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Bang ML, Bogomolovas J, Chen J. Understanding the molecular basis of cardiomyopathy. Am J Physiol Heart Circ Physiol 2022; 322:H181-H233. [PMID: 34797172 PMCID: PMC8759964 DOI: 10.1152/ajpheart.00562.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Inherited cardiomyopathies are a major cause of mortality and morbidity worldwide and can be caused by mutations in a wide range of proteins located in different cellular compartments. The present review is based on Dr. Ju Chen's 2021 Robert M. Berne Distinguished Lectureship of the American Physiological Society Cardiovascular Section, in which he provided an overview of the current knowledge on the cardiomyopathy-associated proteins that have been studied in his laboratory. The review provides a general summary of the proteins in different compartments of cardiomyocytes associated with cardiomyopathies, with specific focus on the proteins that have been studied in Dr. Chen's laboratory.
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Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan Unit, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Julius Bogomolovas
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| | - Ju Chen
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
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Genetic Testing in Patients with Hypertrophic Cardiomyopathy. Int J Mol Sci 2021; 22:ijms221910401. [PMID: 34638741 PMCID: PMC8509044 DOI: 10.3390/ijms221910401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a common inherited heart disease with an estimated prevalence of up to 1 in 200 individuals. In the majority of cases, HCM is considered a Mendelian disease, with mainly autosomal dominant inheritance. Most pathogenic variants are usually detected in genes for sarcomeric proteins. Nowadays, the genetic basis of HCM is believed to be rather complex. Thousands of mutations in more than 60 genes have been described in association with HCM. Nevertheless, screening large numbers of genes results in the identification of many genetic variants of uncertain significance and makes the interpretation of the results difficult. Patients lacking a pathogenic variant are now believed to have non-Mendelian HCM and probably have a better prognosis than patients with sarcomeric pathogenic mutations. Identifying the genetic basis of HCM creates remarkable opportunities to understand how the disease develops, and by extension, how to disrupt the disease progression in the future. The aim of this review is to discuss the brief history and recent advances in the genetics of HCM and the application of molecular genetic testing into common clinical practice.
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Next-generation Sequencing in Bone Marrow Failure Syndromes and Isolated Cytopenias: Experience of the Spanish Network on Bone Marrow Failure Syndromes. Hemasphere 2021; 5:e539. [PMID: 33718801 PMCID: PMC7951136 DOI: 10.1097/hs9.0000000000000539] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/11/2021] [Indexed: 11/26/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFSs) are a group of congenital rare diseases characterized by bone marrow failure, congenital anomalies, high genetic heterogeneity, and predisposition to cancer. Appropriate treatment and cancer surveillance ideally depend on the identification of the mutated gene. A next-generation sequencing (NGS) panel of genes could be 1 initial genetic screening test to be carried out in a comprehensive study of IBMFSs, allowing molecular detection in affected patients. We designed 2 NGS panels of IBMFS genes: version 1 included 129 genes and version 2 involved 145 genes. The cohort included a total of 204 patients with suspected IBMFSs without molecular diagnosis. Capture-based targeted sequencing covered > 99% of the target regions of 145 genes, with more than 20 independent reads. No differences were seen between the 2 versions of the panel. The NGS tool allowed a total of 91 patients to be diagnosed, with an overall molecular diagnostic rate of 44%. Among the 167 patients with classified IBMFSs, 81 patients (48%) were diagnosed. Unclassified IBMFSs involved a total of 37 patients, of whom 9 patients (24%) were diagnosed. The preexisting diagnosis of 6 clinically classified patients (6%) was amended, implying a change of therapy for some of them. Our NGS IBMFS gene panel assay is a useful tool in the molecular diagnosis of IBMFSs and a reasonable option as the first tier genetic test in these disorders.
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Guelly C, Abilova Z, Nuralinov O, Panzitt K, Akhmetova A, Rakhimova S, Kozhamkulov U, Kairov U, Molkenov A, Seisenova A, Trajanoski S, Abildinova Rashbayeva G, Kaussova G, Windpassinger C, Lee JH, Zhumadilov Z, Bekbossynova M, Akilzhanova A. Patients with coronary heart disease, dilated cardiomyopathy and idiopathic ventricular tachycardia share overlapping patterns of pathogenic variation in cardiac risk genes. PeerJ 2021; 9:e10711. [PMID: 33552729 PMCID: PMC7821765 DOI: 10.7717/peerj.10711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022] Open
Abstract
Background Ventricular tachycardia (VT) is a major cause of sudden cardiac death (SCD). Clinical investigations can sometimes fail to identify the underlying cause of VT and the event is classified as idiopathic (iVT). VT contributes significantly to the morbidity and mortality in patients with coronary artery disease (CAD) and dilated cardiomyopathy (DCM). Since mutations in arrhythmia-associated genes frequently determine arrhythmia susceptibility screening for disease-predisposing variants could improve VT diagnostics and prevent SCD in patients. Methods Ninety-two patients diagnosed with coronary heart disease (CHD), DCM, or iVT were included in our study. We evaluated genetic profiles and variants in known cardiac risk genes by targeted next generation sequencing (NGS) using a newly designed custom panel of 96 genes. We hypothesized that shared morphological and phenotypical features among these subgroups may have an overlapping molecular base. To our knowledge, this was the first study of the deep sequencing of 96 targeted cardiac genes in Kazakhstan. The clinical significance of the sequence variants was interpreted according to the guidelines developed by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) in 2015. The ClinVar and Varsome databases were used to determine the variant classifications. Results Targeted sequencing and stepwise filtering of the annotated variants identified a total of 307 unique variants in 74 genes, totally 456 variants in the overall study group. We found 168 mutations listed in the Human Genome Mutation Database (HGMD) and another 256 rare/unique variants with elevated pathogenic potential. There was a predominance of high- to intermediate pathogenicity variants in LAMA2, MYBPC3, MYH6, KCNQ1, GAA, and DSG2 in CHD VT patients. Similar frequencies were observed in DCM VT, and iVT patients, pointing to a common molecular disease association. TTN, GAA, LAMA2, and MYBPC3 contained the most variants in the three subgroups which confirm the impact of these genes in the complex pathogenesis of cardiomyopathies and VT. The classification of 307 variants according to ACMG guidelines showed that nine (2.9%) variants could be classified as pathogenic, nine (2.9%) were likely pathogenic, 98 (31.9%) were of uncertain significance, 73 (23.8%) were likely benign, and 118 (38.4%) were benign. CHD VT patients carry rare genetic variants with increased pathogenic potential at a comparable frequency to DCM VT and iVT patients in genes related to sarcomere function, nuclear function, ion flux, and metabolism. Conclusions In this study we showed that in patients with VT secondary to coronary artery disease, DCM, or idiopathic etiology multiple rare mutations and clinically significant sequence variants in classic cardiac risk genes associated with cardiac channelopathies and cardiomyopathies were found in a similar pattern and at a comparable frequency.
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Affiliation(s)
- Christian Guelly
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Zhannur Abilova
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | - Katrin Panzitt
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ainur Seisenova
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Slave Trajanoski
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | | | | | | | - Joseph H Lee
- Sergievsky Center Taub Institute, Columbia University Medical Center, New York, NY, United States of America
| | - Zhaxybay Zhumadilov
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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Alessi CE, Wu Q, Whitaker CH, Felice KJ. Laing Myopathy: Report of 4 New Families With Novel MYH7 Mutations, Double Mutations, and Severe Phenotype. J Clin Neuromuscul Dis 2020; 22:22-34. [PMID: 32833721 DOI: 10.1097/cnd.0000000000000297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Laing distal myopathy (LDM) is an autosomal dominant disorder caused by mutations in the slow skeletal muscle fiber myosin heavy chain (MYH7) gene on chromosome 14q11.2. The classic LDM phenotype-including early-onset, initial involvement of foot dorsiflexors and great toe extensors, followed by weakness of neck flexors and finger extensors-is well documented. Since the original report by Laing et al in 1995, the spectrum of MYH7-related myopathies has expanded to include congenital myopathies, late-onset myopathies, myosin storage myopathy, and scapuloperoneal myopathies. Most patients with LDM harbor mutations in the midrod domain of the MYH7 gene, but rare cases document disease-associated mutations in the globular head region. In this report, we add to the medical literature by describing the clinicopathological findings in 8 affected family members from 4 new LDM families-including 2 with novel MYH7 mutations (Y162D and A1438P), one with dual mutations (V39M and K1617del), and one family (E1508del) with severe early-onset weakness associated with contractures, respiratory insufficiency, and dilated cardiomyopathy. Our families highlight the ever-expanding clinical spectrum and genetic variation of the skeletal myopathies related to MYH7 gene mutations.
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Affiliation(s)
| | - Qian Wu
- Pathology and Laboratory Medicine, University of Connecticut School of Medicine, Farmington, CT; and
| | - Charles H Whitaker
- Department of Neuromuscular Medicine, Muscular Dystrophy Association Care Center, Hospital for Special Care, New Britain, CT
| | - Kevin J Felice
- Department of Neuromuscular Medicine, Muscular Dystrophy Association Care Center, Hospital for Special Care, New Britain, CT
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Merlo M, Masè M, Cannatà A, Zaffalon D, Lardieri G, Limongelli G, Imazio M, Canepa M, Castelletti S, Bauce B, Biagini E, Livi U, Severini GM, Dal Ferro M, Marra MP, Basso C, Autore C, Sinagra G. Management of nonischemic-dilated cardiomyopathies in clinical practice: a position paper of the working group on myocardial and pericardial diseases of Italian Society of Cardiology. J Cardiovasc Med (Hagerstown) 2020; 21:927-943. [PMID: 32740436 DOI: 10.2459/jcm.0000000000001050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
: Nonischemic-dilated cardiomyopathy (NIDCM) is an entity that gathers extremely heterogeneous diseases. This awareness, although leading to continuous improvement in survival, has increased the complexity of NIDCM patients' management. Even though the endorsed 'red-flags' approach helps clinicians in pursuing an accurate etiological definition in clinical practice, it is not clear when and how peripheral centers should interact with referral centers with specific expertise in challenging scenarios (e.g. postmyocarditis and genetically determined dilated cardiomyopathy) and with easier access to second-line diagnostic tools and therapies. This position paper will summarize each step in NIDCM management, highlighting the multiple interactions between peripheral and referral centers, from first-line diagnostic workup and therapy to advanced heart failure management and long-term follow-up.
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Affiliation(s)
- Marco Merlo
- Cardiothoracovascular Department , Center for Diagnosis and Management of Cardiomyopathies, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), University of Trieste, Trieste
| | - Marco Masè
- Cardiothoracovascular Department , Center for Diagnosis and Management of Cardiomyopathies, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), University of Trieste, Trieste
| | - Antonio Cannatà
- Cardiothoracovascular Department , Center for Diagnosis and Management of Cardiomyopathies, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), University of Trieste, Trieste
| | - Denise Zaffalon
- Cardiothoracovascular Department , Center for Diagnosis and Management of Cardiomyopathies, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), University of Trieste, Trieste
| | - Gerardina Lardieri
- Cardiology Department, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), Hospital of Gorizia and Monfalcone
| | - Giuseppe Limongelli
- Department of Translational Medical Sciences, Inherited and Rare Heart Disease, Vanvitelli Cardiology, University of Campania Luigi Vanvitelli, Caserta
| | - Massimo Imazio
- University Cardiology, A.O.U. Città della Salute e della Scienza di Torino, Torino
| | - Marco Canepa
- Cardiovascular Disease Unit, IRCCS Ospedale Policlinico San Martino - IRCCS Italian Cardiovascular Network.,Department of Internal Medicine, University of Genova, Genova
| | - Silvia Castelletti
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin, Milan
| | - Barbara Bauce
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padua, Padova
| | - Elena Biagini
- Azienda Ospedaliero - Universitaria, Policlinico di Sant'Orsola, Cardiology Unit, Cardio-Thoracic-Vascular Department, Bologna, Italy
| | - Ugolino Livi
- Cardiothoracic Department, University Hospital of Udine, Udine
| | | | - Matteo Dal Ferro
- Cardiothoracovascular Department , Center for Diagnosis and Management of Cardiomyopathies, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), University of Trieste, Trieste
| | - Martina Perazzolo Marra
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padua, Padova
| | - Cristina Basso
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padua, Padova
| | - Camillo Autore
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Psychology, Sapienza University, Rome, Italy
| | - Gianfranco Sinagra
- Cardiothoracovascular Department , Center for Diagnosis and Management of Cardiomyopathies, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), University of Trieste, Trieste
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(Complex approach towards patients with hypertrophic cardiomyopathy and indications to genetic testing). COR ET VASA 2020. [DOI: 10.33678/cor.2020.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bonaventura J, Norambuena P, Votýpka P, Hnátová H, Adlová R, Macek M, Veselka J. Patients with hypertrophic obstructive cardiomyopathy after alcohol septal ablation have favorable long-term outcome irrespective of their genetic background. Cardiovasc Diagn Ther 2020; 10:193-200. [PMID: 32420099 DOI: 10.21037/cdt.2020.01.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background The genetic background of patients with hypertrophic cardiomyopathy (HCM) treated with alcohol septal ablation (ASA) and its relationship to the outcomes are not known. We aimed to investigate whether the outcome of genotype positive (G+) patients differs from genotype negative (G-) patients treated with ASA. Methods We included 129 HCM patients (mean age 54±13 years) treated with ASA in a tertiary cardiovascular center and performed next generation sequencing (NGS) based genomic testing. All patients were followed-up three months after the procedure and yearly thereafter. Results A total of 30 (23%) HCM patients were G+ patients. At the 3-months follow-up, both groups of patients had similar left ventricular outflow tract PG (16.9±15.7 mmHg in G+ vs. 16.3±18.8 mmHg in G-, P=0.73) and symptoms (follow-up NYHA class 1.40±0.62 vs. 1.37±0.53, P=0.99, follow-up CCS class 0.23±0.52 vs. 0.36±0.65, P=0.36). The independent predictors of all-cause mortality were baseline interventricular septum (IVS) thickness (HR 1.12, 95% CI: 1.00-1.26, P=0.049) and age at the time of ASA (HR 1.11, 95% CI: 1.06-1.17, P<0.01). The adjusted all-cause mortality rate did not differ significantly between G+ and G- patients (P=0.52). The adjusted combined mortality event rate did not differ between both groups (P=0.78). Conclusions Despite more severe phenotype in G+ HCM patients, ASA is an equally effective treatment for LVOTO in G+ patients as it is for treating LVOTO in G- patients. The long-term outcome after ASA is similar in G+ and G- patients.
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Affiliation(s)
- Jiří Bonaventura
- Department of Cardiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Patricia Norambuena
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Pavel Votýpka
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Hana Hnátová
- Department of Cardiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Radka Adlová
- Department of Cardiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Milan Macek
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Josef Veselka
- Department of Cardiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
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Yeh JK, Liu WH, Wang CY, Lu JJ, Chen CH, Wu-Chou YH, Chang PY, Chang SC, Yang CH, Tsai ML, Ho MY, Hsieh IC, Wen MS. Targeted Next Generation Sequencing for Genetic Mutations of Dilated Cardiomyopathy. ACTA CARDIOLOGICA SINICA 2019; 35:571-584. [PMID: 31879508 PMCID: PMC6859096 DOI: 10.6515/acs.201911_35(6).20190402a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 04/02/2019] [Indexed: 01/19/2023]
Abstract
BACKGROUND Approximately one-third of cases of dilated cardiomyopathy (DCM) are caused by genetic mutations. With new sequencing technologies, numerous variants have been associated with this inherited cardiomyopathy, however the prevalence and genotype-phenotype correlations in different ethnic cohorts remain unclear. This study aimed to investigate the variants in Chinese DCM patients and correlate them with clinical presentations and prognosis. METHODS AND RESULTS From September 2013 to December 2016, 70 index patients underwent DNA sequencing for 12 common disease-causing genes with next generation sequencing. Using a bioinformatics filtering process, 12 rare truncating variants (7 nonsense variants, 4 frameshift variants, and 1 splice site variant) and 29 rare missense variants were identified. Of these, 3 patients were double heterozygotes and 10 patients were compound heterozygotes. Overall, 47.1% (33/70) of the index patients had the seputatively pathogenic variants. The majority (33/41, 80.4%) of these variants were located in titin (TTN). More than 80% of the TTN variants (27/33, 81.8%) were distributed in the A band region of the sarcomere. Patients carrying these variants did not have a different phenotype in disease severity, clinical outcome and reversibility of ventricular function compared with non-carriers. CONCLUSIONS Several new rare variants were identified in a Chinese population in this study, indicating that there are ethnic differences in genetic mutations in DCM patients. TTN remains the major disease-causing gene. Our results could be a reference for future genetic tests in Chinese populations. No specific genotype-phenotype correlations were found, however a prospective large cohort study may be needed to confirm our findings.
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Affiliation(s)
| | - Wei-Hsiu Liu
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
| | - Chao-Yung Wang
- Department of Cardiology
- College of Medicine, Chang Gung University, Taoyuan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
- College of Medicine, Chang Gung University, Taoyuan
| | | | - Yah-Huei Wu-Chou
- Department of Medical Research, Linkou Chang Gung Memorial Hospital and Graduate of Institute of Clinical Medical Science, Chang Gung University, Taoyuan, Taiwan
| | - Pi-Yueh Chang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
| | - Shih-Cheng Chang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital
| | | | | | | | - I-Chang Hsieh
- Department of Cardiology
- College of Medicine, Chang Gung University, Taoyuan
| | - Ming-Shien Wen
- Department of Cardiology
- College of Medicine, Chang Gung University, Taoyuan
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Brodehl A, Ebbinghaus H, Deutsch MA, Gummert J, Gärtner A, Ratnavadivel S, Milting H. Human Induced Pluripotent Stem-Cell-Derived Cardiomyocytes as Models for Genetic Cardiomyopathies. Int J Mol Sci 2019; 20:ijms20184381. [PMID: 31489928 PMCID: PMC6770343 DOI: 10.3390/ijms20184381] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
In the last few decades, many pathogenic or likely pathogenic genetic mutations in over hundred different genes have been described for non-ischemic, genetic cardiomyopathies. However, the functional knowledge about most of these mutations is still limited because the generation of adequate animal models is time-consuming and challenging. Therefore, human induced pluripotent stem cells (iPSCs) carrying specific cardiomyopathy-associated mutations are a promising alternative. Since the original discovery that pluripotency can be artificially induced by the expression of different transcription factors, various patient-specific-induced pluripotent stem cell lines have been generated to model non-ischemic, genetic cardiomyopathies in vitro. In this review, we describe the genetic landscape of non-ischemic, genetic cardiomyopathies and give an overview about different human iPSC lines, which have been developed for the disease modeling of inherited cardiomyopathies. We summarize different methods and protocols for the general differentiation of human iPSCs into cardiomyocytes. In addition, we describe methods and technologies to investigate functionally human iPSC-derived cardiomyocytes. Furthermore, we summarize novel genome editing approaches for the genetic manipulation of human iPSCs. This review provides an overview about the genetic landscape of inherited cardiomyopathies with a focus on iPSC technology, which might be of interest for clinicians and basic scientists interested in genetic cardiomyopathies.
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Affiliation(s)
- Andreas Brodehl
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Hans Ebbinghaus
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Marcus-André Deutsch
- Department of Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Jan Gummert
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
- Department of Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Anna Gärtner
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Sandra Ratnavadivel
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
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Brodehl A, Rezazadeh S, Williams T, Munsie NM, Liedtke D, Oh T, Ferrier R, Shen Y, Jones SJM, Stiegler AL, Boggon TJ, Duff HJ, Friedman JM, Gibson WT, Childs SJ, Gerull B. Mutations in ILK, encoding integrin-linked kinase, are associated with arrhythmogenic cardiomyopathy. Transl Res 2019; 208:15-29. [PMID: 30802431 PMCID: PMC7412573 DOI: 10.1016/j.trsl.2019.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/17/2019] [Accepted: 02/12/2019] [Indexed: 12/11/2022]
Abstract
Arrhythmogenic cardiomyopathy is a genetic heart muscle disorder characterized by fibro-fatty replacement of cardiomyocytes leading to life-threatening ventricular arrhythmias, heart failure, and sudden cardiac death. Mutations in genes encoding cardiac junctional proteins are known to cause about half of cases, while remaining genetic causes are unknown. Using exome sequencing, we identified 2 missense variants (p.H33N and p.H77Y) that were predicted to be damaging in the integrin-linked kinase (ILK) gene in 2 unrelated families. The p.H33N variant was found to be de novo. ILK links integrins and the actin cytoskeleton, and is essential for the maintenance of normal cardiac function. Both of the new variants are located in the ILK ankyrin repeat domain, which binds to the first LIM domain of the adaptor proteins PINCH1 and PINCH2. In silico binding studies proposed that the human variants disrupt the ILK-PINCH complex. Recombinant mutant ILK expressed in H9c2 rat myoblast cells shows aberrant prominent cytoplasmic localization compared to the wild-type. Expression of human wild-type and mutant ILK under the control of the cardiac-specific cmlc2 promotor in zebrafish shows that p.H77Y and p.P70L, a variant previously reported in a dilated cardiomyopathy family, cause cardiac dysfunction and death by about 2-3 weeks of age. Our findings provide genetic and functional evidence that ILK is a cardiomyopathy disease gene and highlight its relevance for diagnosis and genetic counseling of inherited cardiomyopathies.
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Affiliation(s)
- Andreas Brodehl
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Saman Rezazadeh
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Tatjana Williams
- Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Nicole M Munsie
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Daniel Liedtke
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Tracey Oh
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Raechel Ferrier
- Department of Medical Genetics, Alberta Health Services, Calgary, Alberta, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Amy L Stiegler
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Henry J Duff
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | | | - Sarah J Childs
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Brenda Gerull
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada; Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany.
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12
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Chen R, Ge T, Jiang W, Huo J, Chang Q, Geng J, Shan Q. Identification of biomarkers correlated with hypertrophic cardiomyopathy with co‐expression analysis. J Cell Physiol 2019; 234:21999-22008. [PMID: 31059139 DOI: 10.1002/jcp.28762] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Ran Chen
- Department of Cardiology The First Affiliated Hospital of Nanjing Medical University Nanjing P.R. China
| | - Tiantian Ge
- Department of Cardiology The First Affiliated Hospital of Nanjing Medical University Nanjing P.R. China
| | - Wanying Jiang
- Department of Cardiology The First Affiliated Hospital of Nanjing Medical University Nanjing P.R. China
| | - Junyu Huo
- Department of Cardiology The First Affiliated Hospital of Nanjing Medical University Nanjing P.R. China
| | - Qing Chang
- Department of Cardiology The First Affiliated Hospital of Nanjing Medical University Nanjing P.R. China
| | - Jie Geng
- Department of Cardiology The First Affiliated Hospital of Nanjing Medical University Nanjing P.R. China
| | - Qijun Shan
- Department of Cardiology The First Affiliated Hospital of Nanjing Medical University Nanjing P.R. China
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13
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Bonaventura J, Norambuena P, Tomašov P, Jindrová D, Šedivá H, Macek M, Veselka J. The utility of the Mayo Score for predicting the yield of genetic testing in patients with hypertrophic cardiomyopathy. Arch Med Sci 2019; 15:641-649. [PMID: 31110529 PMCID: PMC6524174 DOI: 10.5114/aoms.2018.78767] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/14/2018] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION The yield of genetic testing in hypertrophic cardiomyopathy (HCM) is variable. The Mayo HCM Genotype Predictor score (Mayo Score) provides the pre-test probability of a positive HCM genetic test. In the original cohort of Mayo Score patients, only 9 HCM-associated myofilament genes were evaluated. The aim of this study was to validate the Mayo Score in the national HCM cohort and assess the yield of genetic testing using next generation sequencing (NGS) evaluating up to 229 genes. MATERIAL AND METHODS We included 336 consecutive unrelated HCM patients (41% women, mean age: 53 ±15 years). We performed NGS-based genomic testing with classification of identified variants according to American College of Medical Genetics and Genomics guidelines. NGS findings were compared with the Mayo Score (ranging from -1 to 5) based on clinical and echocardiographic variables. RESULTS We identified 72 variants classified as pathogenic or likely pathogenic in 70 (21%) HCM patients. One patient with the highest Mayo Score of 5 had a pathogenic mutation (100% yield). Patients with a Mayo Score of 4 had a pathogenic mutation in 71% of cases. Patients with a Mayo Score of 3 or 2 had a pathogenic mutation in 50 and 35% of cases, respectively. The yield of genetic testing in patients with a Mayo Score of -1 to 1 was low (6-21%). CONCLUSIONS The overall yield of genetic testing using NGS evaluating up to 229 genes was low. The yield of genetic testing was consistently predicted with Mayo Score values.
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Affiliation(s)
- Jiří Bonaventura
- Department of Cardiology, 2 Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Patricia Norambuena
- Department of Biology and Medical Genetics, 2 Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Pavol Tomašov
- Department of Cardiology, 2 Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Denisa Jindrová
- Department of Cardiology, 2 Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Hana Šedivá
- Department of Cardiology, 2 Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Milan Macek
- Department of Biology and Medical Genetics, 2 Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Josef Veselka
- Department of Cardiology, 2 Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
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14
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Sun Y, Man J, Wan Y, Pan G, Du L, Li L, Yang Y, Qiu L, Gao Q, Dan H, Mao L, Cheng Z, Fan C, Yu J, Lin M, Kristiansen K, Shen Y, Wei X. Targeted next-generation sequencing as a comprehensive test for Mendelian diseases: a cohort diagnostic study. Sci Rep 2018; 8:11646. [PMID: 30076350 PMCID: PMC6076228 DOI: 10.1038/s41598-018-30151-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/23/2018] [Indexed: 11/18/2022] Open
Abstract
With the development of next generation sequencing, more and more common inherited diseases have been reported. However, accurate and convenient molecular diagnosis cannot be achieved easily because of the enormous size of disease causing mutations. In this study, we introduced a new single-step method for the genetic analysis of patients and carriers in real clinical settings. All kinds of disease causing mutations can be detected at the same time in patients with Mendelian diseases or carriers. First, we evaluated this technology using YH cell line DNA and 9 samples with known mutations. Accuracy and stability of 99.80% and 99.58% were achieved respectively. Then, a total of 303 patients were tested using our targeted NGS approaches, 50.17% of which were found to have deleterious mutations and molecular confirmation of the clinical diagnosis. We identified 219 disease causing mutations, 43.84% (96/219) of which has never been reported before. Additionally, we developed a new deleteriousness prediction method for nonsynonymous SNVs, and an automating annotation and diagnosis system for Mendelian diseases, thus greatly assisting and enhancing Mendelian diseases diagnosis and helping to make a precise diagnosis for patients with Mendelian diseases.
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Affiliation(s)
- Yan Sun
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China
| | - Jianfen Man
- BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China
| | - Yang Wan
- Fuyang People's Hospital, Fuyang, 236000, China
| | - Gao Pan
- BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China
| | - Lique Du
- BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China
| | - Long Li
- BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China
| | - Yun Yang
- BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China
| | - Liru Qiu
- The Nephrology Division of Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qing Gao
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Handong Dan
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | | | | | - Chen Fan
- BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China
| | - Jing Yu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mufei Lin
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Karsten Kristiansen
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Yin Shen
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China.
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15
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Zhou N, Qin S, Liu Y, Tang L, Zhao W, Pan C, Qiu Z, Wang X, Shu X. Whole-exome sequencing identifies rare compound heterozygous mutations in the MYBPC3 gene associated with severe familial hypertrophic cardiomyopathy. Eur J Med Genet 2018. [PMID: 29524613 DOI: 10.1016/j.ejmg.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Most patients with hypertrophic cardiomyopathy have single-gene autosomal dominant mutations in loci that encode for sarcomeric proteins. The aim of this study was to determine whether pathogenic mutations were present by whole-exome sequencing (WES) in two families with hypertrophic cardiomyopathy (HCM) that presented during adolescence. Blood samples and clinical data were collected from individuals in two families with HCM. DNA was extracted. Mutations were identified using whole-exome sequencing (WES), and the genotypes of family members were identified using Sanger sequencing. Compound heterozygous mutations in the MYBPC3 gene (c.659A > G, p.Tyr220Cys; c.772G > A, p.Glu258Lys,NM_000256, Family 1), (c.873delG, p. Ile292PhefsTer8; c.3G > A, p.Met1?, NM_000256, Family 2) were identified by WES. Patient 1 carried the maternally inherited c.659A > G mutation and the paternally inherited c.772G > A mutation. Patient 2 carried the maternally inherited frameshift mutation c.873delG and the paternally inherited mutation c.3G > A. Two families with HCM presenting during adolescence (age of onset is about 11 years old) demonstrated compound heterozygous mutations in the MYBPC3 gene. These findings suggested an association of MYBPC3 mutations with the early onset of symptoms and worsened prognoses. Our study highlights the importance of genetic screening of all family members in cases of HCM.
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Affiliation(s)
- Nianwei Zhou
- Department of Echocardiography, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Disease, Shanghai Institute of Medical Imaging, 200032 Shanghai, China
| | - Shengmei Qin
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Disease, Shanghai Institute of Medical Imaging, 200032 Shanghai, China
| | - Yili Liu
- Department of Clinical Laboratory, Tongji Hospital, Tongji Univesity, 200032 Shanghai, China
| | - Lu Tang
- Department of Echocardiography, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Disease, Shanghai Institute of Medical Imaging, 200032 Shanghai, China
| | - Weipeng Zhao
- Department of Echocardiography, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Disease, Shanghai Institute of Medical Imaging, 200032 Shanghai, China
| | - Cuizhen Pan
- Department of Echocardiography, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Disease, Shanghai Institute of Medical Imaging, 200032 Shanghai, China
| | - Zilong Qiu
- Institute of Neuroscience, State Kay Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xiaolin Wang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, 200032 Shanghai, China.
| | - Xianhong Shu
- Department of Echocardiography, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Disease, Shanghai Institute of Medical Imaging, 200032 Shanghai, China.
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16
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Kalayinia S, Goodarzynejad H, Maleki M, Mahdieh N. Next generation sequencing applications for cardiovascular disease. Ann Med 2018; 50:91-109. [PMID: 29027470 DOI: 10.1080/07853890.2017.1392595] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The Human Genome Project (HGP), as the primary sequencing of the human genome, lasted more than one decade to be completed using the traditional Sanger's method. At present, next-generation sequencing (NGS) technology could provide the genome sequence data in hours. NGS has also decreased the expense of sequencing; therefore, nowadays it is possible to carry out both whole-genome (WGS) and whole-exome sequencing (WES) for the variations detection in patients with rare genetic diseases as well as complex disorders such as common cardiovascular diseases (CVDs). Finding new variants may contribute to establishing a risk profile for the pathology process of diseases. Here, recent applications of NGS in cardiovascular medicine are discussed; both Mendelian disorders of the cardiovascular system and complex genetic CVDs including inherited cardiomyopathy, channelopathies, stroke, coronary artery disease (CAD) and are considered. We also state some future use of NGS in clinical practice for increasing our information about the CVDs genetics and the limitations of this new technology. Key messages Traditional Sanger's method was the mainstay for Human Genome Project (HGP); Sanger sequencing has high fidelity but is slow and costly as compared to next generation methods. Within cardiovascular medicine, NGS has been shown to be successful in identifying novel causative mutations and in the diagnosis of Mendelian diseases which are caused by a single variant in a single gene. NGS has provided the opportunity to perform parallel analysis of a great number of genes in an unbiased approach (i.e. without knowing the underlying biological mechanism) which probably contribute to advance our knowledge regarding the pathology of complex diseases such as CVD.
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Affiliation(s)
- Samira Kalayinia
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
| | | | - Majid Maleki
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
| | - Nejat Mahdieh
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
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17
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Demougeot L, Houdayer F, Pélissier A, Mohrez F, Thevenon J, Duffourd Y, Nambot S, Gautier E, Binquet C, Rossi M, Sanlaville D, Béjean S, Peyron C, Thauvin-Robinet C, Faivre L. [Changes in clinical practice related to the arrival of next-generation sequencing in the genetic diagnosis of developmental diseases]. Arch Pediatr 2018; 25:77-83. [PMID: 29395884 DOI: 10.1016/j.arcped.2017.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 09/29/2017] [Accepted: 12/10/2017] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The arrival of high-throughput sequencing (HTS) has led to a sweeping change in the diagnosis of developmental abnormalities (DA) with or without intellectual deficiency (ID). With the prospect of deploying these new technologies, two questions have been raised: the representations of HTS among geneticists and the costs incurred due to these analyses. METHODS Geneticists attending a clinical genetics seminar were invited to complete a questionnaire. The statistical analysis was essentially descriptive and an analysis of costs was undertaken. RESULTS Of those responding to the questionnaire, 48% had already prescribed exome analysis and 25% had already had the occasion to disclose the results of such analyses. Ninety-six percent were aware that whole-exome sequencing (WES) had certain limits and 74% expressed misgivings concerning its use in medical practice. In parallel, the evaluation of costs showed that WES was less expensive than conventional procedures. DISCUSSION The survey revealed that geneticists had already come to terms with HTS as early as 2015. Among the major concerns expressed were the complexity of interpreting these tests and the many ethical implications. Geneticists seemed to be aware of the advantages but also the limits of these new technologies. The cost analysis raises questions about the place of HTS and in particular WES in the diagnostic work-up: should it be used early to obtain an etiological diagnosis rather than as the last resort? CONCLUSION It is essential for future generations of doctors and for the families concerned to learn about the concepts of HTS, which is set to become a major feature of new genomic medicine.
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Affiliation(s)
- L Demougeot
- Fédération hospitalo-universitaire médecine translationnelle et anomalies du développement (TRANSLAD), centre hospitalier universitaire de Dijon, 21079 Dijon, France; Filière de santé maladies rares anomalies du développement - déficience intellectuelle de causes rares (AnDDI-Rares), 21079 Dijon, France
| | - F Houdayer
- Centre de référence des anomalies de développement, service de génétique, hôpital Femme-Mère-Enfant, hospices Civils de Lyon, 69677 Bron, France
| | - A Pélissier
- Laboratoire d'économie et de gestion, pôle d'économie et de gestion, université de Bourgogne, 21066 Dijon, France
| | - F Mohrez
- Laboratoire d'économie et de gestion, pôle d'économie et de gestion, université de Bourgogne, 21066 Dijon, France
| | - J Thevenon
- Fédération hospitalo-universitaire médecine translationnelle et anomalies du développement (TRANSLAD), centre hospitalier universitaire de Dijon, 21079 Dijon, France; Filière de santé maladies rares anomalies du développement - déficience intellectuelle de causes rares (AnDDI-Rares), 21079 Dijon, France; Centre de génétique et centre de référence anomalies du développement et syndromes malformatifs de l'interrégion Est, centre hospitalier universitaire de Dijon, 21079 Dijon, France; Équipe génétique des anomalies du développement, UMR Inserm U1231, université de Bourgogne, 21079 Dijon, France
| | - Y Duffourd
- Fédération hospitalo-universitaire médecine translationnelle et anomalies du développement (TRANSLAD), centre hospitalier universitaire de Dijon, 21079 Dijon, France; Équipe génétique des anomalies du développement, UMR Inserm U1231, université de Bourgogne, 21079 Dijon, France
| | - S Nambot
- Fédération hospitalo-universitaire médecine translationnelle et anomalies du développement (TRANSLAD), centre hospitalier universitaire de Dijon, 21079 Dijon, France; Centre de génétique et centre de référence anomalies du développement et syndromes malformatifs de l'interrégion Est, centre hospitalier universitaire de Dijon, 21079 Dijon, France; Équipe génétique des anomalies du développement, UMR Inserm U1231, université de Bourgogne, 21079 Dijon, France
| | - E Gautier
- Fédération hospitalo-universitaire médecine translationnelle et anomalies du développement (TRANSLAD), centre hospitalier universitaire de Dijon, 21079 Dijon, France
| | - C Binquet
- Centre d'investigation clinique, centre hospitalier universitaire de Dijon, 21079 Dijon, France
| | - M Rossi
- Filière de santé maladies rares anomalies du développement - déficience intellectuelle de causes rares (AnDDI-Rares), 21079 Dijon, France; Centre de référence des anomalies de développement, service de génétique, hôpital Femme-Mère-Enfant, hospices Civils de Lyon, 69677 Bron, France
| | - D Sanlaville
- Filière de santé maladies rares anomalies du développement - déficience intellectuelle de causes rares (AnDDI-Rares), 21079 Dijon, France; Centre de référence des anomalies de développement, service de génétique, hôpital Femme-Mère-Enfant, hospices Civils de Lyon, 69677 Bron, France
| | - S Béjean
- Laboratoire d'économie et de gestion, pôle d'économie et de gestion, université de Bourgogne, 21066 Dijon, France
| | - C Peyron
- Laboratoire d'économie et de gestion, pôle d'économie et de gestion, université de Bourgogne, 21066 Dijon, France
| | - C Thauvin-Robinet
- Fédération hospitalo-universitaire médecine translationnelle et anomalies du développement (TRANSLAD), centre hospitalier universitaire de Dijon, 21079 Dijon, France; Filière de santé maladies rares anomalies du développement - déficience intellectuelle de causes rares (AnDDI-Rares), 21079 Dijon, France; Centre de génétique et centre de référence anomalies du développement et syndromes malformatifs de l'interrégion Est, centre hospitalier universitaire de Dijon, 21079 Dijon, France; Équipe génétique des anomalies du développement, UMR Inserm U1231, université de Bourgogne, 21079 Dijon, France
| | - L Faivre
- Fédération hospitalo-universitaire médecine translationnelle et anomalies du développement (TRANSLAD), centre hospitalier universitaire de Dijon, 21079 Dijon, France; Filière de santé maladies rares anomalies du développement - déficience intellectuelle de causes rares (AnDDI-Rares), 21079 Dijon, France; Centre de génétique et centre de référence anomalies du développement et syndromes malformatifs de l'interrégion Est, centre hospitalier universitaire de Dijon, 21079 Dijon, France; Équipe génétique des anomalies du développement, UMR Inserm U1231, université de Bourgogne, 21079 Dijon, France.
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18
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Wang J, Wan K, Sun J, Li W, Liu H, Han Y, Chen Y. Phenotypic diversity identified by cardiac magnetic resonance in a large hypertrophic cardiomyopathy family with a single MYH7 mutation. Sci Rep 2018; 8:973. [PMID: 29343710 PMCID: PMC5772531 DOI: 10.1038/s41598-018-19372-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/29/2017] [Indexed: 02/05/2023] Open
Abstract
Limited data is available on phenotypic variations with the same genotype in hypertrophic cardiomyopathy (HCM). The present study aims to explore the relationship between genotype and phenotype characterized by cardiovascular magnetic resonance (CMR) in a large Chinese family. A proband diagnosed with HCM from a multigenerational family underwent next-generation sequencing based on a custom sureSelect panel, including 117 candidate pathogenic genes associated with cardiomyopathies. All genetic results were confirmed by the Sanger sequencing method. All confirmed mutation carriers underwent CMR exam and myocardial tissue characterization using T1 mapping and late gadolinium enhancement (LGE) on a 3T scanner (Siemens Trio, Gemany). After clinical and genetic screening of 36 (including the proband) members of a large Chinese family, nineteen family members are determined to carry the single p.T1377M (c.4130C>T) mutation in the MYH7 gene. Of these 19 mutation carriers, eight are diagnosed with HCM, one was considered as borderline affected and ten are not clinically or phenotypically affected. Different HCM phenotypes are present in the nine affected individuals in this family. In addition, we have found different tissue characteristics assessed by T1 mapping and LGE in these individuals. We describe a family that demonstrates the diverse HCM phenotypes associated with a single MYH7 mutation.
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Affiliation(s)
- Jie Wang
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ke Wan
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiayu Sun
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, P. R. China
| | - Weihao Li
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hong Liu
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yuchi Han
- Department of Medicine (Cardiovascular Division), University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yucheng Chen
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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19
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Die hypertrophe Kardiomyopathie. MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-017-0155-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Zusammenfassung
Die hypertrophe Kardiomyopathie (HCM) ist die häufigste Kardiomyopathie mit mendelschem autosomal-dominanten Erbgang. Die Folgen der ausgeprägten Hypertrophie des Herzmuskels, in Verbindung mit (HOCM) oder ohne (HNCM) Obstruktion des linksventrikulären Ausflusstraktes reichen von benignen klinischen Verläufen bis hin zu schwersten Verläufen der Herzinsuffizienz und des plötzlichen Herztodes. Die neuen Leitlinien der Europäischen Gesellschaft für Kardiologie, veröffentlicht in 2014, fassen die aktuelle Evidenz beinahe aller Aspekte der Versorgung von Patienten zusammen. Erstmals werden hier klare Empfehlungen zum Vorgehen bei der genetischen Diagnostik ausgesprochen. Die genetische Testung unter Verwendung der Hochdurchsatzsequenzierung wird aktuell kontrovers und emotional diskutiert, könnte aber künftig das Verständnis der HCM und damit möglicherweise auch die Versorgung der Patienten mit HCM verbessern. Aus der Grundlagenforschung entspringen zudem neue translationale Ansätze, die Anlass zur Hoffnung geben, in der Zukunft bei HCM neue und gezielte Therapien (z. B. Gentherapie) anbieten zu können.
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20
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Smagarinsky Y, Burns C, Spinks C, Semsarian C, Ingles J. Development of a communication aid for explaining hypertrophic cardiomyopathy genetic test results. Pilot Feasibility Stud 2017; 3:53. [PMID: 29152326 PMCID: PMC5680798 DOI: 10.1186/s40814-017-0205-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 10/31/2017] [Indexed: 01/10/2023] Open
Abstract
Background Large gene panels are now commonplace for hypertrophic cardiomyopathy (HCM), increasing the yield of uncertain genetic findings. Few resources exist which aim to facilitate communication of HCM genetic test results. We sought to develop, pilot, and refine a communication aid for probands receiving HCM genetic test results. Methods Development was a multi-step process involving expertise of a multidisciplinary team, literature review, and empirical experience. The aid went through an iterative revision process throughout the piloting phase to incorporate feedback. HCM probands attending a specialized multidisciplinary HCM clinic, aged ≥ 18 years and genetic test results available for disclosure between May and August 2016, or recently received their gene results (January–April 2015) were eligible. A purposive sampling strategy was employed, recruiting those attending clinic during the study period or those who could attend without difficulty. Results We developed and pilot tested a genetic counsellor-led communication aid. Based on clinical expertise, the aid addresses (a) what genetic testing is, (b) implications for the patient, (c) reasoning for variant classification, and (d) implications for the family. Pilot data were sought to assess knowledge, feasibility, and acceptability using a self-report survey 2 weeks post-intervention. Twelve of 13 participants completed the follow-up questionnaire. Participants valued the individualised nature of the aid, recommended use of the aid, and indicated genetic knowledge, and family communication was better facilitated. Iterative modification of images helped to more simply depict important genetic concepts. Conclusions We have developed a tool that is feasible, acceptable, and helpful to patients receiving genetic results. This is an important first step, and trial of the aid to assess effectiveness compared to usual care will follow.
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Affiliation(s)
- Yana Smagarinsky
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Charlotte Burns
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Catherine Spinks
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
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21
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Pinto AM, Ariani F, Bianciardi L, Daga S, Renieri A. Exploiting the potential of next-generation sequencing in genomic medicine. Expert Rev Mol Diagn 2017; 16:1037-47. [PMID: 27574853 DOI: 10.1080/14737159.2016.1224181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The review highlights the impact of next-generation sequencing (NGS) on genomic medicine and the consequences of the progression from a single-gene panel technology to a whole exome sequencing approach. AREAS COVERED We brought together literature-based evidences, personal unpublished data and clinical experience to provide a critical overview of the impact of NGS on our daily clinical practice. Expert commentary: NGS has changed the role of clinical geneticist and has broadened the view accomplishing a transition from a monogenic Mendelian perspective to an oligogenic approach to disorders. Thus, it is a compelling new expertise which combines clinical evaluation with big omics data interpretation and moves forward to phenotype re-evaluation in light of data analysis. We introduced the term, 'exotyping', to highlight this holistic approach. Further, the review discusses the impact that the combination of genetic reprogramming and transcriptome analysis will have on the discovery of evidence-based therapies.
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Affiliation(s)
- Anna Maria Pinto
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | - Francesca Ariani
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | | | - Sergio Daga
- a Medical Genetics , University of Siena , Siena , Italy
| | - Alessandra Renieri
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
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22
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Mademont-Soler I, Mates J, Yotti R, Espinosa MA, Pérez-Serra A, Fernandez-Avila AI, Coll M, Méndez I, Iglesias A, del Olmo B, Riuró H, Cuenca S, Allegue C, Campuzano O, Picó F, Ferrer-Costa C, Álvarez P, Castillo S, Garcia-Pavia P, Gonzalez-Lopez E, Padron-Barthe L, Díaz de Bustamante A, Darnaude MT, González-Hevia JI, Brugada J, Fernandez-Aviles F, Brugada R. Additional value of screening for minor genes and copy number variants in hypertrophic cardiomyopathy. PLoS One 2017; 12:e0181465. [PMID: 28771489 PMCID: PMC5542623 DOI: 10.1371/journal.pone.0181465] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/30/2017] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Hypertrophic cardiomyopathy (HCM) is the most prevalent inherited heart disease. Next-generation sequencing (NGS) is the preferred genetic test, but the diagnostic value of screening for minor and candidate genes, and the role of copy number variants (CNVs) deserves further evaluation. METHODS Three hundred and eighty-seven consecutive unrelated patients with HCM were screened for genetic variants in the 5 most frequent genes (MYBPC3, MYH7, TNNT2, TNNI3 and TPM1) using Sanger sequencing (N = 84) or NGS (N = 303). In the NGS cohort we analyzed 20 additional minor or candidate genes, and applied a proprietary bioinformatics algorithm for detecting CNVs. Additionally, the rate and classification of TTN variants in HCM were compared with 427 patients without structural heart disease. RESULTS The percentage of patients with pathogenic/likely pathogenic (P/LP) variants in the main genes was 33.3%, without significant differences between the Sanger sequencing and NGS cohorts. The screening for 20 additional genes revealed LP variants in ACTC1, MYL2, MYL3, TNNC1, GLA and PRKAG2 in 12 patients. This approach resulted in more inconclusive tests (36.0% vs. 9.6%, p<0.001), mostly due to variants of unknown significance (VUS) in TTN. The detection rate of rare variants in TTN was not significantly different to that found in the group of patients without structural heart disease. In the NGS cohort, 4 patients (1.3%) had pathogenic CNVs: 2 deletions in MYBPC3 and 2 deletions involving the complete coding region of PLN. CONCLUSIONS A small percentage of HCM cases without point mutations in the 5 main genes are explained by P/LP variants in minor or candidate genes and CNVs. Screening for variants in TTN in HCM patients drastically increases the number of inconclusive tests, and shows a rate of VUS that is similar to patients without structural heart disease, suggesting that this gene should not be analyzed for clinical purposes in HCM.
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Affiliation(s)
- Irene Mademont-Soler
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Jesus Mates
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Raquel Yotti
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Department of Cardiology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón. Universidad Complutense, Madrid, Spain
| | - Maria Angeles Espinosa
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Department of Cardiology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón. Universidad Complutense, Madrid, Spain
| | - Alexandra Pérez-Serra
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ana Isabel Fernandez-Avila
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Department of Cardiology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón. Universidad Complutense, Madrid, Spain
| | - Monica Coll
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Irene Méndez
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Department of Cardiology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón. Universidad Complutense, Madrid, Spain
| | - Anna Iglesias
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Bernat del Olmo
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Helena Riuró
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Sofía Cuenca
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Department of Cardiology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón. Universidad Complutense, Madrid, Spain
| | - Catarina Allegue
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Oscar Campuzano
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Ferran Picó
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | | | | | | | - Pablo Garcia-Pavia
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Inherited Cardiac Diseases Unit. Department of Cardiology. Hospital Universitario Puerta de Hierro, Francisco de Vitoria University, Madrid, Spain
| | - Esther Gonzalez-Lopez
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Inherited Cardiac Diseases Unit. Department of Cardiology. Hospital Universitario Puerta de Hierro, Francisco de Vitoria University, Madrid, Spain
| | - Laura Padron-Barthe
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Inherited Cardiac Diseases Unit. Department of Cardiology. Hospital Universitario Puerta de Hierro, Francisco de Vitoria University, Madrid, Spain
| | | | | | | | - Josep Brugada
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Arrhythmia Unit, Hospital Clinic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Francisco Fernandez-Aviles
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Department of Cardiology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón. Universidad Complutense, Madrid, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Cardiovascular Genetics Unit, Hospital Universitari Dr. Josep Trueta, Girona, Spain
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23
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Szabadosova V, Boronova I, Ferenc P, Tothova I, Bernasovska J, Zigova M, Kmec J, Bernasovsky I. Analysis of selected genes associated with cardiomyopathy by next-generation sequencing. J Clin Lab Anal 2017; 32. [PMID: 28594148 DOI: 10.1002/jcla.22254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/14/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND As the leading cause of congestive heart failure, cardiomyopathy represents a heterogenous group of heart muscle disorders. Despite considerable progress being made in the genetic diagnosis of cardiomyopathy by detection of the mutations in the most prevalent cardiomyopathy genes, the cause remains unsolved in many patients. High-throughput mutation screening in the disease genes for cardiomyopathy is now possible because of using target enrichment followed by next-generation sequencing. The aim of the study was to analyze a panel of genes associated with dilated or hypertrophic cardiomyopathy based on previously published results in order to identify the subjects at risk. METHODS The method of next-generation sequencing by IlluminaHiSeq 2500 platform was used to detect sequence variants in 16 individuals diagnosed with dilated or hypertrophic cardiomyopathy. Detected variants were filtered and the functional impact of amino acid changes was predicted by computational programs. RESULTS DNA samples of the 16 patients were analyzed by whole exome sequencing. We identified six nonsynonymous variants that were shown to be pathogenic in all used prediction softwares: rs3744998 (EPG5), rs11551768 (MGME1), rs148374985 (MURC), rs78461695 (PLEC), rs17158558 (RET) and rs2295190 (SYNE1). Two of the analyzed sequence variants had minor allele frequency (MAF)<0.01: rs148374985 (MURC), rs34580776 (MYBPC3). CONCLUSION Our data support the potential role of the detected variants in pathogenesis of dilated or hypertrophic cardiomyopathy; however, the possibility that these variants might not be true disease-causing variants but are susceptibility alleles that require additional mutations or injury to cause the clinical phenotype of disease must be considered.
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Affiliation(s)
- Viktoria Szabadosova
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Iveta Boronova
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Peter Ferenc
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Iveta Tothova
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Jarmila Bernasovska
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Michaela Zigova
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Jan Kmec
- Cardiocentre, Faculty Hospital of J.A. Reiman, Presov, Slovakia
| | - Ivan Bernasovsky
- Center of Languages and Cultures of National Minorities, University of Presov, Presov, Slovakia
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24
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Povysil G, Tzika A, Vogt J, Haunschmid V, Messiaen L, Zschocke J, Klambauer G, Hochreiter S, Wimmer K. panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics. Hum Mutat 2017; 38:889-897. [PMID: 28449315 PMCID: PMC5518446 DOI: 10.1002/humu.23237] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/21/2017] [Accepted: 04/22/2017] [Indexed: 11/10/2022]
Abstract
Targeted next‐generation‐sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy‐number variations (CNVs) in addition to single‐nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user‐friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state‐of‐the‐art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user‐selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user‐friendliness rendering it highly suitable for routine clinical diagnostics.
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Affiliation(s)
- Gundula Povysil
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Antigoni Tzika
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Julia Vogt
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Verena Haunschmid
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Ludwine Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Johannes Zschocke
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Günter Klambauer
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Sepp Hochreiter
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
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25
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Gago-Díaz M, Ramos-Luis E, Zoppis S, Zorio E, Molina P, Braza-Boïls A, Giner J, Sobrino B, Amigo J, Blanco-Verea A, Carracedo Á, Brion M. Postmortem genetic testing should be recommended in sudden cardiac death cases due to thoracic aortic dissection. Int J Legal Med 2017; 131:1211-1219. [PMID: 28391405 DOI: 10.1007/s00414-017-1583-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 03/27/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Acute thoracic aortic dissections and ruptures, the main life-threatening complications of the corresponding aneurysms, are an important cause of sudden cardiac death. Despite the usefulness of the molecular diagnosis of these conditions in the clinical setting, the corresponding forensic field remains largely unexplored. The main goal of this study was to explore and validate a new massive parallel sequencing candidate gene assay as a diagnostic tool for acute thoracic aortic dissection autopsy cases. MATERIALS AND METHODS Massive parallel sequencing of 22 thoracic aortic disease candidate genes performed in 17 cases of thoracic aortic dissection using AmpliSeq and Ion Proton technologies. Genetic variants were filtered by location, type, and frequency at the Exome Aggregation Consortium and an internal database and further classified based on the American College of Medical Genetics and Genomics (ACMG) recommendations published in 2015. All prioritized results were confirmed by traditional sequencing. RESULTS From the total of 10 potentially pathogenic genetic variants identified in 7 out of the 17 initial samples, 2 of them were further classified as pathogenic, 2 as likely pathogenic, 1 as possibly benign, and the remaining 5 as variants of uncertain significance, reaching a molecular autopsy yield of 23%, approximately. CONCLUSIONS This massive parallel sequencing candidate gene approach proved useful for the molecular autopsy of aortic dissection sudden cardiac death cases and should therefore be progressively incorporated into the forensic field, being especially beneficial for the anticipated diagnosis and risk stratification of any other family member at risk of developing the same condition.
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Affiliation(s)
- Marina Gago-Díaz
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Eva Ramos-Luis
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Silvia Zoppis
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain.,Laboratorio di Genetica Forense, Sezione di Medicina Legale, Dipartimento S.A.I.M.L.A.L., Università di Roma Sapienza, Rome, Italy
| | - Esther Zorio
- Servicio de Cardiología, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Pilar Molina
- Servicio de Patología, Instituto de Medicina Legal de Valencia, Valencia, Spain
| | | | - Juan Giner
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Beatriz Sobrino
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Jorge Amigo
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Alejandro Blanco-Verea
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - María Brion
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain. .,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain. .,Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Laboratorio 1, Travesía de Choupana S/N, CP: 15706, Santiago de Compostela, Spain.
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26
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Veselka J, Anavekar NS, Charron P. Hypertrophic obstructive cardiomyopathy. Lancet 2017; 389:1253-1267. [PMID: 27912983 DOI: 10.1016/s0140-6736(16)31321-6] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/22/2016] [Accepted: 08/02/2016] [Indexed: 12/23/2022]
Abstract
Hypertrophic obstructive cardiomyopathy is an inherited myocardial disease defined by cardiac hypertrophy (wall thickness ≥15 mm) that is not explained by abnormal loading conditions, and left ventricular obstruction greater than or equal to 30 mm Hg. Typical symptoms include dyspnoea, chest pain, palpitations, and syncope. The diagnosis is usually suspected on clinical examination and confirmed by imaging. Some patients are at increased risk of sudden cardiac death, heart failure, and atrial fibrillation. Patients with an increased risk of sudden cardiac death undergo cardioverter-defibrillator implantation; in patients with severe symptoms related to ventricular obstruction, septal reduction therapy (myectomy or alcohol septal ablation) is recommended. Life-long anticoagulation is indicated after the first episode of atrial fibrillation.
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Affiliation(s)
- Josef Veselka
- Department of Cardiology, 2nd Medical School, Charles University and Motol University Hospital, Prague, Czech Republic.
| | - Nandan S Anavekar
- Departments of Cardiology and Radiology, Mayo Clinic, Rochester, MN, USA
| | - Philippe Charron
- Université Paris Sud, UVSQ, INSERM U1018, CESP, Boulogne-Billancourt, France; APHP, ICAN, Hôpital de la Pitié Salpêtrière, Paris, France
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27
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Wang G, Ji R, Zou W, Penny DJ, Fan Y. Inherited Cardiomyopathies: Genetics and Clinical Genetic Testing. CARDIOVASCULAR INNOVATIONS AND APPLICATIONS 2017. [DOI: 10.15212/cvia.2017.0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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28
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Blue GM, Humphreys D, Szot J, Major J, Chapman G, Bosman A, Kirk EP, Sholler GF, Harvey RP, Dunwoodie SL, Winlaw DS. The promises and challenges of exome sequencing in familial, non-syndromic congenital heart disease. Int J Cardiol 2016; 230:155-163. [PMID: 27989580 DOI: 10.1016/j.ijcard.2016.12.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/30/2016] [Accepted: 12/11/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Exome sequencing is an established strategy to identify causal variants in families with two or more members affected by congenital heart disease (CHD). This unbiased approach, in which both rare and common variants are identified, makes it suitable to research complex, heterogeneous diseases such as CHD. METHODS AND RESULTS Exome sequencing was performed on two affected members of a three generation family with atrial septal defects (ASD), suggesting a dominant inheritance pattern. Variants were filtered using two bioinformatics pipelines and prioritised according to in silico prediction programs. Segregation studies and functional analyses were used to assess co-segregation with disease and effects on protein function, respectively. Following the data and in silico analyses, ten candidate variants were prioritised. Of these, SRPK2 (c.2044C>T[p.Arg682Trp]) and NOTCH1 (c.3835C>T[p.Arg1279Cys]), co-segregated with disease in the family; however, previous functional analyses on SRPK2 make this an unlikely candidate. Functional analyses in the variant (c.3835C>T[p.Arg1279Cys]) of the known CHD gene NOTCH1 demonstrated a non-significant decrease in signalling activity. CONCLUSION This study demonstrates both the potential, as well as the challenges, of applying exome sequencing to complex diseases such as CHD. While in silico evidence and segregation analyses in the NOTCH1 p.Arg1279Cys variant are highly suggestive of pathogenicity, the minimal change in signalling capacity suggests that other variants may be required for CHD development. This study highlights the difficulties of applying exome sequencing in familial, non-syndromic CHD in the clinical environment and a cautionary note in the interpretation of apparently causal abnormalities in silico without supportive functional data.
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Affiliation(s)
- Gillian M Blue
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - David Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Justin Szot
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Joelene Major
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Alexis Bosman
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia
| | - Edwin P Kirk
- Department of Medical Genetics, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Gary F Sholler
- The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - David S Winlaw
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia.
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29
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Affiliation(s)
- Valentina Favalli
- Centre for Inherited Cardiovascular Diseases, IRCCS Foundation, University Hospital, Policlinico San Matteo, Pavia, Italy
| | - Alessandra Serio
- Centre for Inherited Cardiovascular Diseases, IRCCS Foundation, University Hospital, Policlinico San Matteo, Pavia, Italy
| | - Maurizia Grasso
- Centre for Inherited Cardiovascular Diseases, IRCCS Foundation, University Hospital, Policlinico San Matteo, Pavia, Italy
| | - Eloisa Arbustini
- Centre for Inherited Cardiovascular Diseases, IRCCS Foundation, University Hospital, Policlinico San Matteo, Pavia, Italy
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30
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Müller AM, Bockstahler M, Hristov G, Weiß C, Fischer A, Korkmaz-Icöz S, Giannitsis E, Poller W, Schultheiss HP, Katus HA, Kaya Z. Identification of novel antigens contributing to autoimmunity in cardiovascular diseases. Clin Immunol 2016; 173:64-75. [PMID: 27634429 DOI: 10.1016/j.clim.2016.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 12/11/2022]
Abstract
In myocarditis and dilated cardiomyopathy (DCM) patients the immune system may play an important role in disease progression. In this study, we aimed to identify new antigens as a target for autoimmune response that might play a crucial role in these diseases. Therefore, a peptide-array was used to investigate antibody binding profiles in patients with autoimmune myocarditis or DCM compared to healthy controls and thus to identify disease relevant antigens. To analyze the pathogenicity of the identified antigens, an experimental autoimmune myocarditis (EAM) model was used. Hereby, 3 peptide sequences, derived from myosin-binding-protein-C (MYBPC) fast-type, RNA-binding-protein 20 (RBM20), and dystrophin, showed pathogenic effects on the myocardium of mice. In summary, 3 potentially cardiopathogenic peptides (MYBPC fast-type, RBM20, dystrophin) were identified. Thus, this study could serve as a basis for future investigations aimed at determining further antigens leading to pathogenic effects on the myocardium of DCM as well as myocarditis patients.
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Affiliation(s)
- Anna-Maria Müller
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany
| | | | - Georgi Hristov
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Christel Weiß
- Department of Clinical Statistics, Biomathematics, Information Processing, University of Heidelberg/Mannheim, 68167 Mannheim, Germany
| | - Andrea Fischer
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sevil Korkmaz-Icöz
- Department of Cardiac Surgery, University of Heidelberg, 69120 Heidelberg, Germany
| | | | - Wolfgang Poller
- Department of Cardiology and Pneumology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, University of Heidelberg, 69120 Heidelberg, Germany
| | - Heinz-Peter Schultheiss
- Department of Cardiology and Pneumology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Hugo A Katus
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ziya Kaya
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, University of Heidelberg, 69120 Heidelberg, Germany.
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31
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Cecconi M, Parodi MI, Formisano F, Spirito P, Autore C, Musumeci MB, Favale S, Forleo C, Rapezzi C, Biagini E, Davì S, Canepa E, Pennese L, Castagnetta M, Degiorgio D, Coviello DA. Targeted next-generation sequencing helps to decipher the genetic and phenotypic heterogeneity of hypertrophic cardiomyopathy. Int J Mol Med 2016; 38:1111-24. [PMID: 27600940 PMCID: PMC5029966 DOI: 10.3892/ijmm.2016.2732] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/16/2016] [Indexed: 01/05/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is mainly associated with myosin, heavy chain 7 (MYH7) and myosin binding protein C, cardiac (MYBPC3) mutations. In order to better explain the clinical and genetic heterogeneity in HCM patients, in this study, we implemented a target-next generation sequencing (NGS) assay. An Ion AmpliSeq™ Custom Panel for the enrichment of 19 genes, of which 9 of these did not encode thick/intermediate and thin myofilament (TTm) proteins and, among them, 3 responsible of HCM phenocopy, was created. Ninety-two DNA samples were analyzed by the Ion Personal Genome Machine: 73 DNA samples (training set), previously genotyped in some of the genes by Sanger sequencing, were used to optimize the NGS strategy, whereas 19 DNA samples (discovery set) allowed the evaluation of NGS performance. In the training set, we identified 72 out of 73 expected mutations and 15 additional mutations: the molecular diagnosis was achieved in one patient with a previously wild-type status and the pre-excitation syndrome was explained in another. In the discovery set, we identified 20 mutations, 5 of which were in genes encoding non-TTm proteins, increasing the diagnostic yield by approximately 20%: a single mutation in genes encoding non-TTm proteins was identified in 2 out of 3 borderline HCM patients, whereas co-occuring mutations in genes encoding TTm and galactosidase alpha (GLA) altered proteins were characterized in a male with HCM and multiorgan dysfunction. Our combined targeted NGS-Sanger sequencing-based strategy allowed the molecular diagnosis of HCM with greater efficiency than using the conventional (Sanger) sequencing alone. Mutant alleles encoding non-TTm proteins may aid in the complete understanding of the genetic and phenotypic heterogeneity of HCM: co-occuring mutations of genes encoding TTm and non-TTm proteins could explain the wide variability of the HCM phenotype, whereas mutations in genes encoding only the non-TTm proteins are identifiable in patients with a milder HCM status.
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Affiliation(s)
| | - Maria I Parodi
- Laboratory of Human Genetics, E.O. Ospedali Galliera, Genova, Italy
| | | | - Paolo Spirito
- Cardiology Unit, E.O. Ospedali Galliera, Genova, Italy
| | - Camillo Autore
- Cardiology Unit, St. Andrea Hospital, Sapienza University, Rome, Italy
| | - Maria B Musumeci
- Cardiology Unit, St. Andrea Hospital, Sapienza University, Rome, Italy
| | - Stefano Favale
- Cardiology Unit, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Cinzia Forleo
- Cardiology Unit, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Claudio Rapezzi
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola Hospital, University of Bologna, Bologna, Italy
| | - Elena Biagini
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola Hospital, University of Bologna, Bologna, Italy
| | - Sabrina Davì
- Laboratory of Human Genetics, E.O. Ospedali Galliera, Genova, Italy
| | | | - Loredana Pennese
- Laboratory of Human Genetics, E.O. Ospedali Galliera, Genova, Italy
| | | | - Dario Degiorgio
- Laboratory of Human Genetics, E.O. Ospedali Galliera, Genova, Italy
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32
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Kayvanpour E, Sedaghat-Hamedani F, Amr A, Lai A, Haas J, Holzer DB, Frese KS, Keller A, Jensen K, Katus HA, Meder B. Genotype-phenotype associations in dilated cardiomyopathy: meta-analysis on more than 8000 individuals. Clin Res Cardiol 2016; 106:127-139. [DOI: 10.1007/s00392-016-1033-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/23/2016] [Indexed: 02/06/2023]
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33
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Tiziano FD, Palmieri V, Genuardi M, Zeppilli P. The Role of Genetic Testing in the Identification of Young Athletes with Inherited Primitive Cardiac Disorders at Risk of Exercise Sudden Death. Front Cardiovasc Med 2016; 3:28. [PMID: 27617263 PMCID: PMC5000131 DOI: 10.3389/fcvm.2016.00028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/16/2016] [Indexed: 12/23/2022] Open
Abstract
Although relatively rare, inherited primitive cardiac disorders (IPCDs) in athletes have a deep social impact since they often present as sudden cardiac death (SCD) of young and otherwise healthy persons. The diagnosis of these conditions is likely underestimated due to the lack of shared clinical criteria and to the existence of several borderline clinical pictures. We will focus on the clinical and molecular diagnosis of the most common IPCDs, namely hypertrophic cardiomyopathies, long QT syndrome, arrhythmogenic right ventricular cardiomyopathy, and left ventricular non-compaction. Collectively, these conditions account for the majority of SCD episodes and/or cardiologic clinical problems in athletes. In addition to the clinical and instrumental tools for the diagnosis of IPCD, the viral technological advances in genetic testing have facilitated the molecular confirmation of these conditions. However, genetic testing presents several issues: the limited sensitivity (globally, around 50%), the low prognostic predictive value, the probability to find pathogenic variants in different genes in the same patient, and the risk of non-interpretable results. In this review, we will analyze the pros and cons of the different clinical approaches for the presymptomatic identification, the diagnosis and management of IPCD athletes, and we will discuss the indications to the genetic testing for patients and their relatives, particularly focusing on the most complex scenarios, such as presymptomatic tests, uncertain results, and unexpected findings.
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Affiliation(s)
| | - Vincenzo Palmieri
- Unità di Medicina dello Sport, Fondazione Policlinico "A. Gemelli", Università Cattolica del Sacro Cuore , Roma , Italy
| | - Maurizio Genuardi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore , Roma , Italy
| | - Paolo Zeppilli
- Unità di Medicina dello Sport, Fondazione Policlinico "A. Gemelli", Università Cattolica del Sacro Cuore , Roma , Italy
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34
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Raghow R. An 'Omics' Perspective on Cardiomyopathies and Heart Failure. Trends Mol Med 2016; 22:813-827. [PMID: 27499035 DOI: 10.1016/j.molmed.2016.07.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 12/27/2022]
Abstract
Pathological enlargement of the heart, represented by hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM), occurs in response to many genetic and non-genetic factors. The clinical course of cardiac hypertrophy is remarkably variable, ranging from lifelong absence of symptoms to rapidly declining heart function and sudden cardiac death (SCD). Unbiased omics studies have begun to provide a glimpse into the molecular framework underpinning altered mechanotransduction, mitochondrial energetics, oxidative stress, and extracellular matrix in the heart undergoing physiological and pathological hypertrophy. Omics analyses indicate that post-transcriptional regulation of gene expression plays an overriding role in the normal and diseased heart. Studies to date highlight a need for more effective bioinformatics to better integrate patient omics data with their comprehensive clinical histories.
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Affiliation(s)
- Rajendra Raghow
- Department of Pharmacology, College of Medicine, The University of Tennessee Health Science Center and the VA Medical Center, Memphis, TN 38104, USA.
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35
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Rubattu S, Bozzao C, Pennacchini E, Pagannone E, Musumeci BM, Piane M, Germani A, Savio C, Francia P, Volpe M, Autore C, Chessa L. A Next-Generation Sequencing Approach to Identify Gene Mutations in Early- and Late-Onset Hypertrophic Cardiomyopathy Patients of an Italian Cohort. Int J Mol Sci 2016; 17:ijms17081239. [PMID: 27483260 PMCID: PMC5000637 DOI: 10.3390/ijms17081239] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/22/2016] [Accepted: 07/22/2016] [Indexed: 01/08/2023] Open
Abstract
Sequencing of sarcomere protein genes in patients fulfilling the clinical diagnostic criteria for hypertrophic cardiomyopathy (HCM) identifies a disease-causing mutation in 35% to 60% of cases. Age at diagnosis and family history may increase the yield of mutations screening. In order to assess whether Next-Generation Sequencing (NGS) may fulfil the molecular diagnostic needs in HCM, we included 17 HCM-related genes in a sequencing panel run on PGM IonTorrent. We selected 70 HCM patients, 35 with early (≤25 years) and 35 with late (≥65 years) diagnosis of disease onset. All samples had a 98.6% average of target regions, with coverage higher than 20× (mean coverage 620×). We identified 41 different mutations (seven of them novel) in nine genes: MYBPC3 (17/41 = 41%); MYH7 (10/41 = 24%); TNNT2, CAV3 and MYH6 (3/41 = 7.5% each); TNNI3 (2/41 = 5%); GLA, MYL2, and MYL3 (1/41=2.5% each). Mutation detection rate was 30/35 (85.7%) in early-onset and 8/35 (22.9%) in late-onset HCM patients, respectively (p < 0.0001). The overall detection rate for patients with positive family history was 84%, and 90.5% in patients with early disease onset. In our study NGS revealed higher mutations yield in patients with early onset and with a family history of HCM. Appropriate patient selection can increase the yield of genetic testing and make diagnostic testing cost-effective.
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Affiliation(s)
- Speranza Rubattu
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
- Department of Angiocardioneurology, IRCCS Neuromed, 86077 Pozzilli, Italy.
| | - Cristina Bozzao
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
| | - Ermelinda Pennacchini
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
| | - Erika Pagannone
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
| | - Beatrice Maria Musumeci
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
| | - Maria Piane
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
| | - Aldo Germani
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
| | - Camilla Savio
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
| | - Pietro Francia
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
| | - Massimo Volpe
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
- Department of Angiocardioneurology, IRCCS Neuromed, 86077 Pozzilli, Italy.
| | - Camillo Autore
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
| | - Luciana Chessa
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, University Sapienza of Rome, 00185 Rome, Italy.
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Macaron C, Heald B, Burke CA. Using Genetics to Identify Hereditary Colorectal Polyposis and Cancer Syndromes in Your Patient. Curr Gastroenterol Rep 2016; 17:463. [PMID: 26292665 DOI: 10.1007/s11894-015-0463-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The majority of patients with colorectal polyps and cancer do not have a Mendelian cause of the disease. Age, lifestyle, and environmental factors interact with complex genetic traits to contribute to the etiology. However, approximately 5-10 % of patients with colorectal cancer (CRC) and more than 40 % of patients meeting specific clinical features of the hereditary polyposis syndromes have a discoverable, actionable genetic cause which will significantly alter their medical management.
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Affiliation(s)
- Carole Macaron
- Section of Gastroenterology, Department of Veterans Affairs, Louis Stokes Cleveland Medical Center, Cleveland, 44106, OH, USA
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37
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Ingles J, Burns C, Barratt A, Semsarian C. Application of Genetic Testing in Hypertrophic Cardiomyopathy for Preclinical Disease Detection. ACTA ACUST UNITED AC 2015; 8:852-9. [DOI: 10.1161/circgenetics.115.001093] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jodie Ingles
- From the Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney NSW, Australia (J.I., C.B., C.S.); Central Clinical School, Sydney Medical School, University of Sydney, Sydney NSW, Australia (J.I., C.B., C.S.); School of Population Health, Sydney Medical School, University of Sydney, Sydney NSW, Australia (A.B.); and Department of Cardiology, Royal Prince Alfred Hospital, Sydney NSW, Australia (J.I., C.B., C.S.)
| | - Charlotte Burns
- From the Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney NSW, Australia (J.I., C.B., C.S.); Central Clinical School, Sydney Medical School, University of Sydney, Sydney NSW, Australia (J.I., C.B., C.S.); School of Population Health, Sydney Medical School, University of Sydney, Sydney NSW, Australia (A.B.); and Department of Cardiology, Royal Prince Alfred Hospital, Sydney NSW, Australia (J.I., C.B., C.S.)
| | - Alexandra Barratt
- From the Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney NSW, Australia (J.I., C.B., C.S.); Central Clinical School, Sydney Medical School, University of Sydney, Sydney NSW, Australia (J.I., C.B., C.S.); School of Population Health, Sydney Medical School, University of Sydney, Sydney NSW, Australia (A.B.); and Department of Cardiology, Royal Prince Alfred Hospital, Sydney NSW, Australia (J.I., C.B., C.S.)
| | - Christopher Semsarian
- From the Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney NSW, Australia (J.I., C.B., C.S.); Central Clinical School, Sydney Medical School, University of Sydney, Sydney NSW, Australia (J.I., C.B., C.S.); School of Population Health, Sydney Medical School, University of Sydney, Sydney NSW, Australia (A.B.); and Department of Cardiology, Royal Prince Alfred Hospital, Sydney NSW, Australia (J.I., C.B., C.S.)
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38
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Abstract
Approximately 5 to 10% of colorectal cancers develop within a known hereditary syndrome. Specific underlying genetic mutations drive the clinical phenotype and it is imperative to determine the genetic etiology to provide meaningful surveillance and intervention. Recognizing potential patients and families with a hereditary predisposition is the first step in management. Syndromes can be categorized according to polyp burden as polyposis or nonpolyposis. Clinical assessment should start with a personal and family medical history, physical examination, and evaluation for the presence and type of colorectal polyps or cancers. Key information is gained from these simple steps and should guide the specific genetic analysis for diagnosis. Genetic counseling is a critical component to any hereditary colorectal cancer program and should be conducted before genetic testing to provide education about the implications of test results. This review focuses on the thought process that drives initial clinical evaluation and guides genetic testing for patients with suspected hereditary colorectal cancer syndromes.
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Affiliation(s)
- Matthew F. Kalady
- Department of Colorectal Surgery, Digestive Disease Institute, Cleveland, Ohio
- Sanford R. Weiss, MD, Center for Hereditary Colorectal Neoplasia, Cleveland, Ohio
| | - Brandie Heald
- Sanford R. Weiss, MD, Center for Hereditary Colorectal Neoplasia, Cleveland, Ohio
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio
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39
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Next generation sequencing in cardiomyopathy: towards personalized genomics and medicine. Mol Biol Rep 2015; 41:4881-8. [PMID: 24908287 DOI: 10.1007/s11033-014-3418-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Next generation sequencing (NGS) is perhaps one of the most exciting advances in the field of life sciences and biomedical research in the last decade. With the availability of massive parallel sequencing, human DNA blueprint can be decoded to explore the hidden information with reduced time and cost. This technology has been used to understand the genetic aspects of various diseases including cardiomyopathies. Mutations for different cardiomyopathies have been identified and cataloging mutations on phenotypic basis are underway and are expected to lead to new discoveries that may translate to novel diagnostic, prognostic and therapeutic targets. With ease in handling NGS, cost effectiveness and fast data output, NGS is now considered as a diagnostic tool for cardiomyopathy by providing targeted gene sequencing. In addition to the number of genetic variants that are identified in cardiomyopathies, there is a need of quicker and easy way to screen multiple genes associated with the disease. In this review, an attempt has been made to explain the NGS technology, methods and applications in cardiomyopathies and their perspective in clinical practice and challenges which are to be addressed.
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40
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Waldmüller S, Schroeder C, Sturm M, Scheffold T, Imbrich K, Junker S, Frische C, Hofbeck M, Bauer P, Bonin M, Gawaz M, Gramlich M. Targeted 46-gene and clinical exome sequencing for mutations causing cardiomyopathies. Mol Cell Probes 2015; 29:308-14. [DOI: 10.1016/j.mcp.2015.05.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/05/2015] [Accepted: 05/05/2015] [Indexed: 12/18/2022]
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41
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Liu Y, Wei X, Kong X, Guo X, Sun Y, Man J, Du L, Zhu H, Qu Z, Tian P, Mao B, Yang Y. Targeted Next-Generation Sequencing for Clinical Diagnosis of 561 Mendelian Diseases. PLoS One 2015; 10:e0133636. [PMID: 26274329 PMCID: PMC4537117 DOI: 10.1371/journal.pone.0133636] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/30/2015] [Indexed: 12/04/2022] Open
Abstract
Background Targeted next-generation sequencing (NGS) is a cost-effective approach for rapid and accurate detection of genetic mutations in patients with suspected genetic disorders, which can facilitate effective diagnosis. Methodology/Principal Findings We designed a capture array to mainly capture all the coding sequence (CDS) of 2,181 genes associated with 561 Mendelian diseases and conducted NGS to detect mutations. The accuracy of NGS was 99.95%, which was obtained by comparing the genotypes of selected loci between our method and SNP Array in four samples from normal human adults. We also tested the stability of the method using a sample from normal human adults. The results showed that an average of 97.79% and 96.72% of single-nucleotide variants (SNVs) in the sample could be detected stably in a batch and different batches respectively. In addition, the method could detect various types of mutations. Some disease-causing mutations were detected in 69 clinical cases, including 62 SNVs, 14 insertions and deletions (Indels), 1 copy number variant (CNV), 1 microdeletion and 2 microduplications of chromosomes, of which 35 mutations were novel. Mutations were confirmed by Sanger sequencing or real-time polymerase chain reaction (PCR). Conclusions/Significance Results of the evaluation showed that targeted NGS enabled to detect disease-causing mutations with high accuracy, stability, speed and throughput. Thus, the technology can be used for the clinical diagnosis of 561 Mendelian diseases.
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Affiliation(s)
- Yanqiu Liu
- Department of Genetics, Jiangxi Provincial Women and Children Hospital, Nanchang, 330006, China
| | - Xiaoming Wei
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiangdong Kong
- Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xueqin Guo
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yan Sun
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jianfen Man
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Lique Du
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Hui Zhu
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Zelan Qu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Ping Tian
- Department of Obstetrics and Gynecology, Wuhan Medical and Health Center for Women and Children, Wuhan, 430022, China
| | - Bing Mao
- Department of Neurology, Wuhan Medical and Health Center for Women and Children, Wuhan, 430022, China
| | - Yun Yang
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
- * E-mail:
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42
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Wu W, Lu CX, Wang YN, Liu F, Chen W, Liu YT, Han YC, Cao J, Zhang SY, Zhang X. Novel Phenotype-Genotype Correlations of Restrictive Cardiomyopathy With Myosin-Binding Protein C (MYBPC3) Gene Mutations Tested by Next-Generation Sequencing. J Am Heart Assoc 2015; 4:JAHA.115.001879. [PMID: 26163040 PMCID: PMC4608072 DOI: 10.1161/jaha.115.001879] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND MYBPC3 dysfunctions have been proven to induce dilated cardiomyopathy, hypertrophic cardiomyopathy, and/or left ventricular noncompaction; however, the genotype-phenotype correlation between MYBPC3 and restrictive cardiomyopathy (RCM) has not been established. The newly developed next-generation sequencing method is capable of broad genomic DNA sequencing with high throughput and can help explore novel correlations between genetic variants and cardiomyopathies. METHODS AND RESULTS A proband from a multigenerational family with 3 live patients and 1 unrelated patient with clinical diagnoses of RCM underwent a next-generation sequencing workflow based on a custom AmpliSeq panel, including 64 candidate pathogenic genes for cardiomyopathies, on the Ion Personal Genome Machine high-throughput sequencing benchtop instrument. The selected panel contained a total of 64 genes that were reportedly associated with inherited cardiomyopathies. All patients fulfilled strict criteria for RCM with clinical characteristics, echocardiography, and/or cardiac magnetic resonance findings. The multigenerational family with 3 adult RCM patients carried an identical nonsense MYBPC3 mutation, and the unrelated patient carried a missense mutation in the MYBPC3 gene. All of these results were confirmed by the Sanger sequencing method. CONCLUSIONS This study demonstrated that MYBPC3 gene mutations, revealed by next-generation sequencing, were associated with familial and sporadic RCM patients. It is suggested that the next-generation sequencing platform with a selected panel provides a highly efficient approach for molecular diagnosis of hereditary and idiopathic RCM and helps build new genotype-phenotype correlations.
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MESH Headings
- Adult
- Aged
- Cardiomyopathy, Restrictive/diagnosis
- Cardiomyopathy, Restrictive/genetics
- Cardiomyopathy, Restrictive/mortality
- Cardiomyopathy, Restrictive/physiopathology
- Carrier Proteins/genetics
- Codon, Nonsense
- DNA Mutational Analysis/methods
- Echocardiography, Doppler, Color
- Echocardiography, Transesophageal
- Electrocardiography
- Female
- Genetic Association Studies
- Genetic Predisposition to Disease
- Genetic Testing/methods
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Magnetic Resonance Imaging
- Male
- Middle Aged
- Mutation, Missense
- Pedigree
- Phenotype
- Predictive Value of Tests
- Prognosis
- Ventricular Dysfunction, Left/diagnosis
- Ventricular Dysfunction, Left/genetics
- Ventricular Dysfunction, Left/mortality
- Ventricular Dysfunction, Left/physiopathology
- Ventricular Function, Left/genetics
- Workflow
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Affiliation(s)
- Wei Wu
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
| | - Chao-Xia Lu
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
| | - Yi-Ning Wang
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
| | - Fang Liu
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
| | - Wei Chen
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
| | - Yong-Tai Liu
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
| | - Ye-Chen Han
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
| | - Jian Cao
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
| | - Shu-Yang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
- Correspondence to: Shu-Yang Zhang, MD, Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, No. 1 Shuai Fu Yuan, Beijing 100730, China. E-mail:
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Science & Peking Union Medical CollegeBeijing, China
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Md. SSG, Diego-Álvarez D, Buades C, Romera-López A, Pérez-Cabornero L, Valero-Hervás D, Cantalapiedra D, Bioinformatics, Felipe-Ponce V, Hernández-Poveda G, José Roca M, Casañs C, Fernández-Pedrosa V, M. CC, C. ÁA, P. JCT, C. ÓR, Marco G, Gil M, Miñambres R, Ballester A. DIAGNÓSTICO MOLECULAR DE ENFERMEDADES GENÉTICAS: DEL DIAGNÓSTICO GENÉTICO AL DIAGNÓSTICO GENÓMICO CON LA SECUENCIACIÓN MASIVA. REVISTA MÉDICA CLÍNICA LAS CONDES 2015. [DOI: 10.1016/j.rmclc.2015.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Ghemlas I, Li H, Zlateska B, Klaassen R, Fernandez CV, Yanofsky RA, Wu J, Pastore Y, Silva M, Lipton JH, Brossard J, Michon B, Abish S, Steele M, Sinha R, Belletrutti M, Breakey VR, Jardine L, Goodyear L, Sung L, Dhanraj S, Reble E, Wagner A, Beyene J, Ray P, Meyn S, Cada M, Dror Y. Improving diagnostic precision, care and syndrome definitions using comprehensive next-generation sequencing for the inherited bone marrow failure syndromes. J Med Genet 2015; 52:575-84. [PMID: 26136524 DOI: 10.1136/jmedgenet-2015-103270] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/07/2015] [Indexed: 11/04/2022]
Abstract
BACKGROUND Phenotypic overlap among the inherited bone marrow failure syndromes (IBMFSs) frequently limits the ability to establish a diagnosis based solely on clinical features. >70 IBMFS genes have been identified, which often renders genetic testing prolonged and costly. Since correct diagnosis, treatment and cancer surveillance often depend on identifying the mutated gene, strategies that enable timely genotyping are essential. METHODS To overcome these challenges, we developed a next-generation sequencing assay to analyse a panel of 72 known IBMFS genes. Cases fulfilling the clinical diagnostic criteria of an IBMFS but without identified causal genotypes were included. RESULTS The assay was validated by detecting 52 variants previously found by Sanger sequencing. A total of 158 patients with unknown mutations were studied. Of 75 patients with known IBMFS categories (eg, Fanconi anaemia), 59% had causal mutations. Among 83 patients with unclassified IBMFSs, we found causal mutations and established the diagnosis in 18% of the patients. The assay detected mutant genes that had not previously been reported to be associated with the patient phenotypes. In other cases, the assay led to amendments of diagnoses. In 20% of genotype cases, the results indicated a cancer surveillance programme. CONCLUSIONS The novel assay is efficient, accurate and has a major impact on patient care.
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Affiliation(s)
- Ibrahim Ghemlas
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hongbing Li
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Bozana Zlateska
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Robert Klaassen
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | | | - John Wu
- British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | | | | | - Jeff H Lipton
- Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Josee Brossard
- Centre hospitalier universitaire, Sherbrooke, Quebec, Canada
| | - Bruno Michon
- Centre Hospital University Quebec-Pav CHUL, Sainte-Foy, Quebec, Canada
| | - Sharon Abish
- Montreal Children's Hospital, Montreal, Québec, Canada
| | | | - Roona Sinha
- University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Mark Belletrutti
- Stollery Children's Hospital, University of Alberta, Edmonton, Alberta, Canada
| | - Vicky R Breakey
- McMaster Children's Hospital, McMaster University, Hamilton, Ontario, Canada
| | - Lawrence Jardine
- Children's Hospital at London Health Sciences Centre, London, Ontario, Canada
| | - Lisa Goodyear
- Janeway Child Health Centre, St. John's, Newfoundland, Canada
| | - Lillian Sung
- Population Health Sciences, Research Institute, The Hospital For Sick Children, Toronto, Ontario, Canada
| | - Santhosh Dhanraj
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Amanda Wagner
- Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph Beyene
- Program in Population Genomics, Department of Clinical Epidemiology & Biostatistics, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Peter Ray
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Molecular Genetic Laboratory, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen Meyn
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Michaela Cada
- Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yigal Dror
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
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Oliveira TG, Mitne-Neto M, Cerdeira LT, Marsiglia JD, Arteaga-Fernandez E, Krieger JE, Pereira AC. A Variant Detection Pipeline for Inherited Cardiomyopathy–Associated Genes Using Next-Generation Sequencing. J Mol Diagn 2015; 17:420-30. [DOI: 10.1016/j.jmoldx.2015.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 02/11/2015] [Accepted: 02/26/2015] [Indexed: 01/26/2023] Open
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Morini E, Sangiuolo F, Caporossi D, Novelli G, Amati F. Application of Next Generation Sequencing for personalized medicine for sudden cardiac death. Front Genet 2015; 6:55. [PMID: 25784923 PMCID: PMC4345839 DOI: 10.3389/fgene.2015.00055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/05/2015] [Indexed: 11/25/2022] Open
Abstract
Sudden cardiac death (SCD) is a serious public health problem. In the United States, more than 300,000 people are affected by SCD every year. Significantly, sudden deaths represent 20% of the total mortality and 50% of cardiovascular mortality in Western countries. In addition, SCD constitutes one of the most important unsolved challenges in the practice of forensic pathology because of the failure to determine the exact cause of sudden death. In young individuals, SCD is frequently caused by cardiomyopathies and channelopathies, that have generally an autosomal dominant pattern of inheritance. The impact of genetics and genetic testing on the clinical management of these diseases is unquestioned. In particular, genetic tests are an important tool for identifying pre-symptomatic individuals carrying genetic variant that predisposes them to SCD. High-throughput sequencing technologies offer novel opportunities to deeper investigate the genetic background underlying these fatal diseases and to early identify individuals at risk for SCD. In this review, we provide an overview of the development of Next-Generation Sequencing (NGS) technologies and of guidelines useful to design an efficient sequencing protocol and to perform an accurate data analysis. We suggest a flow chart to follow for the set up of a genetic screening protocol for the prevention of cardiac pathologies, in particular SCD events, in young athletes.
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Affiliation(s)
- Elena Morini
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico Rome, Italy ; Department of Biomedicine and Prevention, University of RomeTor Vergata Rome, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of RomeTor Vergata Rome, Italy
| | - Daniela Caporossi
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of RomeTor Vergata Rome, Italy
| | - Francesca Amati
- Department of Biomedicine and Prevention, University of RomeTor Vergata Rome, Italy
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Ho CY, Charron P, Richard P, Girolami F, Van Spaendonck-Zwarts KY, Pinto Y. Genetic advances in sarcomeric cardiomyopathies: state of the art. Cardiovasc Res 2015; 105:397-408. [PMID: 25634555 PMCID: PMC4349164 DOI: 10.1093/cvr/cvv025] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Genetic studies in the 1980s and 1990s led to landmark discoveries that sarcomere mutations cause both hypertrophic and dilated cardiomyopathies. Sarcomere mutations also likely play a role in more complex phenotypes and overlap cardiomyopathies with features of hypertrophy, dilation, diastolic abnormalities, and non-compaction. Identification of the genetic cause of these important conditions provides unique opportunities to interrogate and characterize disease pathogenesis and pathophysiology, starting from the molecular level and expanding from there. With such insights, there is potential for clinical translation that may transform management of patients and families with inherited cardiomyopathies. If key pathways for disease development can be identified, they could potentially serve as targets for novel disease-modifying or disease-preventing therapies. By utilizing gene-based diagnostic testing, we can identify at-risk individuals prior to the onset of clinical disease, allowing for disease-modifying therapy to be initiated early in life, at a time that such treatment may be most successful. In this section, we review the current application of genetics in clinical management, focusing on hypertrophic cardiomyopathy as a paradigm; discuss state-of-the-art genetic testing technology; review emerging knowledge of gene expression in sarcomeric cardiomyopathies; and discuss both the prospects, as well as the challenges, of bringing genetics to medicine.
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Affiliation(s)
- Carolyn Y Ho
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Philippe Charron
- Centre de référence maladies cardiaques héréditaires, ICAN, Inserm UMR_1166, Hôpital Pitié-Salpêtrière, AP-HP, Paris, France Université de Versailles-Saint Quentin, Hôpital Ambroise Paré, AP-HP, Boulogne-Billancourt, France
| | - Pascale Richard
- Centre de référence maladies cardiaques héréditaires, ICAN, Inserm UMR_1166, Hôpital Pitié-Salpêtrière, AP-HP, Paris, France
| | | | - Karin Y Van Spaendonck-Zwarts
- Department of Clinical Genetics, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Yigal Pinto
- Department of Cardiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
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Heald B, Church J. Genetic testing for hereditary colorectal cancer syndromes: a significant change in technology and its clinical implications. Colorectal Dis 2014; 16:942-6. [PMID: 25283074 DOI: 10.1111/codi.12792] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 08/18/2014] [Indexed: 02/08/2023]
Affiliation(s)
- B Heald
- Digestive Disease Institute, Sanford R. Weiss M.D. Center for Hereditary Colorectal Neoplasia, Cleveland Clinic, Cleveland, Ohio, USA; Department of Colorectal Surgery, Digestive Disease Institute, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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Blue GM, Kirk EP, Giannoulatou E, Dunwoodie SL, Ho JW, Hilton DC, White SM, Sholler GF, Harvey RP, Winlaw DS. Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Familial Congenital Heart Disease. J Am Coll Cardiol 2014; 64:2498-506. [DOI: 10.1016/j.jacc.2014.09.048] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/18/2014] [Accepted: 09/16/2014] [Indexed: 01/06/2023]
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Gómez J, Reguero JR, Morís C, Martín M, Alvarez V, Alonso B, Iglesias S, Coto E. Mutation analysis of the main hypertrophic cardiomyopathy genes using multiplex amplification and semiconductor next-generation sequencing. Circ J 2014; 78:2963-71. [PMID: 25342278 DOI: 10.1253/circj.cj-14-0628] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Mutations in at least 30 genes have been linked to hypertrophic cardiomyopathy (HCM). Due to the large size of the main HCM genes, Sanger sequencing is labor intensive and expensive. The purpose was to develop a next-generation sequencing (NGS) procedure for the main HCM genes. METHODS AND RESULTS: Multiplex amplification of the coding exons of MYH7,MYBPC3,TNNT2,TNNI3,ACTC1,TNNC1,MYL2,MYL3, and TPM1 was designated, followed by NGS with the Ion Torrent PGM (Life Technologies). A total of 8 pools containing DNA from HCM patients were sequenced in a 2-step approach. First, a total of 60 patients (validation cohort) underwent both PGM and Sanger sequencing for the 9 genes. No false-negative variants were found on NGS (100% sensitivity), and a specificity of 97% and 80% was achieved for single-nucleotide and insertion/deletion variants, respectively. Second, the PGM was used to search for mutations in a total of 76 cases not previously studied (discovery cohort). A total of 19 putative mutations were identified in the discovery pools, which were confirmed and assigned to specific patients on Sanger sequencing. CONCLUSIONS An NGS procedure has been developed for the main sarcomeric genes that would facilitate the screening of large cohorts of patients. In addition, this procedure would facilitate the uncovering of rare gene variants on a population scale.
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Affiliation(s)
- Juan Gómez
- Molecular Genetics Dept-Laboratory of Medicine-Renal Foundation (IRSIN-FRIAT), Hospital Central Asturias
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