact of the variants. METHODS We selected 11 variants from known LQTS patients and two variants for which diagnosis was problematic. Using the Gibson assembly strategy, we efficiently introduced mutations in hERG cDNA despite GC-rich sequences. A pH-sensitive fluorescent tag was fused to hERG for efficient evaluation of channel trafficking. An optimised 35-s patch-clamp protocol was developed to evaluate hERG channel activity in transfected cells. R software was used to speed up analyses. RESULTS In the present work, we observed a good correlation between cell surface expression, assessed by the pH-sensitive tag, and current densities. Also, we showed that the new biophysical protocol allows a significant gain of time in recording ion channel properties and provides extensive information on WT and variant channel biophysical parameters, that can all be recapitulated in a single parameter defined herein as the repolarisation power. The impacts of the variants on channel structure were also reported where structural information was available. These three readouts (trafficking, repolarisation power and structural impact) define three pathogenicity indexes that may help clinical diagnosis. CONCLUSIONS Fast-track characterisation of KCNH2 genetic variants shows its relevance to discriminate mutants that affect hERG channel activity from variants with undetectable effects. It also helped the diagnosis of two new variants. This information is meant to fill a patient database, as a basis for personalised medicine. The next steps will be to further accelerate the process using an automated patch-clamp system.
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Affiliation(s)
| | - Sylvain Feliciangeli
- Labex ICST, Université Côte d'Azur, INSERMCentre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et CellulaireValbonneFrance
| | - Mélissa Ménard
- l'Institut du ThoraxInserm UMR 1087/CNRS UMR 6291NantesFrance
| | - Frank Chatelain
- Labex ICST, Université Côte d'Azur, INSERMCentre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et CellulaireValbonneFrance
| | - Malak Alameh
- l'Institut du ThoraxInserm UMR 1087/CNRS UMR 6291NantesFrance
| | - Jérôme Montnach
- l'Institut du ThoraxInserm UMR 1087/CNRS UMR 6291NantesFrance
| | | | | | - Julien Barc
- l'Institut du ThoraxInserm UMR 1087/CNRS UMR 6291NantesFrance
| | - Isabelle Baró
- l'Institut du ThoraxInserm UMR 1087/CNRS UMR 6291NantesFrance
| | | | - Vincent Probst
- CHU Nantes, l'Institut du Thorax, INSERM, CNRSUNIV NantesNantesFrance
| | - Florence Kyndt
- CHU Nantes, l'Institut du Thorax, INSERM, CNRSUNIV NantesNantesFrance
| | - Isabelle Denjoy
- Service de Cardiologie et CNMR Maladies Cardiaques Héréditaires RaresHôpital BichatParisFrance
| | - Florian Lesage
- Labex ICST, Université Côte d'Azur, INSERMCentre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et CellulaireValbonneFrance
| | | | - Michel De Waard
- l'Institut du ThoraxInserm UMR 1087/CNRS UMR 6291NantesFrance
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2
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Gao J, Shen W. Xenopus in revealing developmental toxicity and modeling human diseases. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115809. [PMID: 33096388 DOI: 10.1016/j.envpol.2020.115809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/01/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
The Xenopus model offers many advantages for investigation of the molecular, cellular, and behavioral mechanisms underlying embryo development. Moreover, Xenopus oocytes and embryos have been extensively used to study developmental toxicity and human diseases in response to various environmental chemicals. This review first summarizes recent advances in using Xenopus as a vertebrate model to study distinct types of tissue/organ development following exposure to environmental toxicants, chemical reagents, and pharmaceutical drugs. Then, the successful use of Xenopus as a model for diseases, including fetal alcohol spectrum disorders, autism, epilepsy, and cardiovascular disease, is reviewed. The potential application of Xenopus in genetic and chemical screening to protect against embryo deficits induced by chemical toxicants and related diseases is also discussed.
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Affiliation(s)
- Juanmei Gao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; College of Life and Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
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El Moheb MN, Refaat MM. A cardiac sodium channel mutation associated with epinephrine-induced marked QT-prolongation. J Cardiovasc Electrophysiol 2020; 31:2116-2117. [PMID: 32437005 DOI: 10.1111/jce.14572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Mohamad N El Moheb
- Division of Trauma Emergency Surgery and Surgical Critical Care, Massachusetts General Hospital, Boston, Massachusetts
| | - Marwan M Refaat
- Division of Cardiology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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Jalkh N, Mehawej C, Chouery E. Actionable Exomic Secondary Findings in 280 Lebanese Participants. Front Genet 2020; 11:208. [PMID: 32231684 PMCID: PMC7083077 DOI: 10.3389/fgene.2020.00208] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
The expanded use of NGS tests in genetic diagnosis enables the massive generation of data related to each individual, among which some findings are of medical value. Over the last three and a half years, 280 unrelated Lebanese patients, presenting a wide spectrum of genetic disorders were referred to our center for genetic evaluation by WES. Molecular diagnosis was established in 56% of the cases, as was previously reported. The current study evaluates secondary findings in these patients in 59 genes, linked to conditions mostly responsive to medical interventions, as per the ACMG guidelines. Our analysis allowed us to detect 19 pathogenic/likely pathogenic variants in 24 individuals from our cohort. Dominant actionable variants were found in 17 individuals representing 6% of the studied population. Genes associated with dominant cardiac diseases were the most frequently mutated: variants were found in 2.1% of our cohort. Genetic predisposition to cancer syndromes was observed in 1.07% of the cases. In parallel to dominant disease alleles, our analysis identified a recessive pathogenic disease allele in 2.5% of the individuals included in this study. Of interest, some variants were detected in different patients from our cohort thus urging the study of their prevalence in our population and the implementation, when needed, of specific genetic testing in the neonatal screening panel. In conclusion, here we report the first study estimating the actionable pathogenic variant load in the Lebanese population. Communicating current findings to the patients will enable them to benefit from a multi-disciplinary approach. Furthermore, tailoring the ACMG guidelines to the population is suggested, especially in highly consanguineous populations where the information related to recessive alleles might be highly beneficial to patients and their families.
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Affiliation(s)
- Nadine Jalkh
- Unité de Génétique Médicale, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Cybel Mehawej
- Unité de Génétique Médicale, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Eliane Chouery
- Unité de Génétique Médicale, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
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Vanoye CG, Desai RR, Fabre KL, Gallagher SL, Potet F, DeKeyser JM, Macaya D, Meiler J, Sanders CR, George AL. High-Throughput Functional Evaluation of KCNQ1 Decrypts Variants of Unknown Significance. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e002345. [PMID: 30571187 DOI: 10.1161/circgen.118.002345] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND The explosive growth in known human gene variation presents enormous challenges to current approaches for variant classification that have implications for diagnosis and treatment of many genetic diseases. For disorders caused by mutations in cardiac ion channels as in congenital arrhythmia syndromes, in vitro electrophysiological evidence has high value in discriminating pathogenic from benign variants, but these data are often lacking because assays are cost, time, and labor intensive. METHODS We implemented a strategy for performing high-throughput functional evaluations of ion channel variants that repurposed an automated electrophysiological recording platform developed previously for drug discovery. RESULTS We demonstrated the success of this approach by evaluating 78 variants in KCNQ1, a major gene involved in genetic disorders of cardiac arrhythmia susceptibility. We benchmarked our results with traditional electrophysiological approaches and observed a high level of concordance. This strategy also enabled studies of dominant-negative behavior of variants exhibiting severe loss-of-function. Overall, our results provided functional data useful for reclassifying >65% of the studied KCNQ1 variants. CONCLUSIONS Our results illustrate an efficient and high-throughput paradigm linking genotype to function for a human cardiac ion channel that will enable data-driven classification of large numbers of variants and create new opportunities for precision medicine.
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Affiliation(s)
- Carlos G Vanoye
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Reshma R Desai
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Katarina L Fabre
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Shannon L Gallagher
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Franck Potet
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Jean-Marc DeKeyser
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | | | - Jens Meiler
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, TN (J.M.).,the Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN (J.M.,C.R.S.)
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN (C.R.S.).,the Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN (J.M.,C.R.S.)
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
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Chavali NV, Kryshtal DO, Parikh SS, Wang L, Glazer AM, Blackwell DJ, Kroncke BM, Shoemaker MB, Knollmann BC. Patient-independent human induced pluripotent stem cell model: A new tool for rapid determination of genetic variant pathogenicity in long QT syndrome. Heart Rhythm 2019; 16:1686-1695. [PMID: 31004778 DOI: 10.1016/j.hrthm.2019.04.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Commercial genetic testing for long QT syndrome (LQTS) has rapidly expanded, but the inability to accurately predict whether a rare variant is pathogenic has limited its clinical benefit. Novel missense variants are routinely reported as variant of unknown significance (VUS) and cannot be used to screen family members at risk for sudden cardiac death. Better approaches to determine the pathogenicity of VUS are needed. OBJECTIVE The purpose of this study was to rapidly determine the pathogenicity of a CACNA1C variant reported by commercial genetic testing as a VUS using a patient-independent human induced pluripotent stem cell (hiPSC) model. METHODS Using CRISPR/Cas9 genome editing, CACNA1C-p.N639T was introduced into a previously established hiPSC from an unrelated healthy volunteer, thereby generating a patient-independent hiPSC model. Three independent heterozygous N639T hiPSC lines were generated and differentiated into cardiomyocytes (CM). Electrophysiological properties of N639T hiPSC-CM were compared to those of isogenic and population control hiPSC-CM by measuring the extracellular field potential (EFP) of 96-well hiPSC-CM monolayers and by patch clamp. RESULTS Significant EFP prolongation was observed only in optically stimulated but not in spontaneously beating N639T hiPSC-CM. Patch-clamp studies revealed that N639T prolonged the ventricular action potential by slowing voltage-dependent inactivation of CaV1.2 currents. Heterologous expression studies confirmed the effect of N639T on CaV1.2 inactivation. CONCLUSION The patient-independent hiPSC model enabled rapid generation of functional data to support reclassification of a CACNA1C VUS to likely pathogenic, thereby establishing a novel LQTS type 8 mutation. Furthermore, our results indicate the importance of controlling beating rates to evaluate the functional significance of LQTS VUS in high-throughput hiPSC-CM assays.
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Affiliation(s)
- Nikhil V Chavali
- Vanderbilt University School of Medicine, Nashville, Tennessee; Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Nashville, Tennessee
| | - Dmytro O Kryshtal
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Nashville, Tennessee
| | - Shan S Parikh
- Vanderbilt University School of Medicine, Nashville, Tennessee; Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Nashville, Tennessee
| | - Lili Wang
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Nashville, Tennessee
| | - Andrew M Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Nashville, Tennessee
| | - Daniel J Blackwell
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Nashville, Tennessee
| | - Brett M Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Nashville, Tennessee
| | - Moore Benjamin Shoemaker
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Nashville, Tennessee
| | - Bjorn C Knollmann
- Vanderbilt University School of Medicine, Nashville, Tennessee; Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Nashville, Tennessee.
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Nenni MJ, Fisher ME, James-Zorn C, Pells TJ, Ponferrada V, Chu S, Fortriede JD, Burns KA, Wang Y, Lotay VS, Wang DZ, Segerdell E, Chaturvedi P, Karimi K, Vize PD, Zorn AM. Xenbase: Facilitating the Use of Xenopus to Model Human Disease. Front Physiol 2019; 10:154. [PMID: 30863320 PMCID: PMC6399412 DOI: 10.3389/fphys.2019.00154] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/08/2019] [Indexed: 01/02/2023] Open
Abstract
At a fundamental level most genes, signaling pathways, biological functions and organ systems are highly conserved between man and all vertebrate species. Leveraging this conservation, researchers are increasingly using the experimental advantages of the amphibian Xenopus to model human disease. The online Xenopus resource, Xenbase, enables human disease modeling by curating the Xenopus literature published in PubMed and integrating these Xenopus data with orthologous human genes, anatomy, and more recently with links to the Online Mendelian Inheritance in Man resource (OMIM) and the Human Disease Ontology (DO). Here we review how Xenbase supports disease modeling and report on a meta-analysis of the published Xenopus research providing an overview of the different types of diseases being modeled in Xenopus and the variety of experimental approaches being used. Text mining of over 50,000 Xenopus research articles imported into Xenbase from PubMed identified approximately 1,000 putative disease- modeling articles. These articles were manually assessed and annotated with disease ontologies, which were then used to classify papers based on disease type. We found that Xenopus is being used to study a diverse array of disease with three main experimental approaches: cell-free egg extracts to study fundamental aspects of cellular and molecular biology, oocytes to study ion transport and channel physiology and embryo experiments focused on congenital diseases. We integrated these data into Xenbase Disease Pages to allow easy navigation to disease information on external databases. Results of this analysis will equip Xenopus researchers with a suite of experimental approaches available to model or dissect a pathological process. Ideally clinicians and basic researchers will use this information to foster collaborations necessary to interrogate the development and treatment of human diseases.
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Affiliation(s)
- Mardi J Nenni
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Malcolm E Fisher
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Christina James-Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Troy J Pells
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Virgilio Ponferrada
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Stanley Chu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Joshua D Fortriede
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Kevin A Burns
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Ying Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Vaneet S Lotay
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Dong Zhou Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Erik Segerdell
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
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Bezzerides VJ, Zhang D, Pu WT. Modeling Inherited Arrhythmia Disorders Using Induced Pluripotent Stem Cell-Derived Cardiomyocytes. Circ J 2016; 81:12-21. [PMID: 27916777 DOI: 10.1253/circj.cj-16-1113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inherited arrhythmia disorders (IADs) are a group of potentially lethal diseases that remain diagnostic and management challenges. Although the genetic basis for many of these disorders is well known, the pathogenicity of individual mutations and the resulting clinical outcomes are difficult to predict. Treatment options remain imperfect, and optimizing therapy for individual patients can be difficult. Recent advances in the derivation of induced pluripotent stem cells (iPSCs) from patients and creation of genetically engineered human models using CRISPR/Cas9 has the potential to dramatically advance translational arrhythmia research. In this review, we discuss the current state of modeling IADs using human iPSC-derived cardiomyocytes. We also discuss current limitations and areas for further study.
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Novelli V, Gambelli P, Memmi M, Napolitano C. Challenges in Molecular Diagnostics of Channelopathies in the Next-Generation Sequencing Era: Less Is More? Front Cardiovasc Med 2016; 3:29. [PMID: 27672637 PMCID: PMC5018689 DOI: 10.3389/fcvm.2016.00029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/26/2016] [Indexed: 12/15/2022] Open
Affiliation(s)
- Valeria Novelli
- Medical Genetics Unit, Fondazione Policlinico Universitario A. Gemelli, Rome, Italy; Centro Studi "Benito Stirpe" per la prevenzione della morte improvvisa nel giovane atleta, Rome, Italy
| | - Patrick Gambelli
- Molecular Cardiology, IRCCS Fondazione Salvatore Maugeri , Pavia , Italy
| | - Mirella Memmi
- Molecular Cardiology, IRCCS Fondazione Salvatore Maugeri , Pavia , Italy
| | - Carlo Napolitano
- Molecular Cardiology, IRCCS Fondazione Salvatore Maugeri , Pavia , Italy
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