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Ommen SR, Ho CY, Asif IM, Balaji S, Burke MA, Day SM, Dearani JA, Epps KC, Evanovich L, Ferrari VA, Joglar JA, Khan SS, Kim JJ, Kittleson MM, Krittanawong C, Martinez MW, Mital S, Naidu SS, Saberi S, Semsarian C, Times S, Waldman CB. 2024 AHA/ACC/AMSSM/HRS/PACES/SCMR Guideline for the Management of Hypertrophic Cardiomyopathy: A Report of the American Heart Association/American College of Cardiology Joint Committee on Clinical Practice Guidelines. J Am Coll Cardiol 2024; 83:2324-2405. [PMID: 38727647 DOI: 10.1016/j.jacc.2024.02.014] [Citation(s) in RCA: 1] [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] [Indexed: 05/20/2024]
Abstract
AIM The "2024 AHA/ACC/AMSSM/HRS/PACES/SCMR Guideline for the Management of Hypertrophic Cardiomyopathy" provides recommendations to guide clinicians in the management of patients with hypertrophic cardiomyopathy. METHODS A comprehensive literature search was conducted from September 14, 2022, to November 22, 2022, encompassing studies, reviews, and other evidence on human subjects that were published in English from PubMed, EMBASE, the Cochrane Library, the Agency for Healthcare Research and Quality, and other selected databases relevant to this guideline. Additional relevant studies, published through May 23, 2023, during the guideline writing process, were also considered by the writing committee and added to the evidence tables, where appropriate. STRUCTURE Hypertrophic cardiomyopathy remains a common genetic heart disease reported in populations globally. Recommendations from the "2020 AHA/ACC Guideline for the Diagnosis and Treatment of Patients With Hypertrophic Cardiomyopathy" have been updated with new evidence to guide clinicians.
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Ommen SR, Ho CY, Asif IM, Balaji S, Burke MA, Day SM, Dearani JA, Epps KC, Evanovich L, Ferrari VA, Joglar JA, Khan SS, Kim JJ, Kittleson MM, Krittanawong C, Martinez MW, Mital S, Naidu SS, Saberi S, Semsarian C, Times S, Waldman CB. 2024 AHA/ACC/AMSSM/HRS/PACES/SCMR Guideline for the Management of Hypertrophic Cardiomyopathy: A Report of the American Heart Association/American College of Cardiology Joint Committee on Clinical Practice Guidelines. Circulation 2024; 149:e1239-e1311. [PMID: 38718139 DOI: 10.1161/cir.0000000000001250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
AIM The "2024 AHA/ACC/AMSSM/HRS/PACES/SCMR Guideline for the Management of Hypertrophic Cardiomyopathy" provides recommendations to guide clinicians in the management of patients with hypertrophic cardiomyopathy. METHODS A comprehensive literature search was conducted from September 14, 2022, to November 22, 2022, encompassing studies, reviews, and other evidence on human subjects that were published in English from PubMed, EMBASE, the Cochrane Library, the Agency for Healthcare Research and Quality, and other selected databases relevant to this guideline. Additional relevant studies, published through May 23, 2023, during the guideline writing process, were also considered by the writing committee and added to the evidence tables, where appropriate. STRUCTURE Hypertrophic cardiomyopathy remains a common genetic heart disease reported in populations globally. Recommendations from the "2020 AHA/ACC Guideline for the Diagnosis and Treatment of Patients With Hypertrophic Cardiomyopathy" have been updated with new evidence to guide clinicians.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Victor A Ferrari
- AHA/ACC Joint Committee on Clinical Practice Guidelines liaison
- SCMR representative
| | | | - Sadiya S Khan
- ACC/AHA Joint Committee on Performance Measures representative
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Mio C, Zucco J, Fabbro D, Bregant E, Baldan F, Allegri L, D'Elia AV, Collini V, Imazio M, Damante G, Faletra F. The impact of the European Society of Cardiology guidelines and whole exome sequencing on genetic testing in hereditary cardiac diseases. Clin Genet 2024. [PMID: 38837338 DOI: 10.1111/cge.14569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/14/2024] [Accepted: 05/26/2024] [Indexed: 06/07/2024]
Abstract
In the last decade, an incredible improvement has been made in elucidating the genetic bases of cardiomyopathies. Here we report the impact of either the European Society of Cardiology (ESC) guidelines or the use of whole exome sequencing (WES) in terms of a number of variants of uncertain significance (VUS) and missed diagnoses in a series of 260 patients affected by inherited cardiac disorders. Samples were analyzed using a targeted gene panel of 128 cardiac-related genes and/or WES in a subset of patients, with a three-tier approach. Analyzing (i) only a subset of genes related to the clinical presentation, strictly following the ESC guidelines, 20.77% positive test were assessed. The incremental diagnostic rate for (ii) the whole gene panel, and (iii) the WES was 4.71% and 11.67%, respectively. The diverse analytical approaches increased the number of VUSs and incidental findings. Indeed, the use of WES highlights that there is a small percentage of syndromic conditions that standard analysis would not have detected. Moreover, the use of targeted sequencing coupled with "narrow" analytical approach prevents the detection of variants in actionable genes that could allow for preventive treatment. Our data suggest that genetic testing might aid clinicians in the diagnosis of inheritable cardiac disorders.
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Affiliation(s)
- Catia Mio
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Jessica Zucco
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Dora Fabbro
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Elisa Bregant
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Federica Baldan
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Lorenzo Allegri
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Angela Valentina D'Elia
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Valentino Collini
- Cardiology, Cardiothoracic Department, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Massimo Imazio
- Department of Medicine (DMED), University of Udine, Udine, Italy
- Cardiology, Cardiothoracic Department, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Giuseppe Damante
- Department of Medicine (DMED), University of Udine, Udine, Italy
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Flavio Faletra
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
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Mukhopadhyay S, Dixit P, Khanom N, Sanghera G, McGurk KA. The Genetic Factors Influencing Cardiomyopathies and Heart Failure across the Allele Frequency Spectrum. J Cardiovasc Transl Res 2024:10.1007/s12265-024-10520-y. [PMID: 38771459 DOI: 10.1007/s12265-024-10520-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024]
Abstract
Heart failure (HF) remains a major cause of mortality and morbidity worldwide. Understanding the genetic basis of HF allows for the development of disease-modifying therapies, more appropriate risk stratification, and personalised management of patients. The advent of next-generation sequencing has enabled genome-wide association studies; moving beyond rare variants identified in a Mendelian fashion and detecting common DNA variants associated with disease. We summarise the latest GWAS and rare variant data on mixed and refined HF aetiologies, and cardiomyopathies. We describe the recent understanding of the functional impact of titin variants and highlight FHOD3 as a novel cardiomyopathy-associated gene. We describe future directions of research in this field and how genetic data can be leveraged to improve the care of patients with HF.
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Affiliation(s)
- Srinjay Mukhopadhyay
- National Heart and Lung Institute, Imperial College London, LMS Building, Hammersmith Campus, London, UK
- School of Medicine, Cardiff University, Wales, UK
| | - Prithvi Dixit
- National Heart and Lung Institute, Imperial College London, LMS Building, Hammersmith Campus, London, UK
| | - Najiyah Khanom
- National Heart and Lung Institute, Imperial College London, LMS Building, Hammersmith Campus, London, UK
| | - Gianluca Sanghera
- National Heart and Lung Institute, Imperial College London, LMS Building, Hammersmith Campus, London, UK
| | - Kathryn A McGurk
- National Heart and Lung Institute, Imperial College London, LMS Building, Hammersmith Campus, London, UK.
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK.
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5
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Kumar KR, Cowley MJ, Davis RL. Next-Generation Sequencing and Emerging Technologies. Semin Thromb Hemost 2024. [PMID: 38692283 DOI: 10.1055/s-0044-1786397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.
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Affiliation(s)
- Kishore R Kumar
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, Australia
| | - Mark J Cowley
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Computational Biology Group, Children's Cancer Institute, University of New South Wales, Randwick, New South Wales, Australia
| | - Ryan L Davis
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
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Kwok SY, Kwong AKY, Shi JZ, Shih CFY, Lee M, Mak CCY, Chui M, Tsao S, Chung BHY. Whole genome sequencing in paediatric channelopathy and cardiomyopathy. Front Cardiovasc Med 2024; 11:1335527. [PMID: 38586174 PMCID: PMC10997036 DOI: 10.3389/fcvm.2024.1335527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/28/2024] [Indexed: 04/09/2024] Open
Abstract
Background Precision medicine in paediatric cardiac channelopathy and cardiomyopathy has a rapid advancement over the past years. Compared to conventional gene panel and exome-based testing, whole genome sequencing (WGS) offers additional coverage at the promoter, intronic regions and the mitochondrial genome. However, the data on use of WGS to evaluate the genetic cause of these cardiovascular conditions in children and adolescents are limited. Methods In a tertiary paediatric cardiology center, we recruited all patients diagnosed with cardiac channelopathy and cardiomyopathy between the ages of 0 and 18 years old, who had negative genetic findings with prior gene panel or exome-based testing. After genetic counselling, blood samples were collected from the subjects and both their parents for WGS analysis. Results A total of 31 patients (11 cardiac channelopathy and 20 cardiomyopathy) were recruited. Four intronic splice-site variants were identified in three cardiomyopathy patients, which were not identified in previous whole exome sequencing. These included a pathogenic variant in TAFAZZIN:c.284+5G>A (Barth syndrome), a variant of unknown significance (VUS) in MYBPC3:c.1224-80G>A and 2 compound heterozygous LP variants in LZTR1 (LZTR1:c.1943-256C>T and LZTR1:c1261-3C>G) in a patient with clinical features of RASopathy. There was an additional diagnostic yield of 1.94% using WGS for identification of intronic variants, on top of conventional gene testing. Conclusion WGS plays a role in identifying additional intronic splice-site variants in paediatric patients with isolated cardiomyopathy. With the demonstrated low extra yield of WGS albeit its ability to provide potential clinically important information, WGS should be considered in selected paediatric cases of cardiac channelopathy and cardiomyopathy in a cost-effective manner.
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Affiliation(s)
- Sit Yee Kwok
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children’s Hospital, Hong Kong, Hong Kong SAR, China
| | - Anna Ka Yee Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Julia Zhuo Shi
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children’s Hospital, Hong Kong, Hong Kong SAR, China
| | - Connie Fong Ying Shih
- Clinical Genetics Service Unit, Hong Kong Children’s Hospital, Hong Kong, Hong Kong SAR, China
| | - Mianne Lee
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Christopher C. Y. Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Martin Chui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Sabrina Tsao
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Brian Hon Yin Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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Singer ES, Crowe J, Holliday M, Isbister JC, Lal S, Nowak N, Yeates L, Burns C, Rajagopalan S, Macciocca I, King I, Wacker J, Ingles J, Weintraub RG, Semsarian C, Bagnall RD. The burden of splice-disrupting variants in inherited heart disease and unexplained sudden cardiac death. NPJ Genom Med 2023; 8:29. [PMID: 37821546 PMCID: PMC10567745 DOI: 10.1038/s41525-023-00373-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023] Open
Abstract
There is an incomplete understanding of the burden of splice-disrupting variants in definitively associated inherited heart disease genes and whether these genes can amplify from blood RNA to support functional confirmation of splicing outcomes. We performed burden testing of rare splice-disrupting variants in people with inherited heart disease and sudden unexplained death compared to 125,748 population controls. ClinGen definitively disease-associated inherited heart disease genes were amplified using RNA extracted from fresh blood, derived cardiomyocytes, and myectomy tissue. Variants were functionally assessed and classified for pathogenicity. We found 88 in silico-predicted splice-disrupting variants in 128 out of 1242 (10.3%) unrelated participants. There was an excess burden of splice-disrupting variants in PKP2 (5.9%), FLNC (2.7%), TTN (2.8%), MYBPC3 (8.2%) and MYH7 (1.3%), in distinct cardiomyopathy subtypes, and KCNQ1 (3.6%) in long QT syndrome. Blood RNA supported the amplification of 21 out of 31 definitive disease-associated inherited heart disease genes. Our functional studies confirmed altered splicing in six variants. Eleven variants of uncertain significance were reclassified as likely pathogenic based on functional studies and six were used for cascade genetic testing in 12 family members. Our study highlights that splice-disrupting variants are a significant cause of inherited heart disease, and that analysis of blood RNA confirms splicing outcomes and supports variant pathogenicity classification.
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Affiliation(s)
- Emma S Singer
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Joshua Crowe
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Mira Holliday
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Julia C Isbister
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Sean Lal
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Natalie Nowak
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Laura Yeates
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Cardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Charlotte Burns
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | | | - Ivan Macciocca
- Murdoch Children's Research Institute, University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Ingrid King
- Murdoch Children's Research Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Julie Wacker
- Department of Cardiology, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Jodie Ingles
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Cardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Robert G Weintraub
- Murdoch Children's Research Institute, University of Melbourne, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Department of Cardiology, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia.
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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8
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Brown EE, Murray B. A Practical Guide to Genetic Testing in Inherited Heart Disease. Card Electrophysiol Clin 2023; 15:241-247. [PMID: 37558295 DOI: 10.1016/j.ccep.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Genetic testing has increasingly been shown to provide critical information regarding the treatment and management of patients with hereditary cardiomyopathies and arrhythmias and is available for a wide variety of conditions. It can provide information regarding arrhythmia risk, lifestyle recommendations, such as exercise avoidance, pharmaceutical therapies, and prognosis. Beyond the proband, genetic testing can be a valuable tool for cascade screening in the family. Genetic testing should be accompanied with genetic counseling, as genetic tests should be accompanied by expert interpretation, support in cascade family evaluation, and psychosocial considerations. Overall, it should be routinely implemented in arrhythmia and cardiomyopathy clinics.
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Affiliation(s)
- Emily E Brown
- Division of Cardiology, Johns Hopkins University, 600 North Wolfe Street, Blalock 572, Baltimore, MD 21287, USA.
| | - Brittney Murray
- Division of Cardiology, Johns Hopkins University, 600 North Wolfe Street, Blalock 572, Baltimore, MD 21287, USA
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9
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Einhorn NR, Patel RS, Bennett JL, McDonald TV. Hypertrophic cardiomyopathy and long QT syndrome in cardiac-only Timothy syndrome. HeartRhythm Case Rep 2023; 9:560-564. [PMID: 37614386 PMCID: PMC10444567 DOI: 10.1016/j.hrcr.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Affiliation(s)
- Nathan R. Einhorn
- Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Ritesh S. Patel
- Department of Internal Medicine, Division of Cardiovascular Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Jennifer L. Bennett
- Department of Internal Medicine, Division of Cardiovascular Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Thomas V. McDonald
- Department of Internal Medicine, Division of Cardiovascular Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida
- USF-Heart Institute, Tampa, Florida
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida
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10
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Chumakova OS, Baulina NM. Advanced searching for hypertrophic cardiomyopathy heritability in real practice tomorrow. Front Cardiovasc Med 2023; 10:1236539. [PMID: 37583586 PMCID: PMC10425241 DOI: 10.3389/fcvm.2023.1236539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease associated with morbidity and mortality at any age. As studies in recent decades have shown, the genetic architecture of HCM is quite complex both in the entire population and in each patient. In the rapidly advancing era of gene therapy, we have to provide a detailed molecular diagnosis to our patients to give them the chance for better and more personalized treatment. In addition to emphasizing the importance of genetic testing in routine practice, this review aims to discuss the possibility to go a step further and create an expanded genetic panel that contains not only variants in core genes but also new candidate genes, including those located in deep intron regions, as well as structural variations. It also highlights the benefits of calculating polygenic risk scores based on a combination of rare and common genetic variants for each patient and of using non-genetic HCM markers, such as microRNAs that can enhance stratification of risk for HCM in unselected populations alongside rare genetic variants and clinical factors. While this review is focusing on HCM, the discussed issues are relevant to other cardiomyopathies.
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Affiliation(s)
- Olga S. Chumakova
- Laboratory of Functional Genomics of Cardiovascular Diseases, National Medical Research Centre of Cardiology Named After E.I. Chazov, Moscow, Russia
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11
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Hort Y, Sullivan P, Wedd L, Fowles L, Stevanovski I, Deveson I, Simons C, Mallett A, Patel C, Furlong T, Cowley MJ, Shine J, Mallawaarachchi A. Atypical splicing variants in PKD1 explain most undiagnosed typical familial ADPKD. NPJ Genom Med 2023; 8:16. [PMID: 37419908 DOI: 10.1038/s41525-023-00362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/26/2023] [Indexed: 07/09/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic cause of kidney failure and is primarily associated with PKD1 or PKD2. Approximately 10% of patients remain undiagnosed after standard genetic testing. We aimed to utilise short and long-read genome sequencing and RNA studies to investigate undiagnosed families. Patients with typical ADPKD phenotype and undiagnosed after genetic diagnostics were recruited. Probands underwent short-read genome sequencing, PKD1 and PKD2 coding and non-coding analyses and then genome-wide analysis. Targeted RNA studies investigated variants suspected to impact splicing. Those undiagnosed then underwent Oxford Nanopore Technologies long-read genome sequencing. From over 172 probands, 9 met inclusion criteria and consented. A genetic diagnosis was made in 8 of 9 (89%) families undiagnosed on prior genetic testing. Six had variants impacting splicing, five in non-coding regions of PKD1. Short-read genome sequencing identified novel branchpoint, AG-exclusion zone and missense variants generating cryptic splice sites and a deletion causing critical intron shortening. Long-read sequencing confirmed the diagnosis in one family. Most undiagnosed families with typical ADPKD have splice-impacting variants in PKD1. We describe a pragmatic method for diagnostic laboratories to assess PKD1 and PKD2 non-coding regions and validate suspected splicing variants through targeted RNA studies.
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Affiliation(s)
- Yvonne Hort
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
| | - Patricia Sullivan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Laura Wedd
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
| | - Lindsay Fowles
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Igor Stevanovski
- Genomic Technologies, Garvan Institute of Medical Research, Sydney, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, Australia
| | - Ira Deveson
- Genomic Technologies, Garvan Institute of Medical Research, Sydney, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Andrew Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Timothy Furlong
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - John Shine
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
| | - Amali Mallawaarachchi
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia.
- Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics, Royal Prince Alfred Hospital, Sydney, Australia.
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12
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Bocher O, Willer CJ, Zeggini E. Unravelling the genetic architecture of human complex traits through whole genome sequencing. Nat Commun 2023; 14:3520. [PMID: 37316478 DOI: 10.1038/s41467-023-39259-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Affiliation(s)
- Ozvan Bocher
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Ismaninger Str. 22, 81675, Munich, Germany.
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13
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Aiyer S, Kalutskaya E, Agdamag AC, Tang WHW. Genetic Evaluation and Screening in Cardiomyopathies: Opportunities and Challenges for Personalized Medicine. J Pers Med 2023; 13:887. [PMID: 37373876 DOI: 10.3390/jpm13060887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Cardiomyopathy is a major cause of heart failure caused by abnormalities of the heart muscles that make it harder for it to fill or eject blood. With technological advances, it is important for patients and families to understand that there are potential monogenic etiologies of cardiomyopathy. A multidisciplinary approach to clinical genetic screening for cardiomyopathies involving genetic counseling and clinical genetic testing is beneficial for patients and families. With early identification of inherited cardiomyopathy, patients can initiate guideline-directed medical therapies earlier, resulting in a greater likelihood of improving prognoses and health outcomes. Identifying impactful genetic variants will also allow for cascade testing to determine at-risk family members through clinical (phenotype) screening and risk stratification. Addressing genetic variants of uncertain significance and causative variants that may change in pathogenicity is also important to consider. This review will dive into the clinical genetic testing approaches for the various cardiomyopathies, the significance of early detection and treatment, the value of family screening, the personalized treatment process associated with genetic evaluation, and current strategies for clinical genetic testing outreach.
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Affiliation(s)
- Sahana Aiyer
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Emilia Kalutskaya
- Boonshoft School of Medicine, Wright State University, Fairborn, OH 45435, USA
| | - Arianne C Agdamag
- Department of Cardiovascular Medicine, Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - W H Wilson Tang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Cardiovascular Medicine, Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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14
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Htet M, Lei S, Bajpayi S, Zoitou A, Chamakioti M, Tampakakis E. The role of noncoding genetic variants in cardiomyopathy. Front Cardiovasc Med 2023; 10:1116925. [PMID: 37283586 PMCID: PMC10239966 DOI: 10.3389/fcvm.2023.1116925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Cardiomyopathies remain one of the leading causes of morbidity and mortality worldwide. Environmental risk factors and genetic predisposition account for most cardiomyopathy cases. As with all complex diseases, there are significant challenges in the interpretation of the molecular mechanisms underlying cardiomyopathy-associated genetic variants. Given the technical improvements and reduced costs of DNA sequence technologies, an increasing number of patients are now undergoing genetic testing, resulting in a continuously expanding list of novel mutations. However, many patients carry noncoding genetic variants, and although emerging evidence supports their contribution to cardiac disease, their role in cardiomyopathies remains largely understudied. In this review, we summarize published studies reporting on the association of different types of noncoding variants with various types of cardiomyopathies. We focus on variants within transcriptional enhancers, promoters, intronic sites, and untranslated regions that are likely associated with cardiac disease. Given the broad nature of this topic, we provide an overview of studies that are relatively recent and have sufficient evidence to support a significant degree of causality. We believe that more research with additional validation of noncoding genetic variants will provide further mechanistic insights on the development of cardiac disease, and noncoding variants will be increasingly incorporated in future genetic screening tests.
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Affiliation(s)
- Myo Htet
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
| | - Shunyao Lei
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Sheetal Bajpayi
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
| | - Asimina Zoitou
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | | | - Emmanouil Tampakakis
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States
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15
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Rayani K, Davies B, Cheung M, Comber D, Roberts JD, Tadros R, Green MS, Healey JS, Simpson CS, Sanatani S, Steinberg C, MacIntyre C, Angaran P, Duff H, Hamilton R, Arbour L, Leather R, Seifer C, Fournier A, Atallah J, Kimber S, Makanjee B, Alqarawi W, Cadrin-Tourigny J, Joza J, Gardner M, Talajic M, Bagnall RD, Krahn AD, Laksman ZWM. Identification and in-silico characterization of splice-site variants from a large cardiogenetic national registry. Eur J Hum Genet 2023; 31:512-520. [PMID: 36138163 PMCID: PMC10172209 DOI: 10.1038/s41431-022-01193-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/23/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022] Open
Abstract
Splice-site variants in cardiac genes may predispose carriers to potentially lethal arrhythmias. To investigate, we screened 1315 probands and first-degree relatives enrolled in the Canadian Hearts in Rhythm Organization (HiRO) registry. 10% (134/1315) of patients in the HiRO registry carry variants within 10 base-pairs of the intron-exon boundary with 78% (104/134) otherwise genotype negative. These 134 probands were carriers of 57 unique variants. For each variant, American College of Medical Genetics and Genomics (ACMG) classification was revisited based on consensus between nine in silico tools. Due in part to the in silico algorithms, seven variants were reclassified from the original report, with the majority (6/7) downgraded. Our analyses predicted 53% (30/57) of variants to be likely/pathogenic. For the 57 variants, an average of 9 tools were able to score variants within splice sites, while 6.5 tools responded for variants outside these sites. With likely/pathogenic classification considered a positive outcome, the ACMG classification was used to calculate sensitivity/specificity of each tool. Among these, Combined Annotation Dependent Depletion (CADD) had good sensitivity (93%) and the highest response rate (131/134, 98%), dbscSNV was also sensitive (97%), and SpliceAI was the most specific (64%) tool. Splice variants remain an important consideration in gene elusive inherited arrhythmia syndromes. Screening for intronic variants, even when restricted to the ±10 positions as performed here may improve genetic testing yield. We compare 9 freely available in silico tools and provide recommendations regarding their predictive capabilities. Moreover, we highlight several novel cardiomyopathy-associated variants which merit further study.
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Affiliation(s)
- Kaveh Rayani
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Brianna Davies
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Cheung
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Drake Comber
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jason D Roberts
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada
| | - Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Universite de Montreal, Montreal, QC, Canada
| | - Martin S Green
- Heart Institute, University of Ottawa, Ottawa, ON, Canada
| | | | | | | | - Christian Steinberg
- Institut Universitaire de Cardiologie et Pneumologie de Quebec, Laval University, Quebec City, QC, Canada
| | - Ciorsti MacIntyre
- Division of Cardiology, QEII Health Sciences Center, Halifax, NS, Canada
| | - Paul Angaran
- St Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Henry Duff
- Libin Cardiovascular Institute, University of Calgary, Calgary, AB, Canada
| | - Robert Hamilton
- Division of Cardiology, The Hospital for Sick Children (SickKids), Toronto, ON, Canada
| | - Laura Arbour
- Division of Medical Genetics, Island Health, Victoria, BC, Canada
| | | | - Colette Seifer
- Section of Cardiology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Anne Fournier
- Division of Pediatric Cardiology, CHU Sainte-Justine, Universite de Montreal, Montreal, QC, Canada
| | - Joseph Atallah
- Division of Pediatric Cardiology, University of Alberta Stollery Children's Hospital, Edmonton, AB, Canada
| | - Shane Kimber
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Bhavanesh Makanjee
- Heart Health Institute, Scarborough Health Network, Scarborough, ON, Canada
| | - Wael Alqarawi
- Heart Institute, University of Ottawa, Ottawa, ON, Canada
| | - Julia Cadrin-Tourigny
- Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Universite de Montreal, Montreal, QC, Canada
| | - Jacqueline Joza
- Division of Cardiology, McGill University Health Centre, Montreal, QC, Canada
| | - Martin Gardner
- Division of Cardiology, QEII Health Sciences Center, Halifax, NS, Canada
| | - Mario Talajic
- Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Universite de Montreal, Montreal, QC, Canada
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Andrew D Krahn
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Zachary W M Laksman
- Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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16
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Zhou W, Ye D, Tester DJ, Bains S, Giudicessi JR, Haglund-Turnquist CM, Orland KM, January CT, Eckhardt LL, Maginot KR, Ackerman MJ. Elucidation of ALG10B as a Novel Long-QT Syndrome-Susceptibility Gene. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:e003726. [PMID: 37071726 PMCID: PMC10844923 DOI: 10.1161/circgen.122.003726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/04/2022] [Indexed: 02/24/2023]
Abstract
BACKGROUND Long-QT syndrome (LQTS) is characterized by QT prolongation and increased risk for syncope, seizures, and sudden cardiac death. The majority of LQTS stems from pathogenic mutations in KCNQ1, KCNH2, or SCN5A. However, ≈10% of patients with LQTS remain genetically elusive. We utilized genome sequencing to identify a novel LQTS genetic substrate in a multigenerational genotype-negative LQTS pedigree. METHODS Genome sequencing was performed on 5 affected family members. Only rare nonsynonymous variants present in all affected family members were considered. The candidate variant was characterized functionally in patient-derived induced pluripotent stem cell and gene-edited, variant corrected, isogenic control induced pluripotent stem cell-derived cardiomyocytes. RESULTS A missense variant (p.G6S) was identified in ALG10B-encoded α-1,2-glucosyltransferase B protein. ALG10B (alpha-1,2-glucosyltransferase B protein) is a known interacting protein of KCNH2-encoded Kv11.1 (HERG [human Ether-à-go-go-related gene]). Compared with isogenic control, ALG10B-p.G6S induced pluripotent stem cell-derived cardiomyocytes showed (1) decreased protein expression of ALG10B (p.G6S, 0.7±0.18, n=8 versus control, 1.25±0.16, n=9; P<0.05), (2) significant retention of HERG in the endoplasmic reticulum (P<0.0005), and (3) a significantly prolonged action potential duration confirmed by both patch clamp (p.G6S, 531.1±38.3 ms, n=15 versus control, 324.1±21.8 ms, n=13; P<0.001) and multielectrode assay (P<0.0001). Lumacaftor-a compound known to rescue HERG trafficking-shortened the pathologically prolonged action potential duration of ALG10B-p.G6S induced pluripotent stem cell-derived cardiomyocytes by 10.6% (n=31 electrodes; P<0.001). CONCLUSIONS Here, we demonstrate that ALG10B-p.G6S downregulates ALG10B, resulting in defective HERG trafficking and action potential duration prolongation. Therefore, ALG10B is a novel LQTS-susceptibility gene underlying the LQTS phenotype observed in a multigenerational pedigree. ALG10B mutation analysis may be warranted, especially in genotype-negative patients with an LQT2-like phenotype.
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Affiliation(s)
- Wei Zhou
- Departments of Cardiovascular Medicine (Division of Heart
Rhythm Services), Pediatric and Adolescent Medicine (Division of Pediatric
Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland
Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - Dan Ye
- Departments of Cardiovascular Medicine (Division of Heart
Rhythm Services), Pediatric and Adolescent Medicine (Division of Pediatric
Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland
Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - David J. Tester
- Departments of Cardiovascular Medicine (Division of Heart
Rhythm Services), Pediatric and Adolescent Medicine (Division of Pediatric
Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland
Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - Sahej Bains
- Departments of Cardiovascular Medicine (Division of Heart
Rhythm Services), Pediatric and Adolescent Medicine (Division of Pediatric
Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland
Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - John R. Giudicessi
- Departments of Cardiovascular Medicine (Division of Heart
Rhythm Services), Pediatric and Adolescent Medicine (Division of Pediatric
Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland
Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
- Departments of Cardiovascular Medicine
(Clinician-Investigator Training Program), Mayo Clinic, Rochester, MN
| | - Carla M. Haglund-Turnquist
- Departments of Cardiovascular Medicine (Division of Heart
Rhythm Services), Pediatric and Adolescent Medicine (Division of Pediatric
Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland
Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - Kate M. Orland
- Department of Medicine, Division of Cardiovascular
Medicine, Cellular and Molecular Arrhythmia Research Program and Inherited
Arrhythmia Clinic, University of Wisconsin-Madison, Madison, WI
| | - Craig T. January
- Department of Medicine, Division of Cardiovascular
Medicine, Cellular and Molecular Arrhythmia Research Program and Inherited
Arrhythmia Clinic, University of Wisconsin-Madison, Madison, WI
| | - Lee L. Eckhardt
- Department of Medicine, Division of Cardiovascular
Medicine, Cellular and Molecular Arrhythmia Research Program and Inherited
Arrhythmia Clinic, University of Wisconsin-Madison, Madison, WI
| | - Kathleen R. Maginot
- Department of Pediatrics, University of Wisconsin School of
Medicine and Public Health, Madison, WI
| | - Michael J. Ackerman
- Departments of Cardiovascular Medicine (Division of Heart
Rhythm Services), Pediatric and Adolescent Medicine (Division of Pediatric
Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland
Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
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17
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Identification of Two Homozygous Variants in MYBPC3 and SMYD1 Genes Associated with Severe Infantile Cardiomyopathy. Genes (Basel) 2023; 14:genes14030659. [PMID: 36980931 PMCID: PMC10048717 DOI: 10.3390/genes14030659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Mutations in cardiac genes are one of the primary causes of infantile cardiomyopathy. In this study, we report the genetic findings of two siblings carrying variations in the MYBPC3 and SMYD1 genes. The first patient is a female proband exhibiting hypertrophic cardiomyopathy (HCM) and biventricular heart failure carrying a truncating homozygous MYBPC3 variant c.1224-52G>A (IVS13-52G>A) and a novel homozygous variant (c.302A>G; p.Asn101Ser) in the SMYD1 gene. The second patient, the proband’s sibling, is a male infant diagnosed with hypertrophic cardiomyopathy and carries the same homozygous MYBPC3 variant. While this specific MYBPC3 variant (c.1224-52G>A, IVS13-52G>A) has been previously reported to be associated with adult-onset hypertrophic cardiomyopathy, this is the first report linking it to infantile cardiomyopathy. In addition, this work describes, for the first time, a novel SMYD1 variant (c.302A>G; p.Asn101Ser) that has never been reported. We performed a histopathological evaluation of tissues collected from both probands and show that these variants lead to myofibrillar disarray, reduced and irregular mitochondrial cristae and cardiac fibrosis. Together, these results provide critical insight into the molecular functionality of these genes in human cardiac physiology.
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18
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Stafford F, Krishnan N, Richardson E, Butters A, Hespe S, Burns C, Gray B, Medi C, Nowak N, Isbister JC, Raju H, Richmond D, Ryan MP, Singer ES, Sy RW, Yeates L, Bagnall RD, Semsarian C, Ingles J. The role of genetic testing in diagnosis and care of inherited cardiac conditions in a specialised multidisciplinary clinic. Genome Med 2022; 14:145. [PMID: 36578016 PMCID: PMC9795753 DOI: 10.1186/s13073-022-01149-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/12/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The diagnostic yield of genetic testing for inherited cardiac diseases is up to 40% and is primarily indicated for screening of at-risk relatives. Here, we evaluate the role of genomics in diagnosis and management among consecutive individuals attending a specialised clinic and identify those with the highest likelihood of having a monogenic disease. METHODS A retrospective audit of 1697 consecutive, unrelated probands referred to a specialised, multidisciplinary clinic between 2002 and 2020 was performed. A concordant clinical and genetic diagnosis was considered solved. Cases were classified as likely monogenic based on a score comprising a positive family history, young age at onset, and severe phenotype, whereas low-scoring cases were considered to have a likely complex aetiology. The impact of a genetic diagnosis was evaluated. RESULTS A total of 888 probands fulfilled the inclusion criteria, and genetic testing identified likely pathogenic or pathogenic (LP/P) variants in 330 individuals (37%) and suspicious variants of uncertain significance (VUS) in 73 (8%). Research-focused efforts identified 46 (5%) variants, missed by conventional genetic testing. Where a variant was identified, this changed or clarified the final diagnosis in a clinically useful way for 51 (13%). The yield of suspicious VUS across ancestry groups ranged from 15 to 20%, compared to only 10% among Europeans. Even when the clinical diagnosis was uncertain, those with the most monogenic disease features had the greatest diagnostic yield from genetic testing. CONCLUSIONS Research-focused efforts can increase the diagnostic yield by up to 5%. Where a variant is identified, this will have clinical utility beyond family screening in 13%. We demonstrate the value of genomics in reaching an overall diagnosis and highlight inequities based on ancestry. Acknowledging our incomplete understanding of disease phenotypes, we propose a framework for prioritising likely monogenic cases to solve their underlying cause of disease.
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Affiliation(s)
- Fergus Stafford
- grid.1013.30000 0004 1936 834XCardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.415306.50000 0000 9983 6924Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Neesha Krishnan
- grid.1013.30000 0004 1936 834XCardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.415306.50000 0000 9983 6924Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Ebony Richardson
- grid.1013.30000 0004 1936 834XCardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.415306.50000 0000 9983 6924Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Alexandra Butters
- grid.1013.30000 0004 1936 834XCardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.415306.50000 0000 9983 6924Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Sophie Hespe
- grid.415306.50000 0000 9983 6924Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Charlotte Burns
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Belinda Gray
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.413249.90000 0004 0385 0051Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Caroline Medi
- grid.413249.90000 0004 0385 0051Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Natalie Nowak
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Julia C. Isbister
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.413249.90000 0004 0385 0051Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Hariharan Raju
- grid.413249.90000 0004 0385 0051Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia ,grid.1004.50000 0001 2158 5405Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - David Richmond
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.413249.90000 0004 0385 0051Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Mark P. Ryan
- grid.413249.90000 0004 0385 0051Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Emma S. Singer
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Raymond W. Sy
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Laura Yeates
- grid.1013.30000 0004 1936 834XCardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.415306.50000 0000 9983 6924Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.413249.90000 0004 0385 0051Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Richard D. Bagnall
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Christopher Semsarian
- grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Sydney, Australia ,grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.413249.90000 0004 0385 0051Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- grid.1013.30000 0004 1936 834XCardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.415306.50000 0000 9983 6924Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia ,grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia ,grid.413249.90000 0004 0385 0051Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
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19
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Molecular Diagnosis of Hypertrophic Cardiomyopathy (HCM): In the Heart of Cardiac Disease. J Clin Med 2022; 12:jcm12010225. [PMID: 36615026 PMCID: PMC9821215 DOI: 10.3390/jcm12010225] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is an inherited myocardial disease with the presence of left ventricular hypertrophy (LVH). The disease is characterized by high locus, allelic and phenotypic heterogeneity, even among members of the same family. The list of confirmed and potentially relevant genes implicating the disease is constantly increasing, with novel genes frequently reported. Heterozygous alterations in the five main sarcomeric genes (MYBPC3, MYH7, TNNT2, TNNI3, and MYL2) are estimated to account for more than half of confirmed cases. The genetic discoveries of recent years have shed more light on the molecular pathogenic mechanisms of HCM, contributing to substantial advances in the diagnosis of the disease. Genetic testing applying next-generation sequencing (NGS) technologies and early diagnosis prior to the clinical manifestation of the disease among family members demonstrate an important improvement in the field.
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20
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O'Shea R, Ma AS, Jamieson RV, Rankin NM. Precision medicine in Australia: now is the time to get it right. Med J Aust 2022; 217:559-563. [PMID: 36436133 PMCID: PMC10100177 DOI: 10.5694/mja2.51777] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022]
Affiliation(s)
| | - Alan S Ma
- University of Sydney, Sydney, NSW.,Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW
| | - Robyn V Jamieson
- University of Sydney, Sydney, NSW.,Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW
| | - Nicole M Rankin
- University of Sydney, Sydney, NSW.,Centre for Health Policy, University of Melbourne, Melbourne, VIC
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21
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Smith HS, Sanchez CE, Maag R, Buentello A, Murdock DR, Metcalf GA, Hadley TD, Riconda DL, Boerwinkle E, Wehrens XH, Ballantyne CM, Gibbs RA, McGuire AL, Pereira S. Patient and Clinician Perceptions of Precision Cardiology Care: Findings From the HeartCare Study. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003605. [PMID: 36282588 PMCID: PMC10163837 DOI: 10.1161/circgen.121.003605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 08/04/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Routine genome-wide screening for cardiovascular disease risk may inform clinical decision-making. However, little is known about whether clinicians and patients would find such testing useful or acceptable within the context of a genomics-enabled learning health system. METHODS We conducted surveys with patients and their clinicians who were participating in the HeartCare Study, a precision cardiology care project that returned results from a next-generation sequencing panel of 158 genes associated with cardiovascular disease risk. Six weeks after return of results, we assessed patients' and clinicians' perceived utility and disutility of HeartCare, the effect of the test on clinical recommendations, and patients' attitudes toward integration of research and clinical care. RESULTS Among 666 HeartCare patients with a result returned during the survey study period, 42.0% completed a full or partial survey. Patient-participants who completed a full survey (n=224) generally had positive perceptions of HeartCare independent of whether they received a positive or negative result. Most patient-participants considered genetic testing for cardiovascular disease risk to have more benefit than risk (88.3%) and agreed that it provided information that they wanted to know (81.2%), while most disagreed that the test caused them to feel confused (77.7%) or overwhelmed (78.0%). For 122 of their patients with positive results, clinicians (n=13) reported making changes in clinical care for 66.4% of patients, recommending changes in health behaviors for 36.9% of patients, and recommending to 33.6% of patients that their family members have clinical testing. CONCLUSIONS Both patients and clinicians thought the HeartCare panel screen for cardiovascular disease risk provided information that was useful in terms of personal or health benefits to the patient and that informed clinical care without causing patients to be confused or overwhelmed. Further research is needed to assess perceptions of genome-wide screening among the US cardiology clinic population.
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Affiliation(s)
- Hadley Stevens Smith
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX
| | - Clarissa E. Sanchez
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX
| | - Ronald Maag
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
| | - Alexandria Buentello
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
| | - David R. Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Ginger A. Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Trevor D. Hadley
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
| | - Daniel L. Riconda
- Dept of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- School of Health Professions, Baylor College of Medicine, Houston, TX
| | - Eric Boerwinkle
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Xander H.T. Wehrens
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX
- Dept of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX
| | - Christie M. Ballantyne
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Amy L. McGuire
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX
| | - Stacey Pereira
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX
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22
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Bagnall RD, Singer ES, Wacker J, Nowak N, Ingles J, King I, Macciocca I, Crowe J, Ronan A, Weintraub RG, Semsarian C. Genetic Basis of Childhood Cardiomyopathy. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003686. [PMID: 36252119 DOI: 10.1161/circgen.121.003686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND The causes of cardiomyopathy in children are less well described than in adults. We evaluated the clinical diagnoses and genetic causes of childhood cardiomyopathy and outcomes of cascade genetic testing in family members. METHODS We recruited children from a pediatric cardiology service or genetic heart diseases clinic. We performed Sanger, gene panel, exome or genome sequencing and classified variants for pathogenicity using American College of Molecular Genetics and Genomics guidelines. RESULTS Cardiomyopathy was diagnosed in 221 unrelated children aged ≤18 years. Children mostly had hypertrophic cardiomyopathy (n=98, 44%) or dilated cardiomyopathy (n=89, 40%). The highest genetic testing diagnostic yields were in restrictive cardiomyopathy (n=16, 80%) and hypertrophic cardiomyopathy (n=65, 66%), and lowest in dilated cardiomyopathy (n=26, 29%) and left ventricular noncompaction (n=3, 25%). Pathogenic variants were primarily found in genes encoding sarcomere proteins, with TNNT2 and TNNI3 variants associated with more severe clinical outcomes. Ten children (4.5%) had multiple pathogenic variants. Genetic test results prompted review of clinical diagnosis in 14 families with syndromic, mitochondrial or metabolic gene variants. Cascade genetic testing in 127 families confirmed 24 de novo variants, recessive inheritance in 8 families, and supported reclassification of 12 variants. CONCLUSIONS Genetic testing of children with cardiomyopathy supports a precise clinical diagnosis, which may inform prognosis.
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Affiliation(s)
- Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., N.N., J.I., J.C., C.S.).,Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., J.I., J.C., C.S.)
| | - Emma S Singer
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., N.N., J.I., J.C., C.S.).,Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., J.I., J.C., C.S.)
| | - Julie Wacker
- Department of Cardiology, Royal Children's Hospital, Melbourne, VIC, Australia; (J.W., R.G.W.)
| | - Natalie Nowak
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., N.N., J.I., J.C., C.S.).,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia (N.N., J.I., C.S.)
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., N.N., J.I., J.C., C.S.).,Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., J.I., J.C., C.S.).,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia (N.N., J.I., C.S.).,Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW, Sydney, NSW, Australia (J.I.).,Murdoch Children's Research Institute, Melbourne, VIC, Australia (J.I., I.K., I.M., R.G.W.)
| | - Ingrid King
- Murdoch Children's Research Institute, Melbourne, VIC, Australia (J.I., I.K., I.M., R.G.W.)
| | - Ivan Macciocca
- Murdoch Children's Research Institute, Melbourne, VIC, Australia (J.I., I.K., I.M., R.G.W.).,University of Melbourne, Melbourne, VIC, Australia (I.M., R.G.W.).,Victorian Clinical Genetics Services, Melbourne, VIC, Australia (I.M.)
| | - Joshua Crowe
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., N.N., J.I., J.C., C.S.).,Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., J.I., J.C., C.S.)
| | - Anne Ronan
- Hunter Genetics Unit (A.R.).,University of Newcastle, Newcastle, NSW, Australia (A.R.)
| | - Robert G Weintraub
- Department of Cardiology, Royal Children's Hospital, Melbourne, VIC, Australia; (J.W., R.G.W.).,Murdoch Children's Research Institute, Melbourne, VIC, Australia (J.I., I.K., I.M., R.G.W.).,University of Melbourne, Melbourne, VIC, Australia (I.M., R.G.W.)
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., N.N., J.I., J.C., C.S.).,Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia (R.D.B., E.S.S., J.I., J.C., C.S.).,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia (N.N., J.I., C.S.)
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23
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Singer ES, Bagnall RD. Splicing Functional Assays Into the Genetic Testing Pipeline. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003949. [PMID: 36350765 DOI: 10.1161/circgen.122.003949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Emma S Singer
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (E.S.S., R.D.B.), The University of Sydney, NSW, Australia.,Faculty of Medicine and Health (E.S.S., R.D.B.), The University of Sydney, NSW, Australia
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (E.S.S., R.D.B.), The University of Sydney, NSW, Australia.,Faculty of Medicine and Health (E.S.S., R.D.B.), The University of Sydney, NSW, Australia
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24
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Whole exome and genome sequencing in mendelian disorders: a diagnostic and health economic analysis. Eur J Hum Genet 2022; 30:1121-1131. [PMID: 35970915 PMCID: PMC9553973 DOI: 10.1038/s41431-022-01162-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/01/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022] Open
Abstract
Whole genome sequencing (WGS) improves Mendelian disorder diagnosis over whole exome sequencing (WES); however, additional diagnostic yields and costs remain undefined. We investigated differences between diagnostic and cost outcomes of WGS and WES in a cohort with suspected Mendelian disorders. WGS was performed in 38 WES-negative families derived from a 64 family Mendelian cohort that previously underwent WES. For new WGS diagnoses, contemporary WES reanalysis determined whether variants were diagnosable by original WES or unique to WGS. Diagnostic rates were estimated for WES and WGS to simulate outcomes if both had been applied to the 64 families. Diagnostic costs were calculated for various genomic testing scenarios. WGS diagnosed 34% (13/38) of WES-negative families. However, contemporary WES reanalysis on average 2 years later would have diagnosed 18% (7/38 families) resulting in a WGS-specific diagnostic yield of 19% (6/31 remaining families). In WES-negative families, the incremental cost per additional diagnosis using WGS following WES reanalysis was AU$36,710 (£19,407;US$23,727) and WGS alone was AU$41,916 (£22,159;US$27,093) compared to WES-reanalysis. When we simulated the use of WGS alone as an initial genomic test, the incremental cost for each additional diagnosis was AU$29,708 (£15,705;US$19,201) whereas contemporary WES followed by WGS was AU$36,710 (£19,407;US$23,727) compared to contemporary WES. Our findings confirm that WGS is the optimal genomic test choice for maximal diagnosis in Mendelian disorders. However, accepting a small reduction in diagnostic yield, WES with subsequent reanalysis confers the lowest costs. Whether WES or WGS is utilised will depend on clinical scenario and local resourcing and availability.
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25
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Wilde AAM, Semsarian C, Márquez MF, Shamloo AS, Ackerman MJ, Ashley EA, Sternick EB, Barajas-Martinez H, Behr ER, Bezzina CR, Breckpot J, Charron P, Chockalingam P, Crotti L, Gollob MH, Lubitz S, Makita N, Ohno S, Ortiz-Genga M, Sacilotto L, Schulze-Bahr E, Shimizu W, Sotoodehnia N, Tadros R, Ware JS, Winlaw DS, Kaufman ES. European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the state of genetic testing for cardiac diseases. Europace 2022; 24:1307-1367. [PMID: 35373836 PMCID: PMC9435643 DOI: 10.1093/europace/euac030] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Arthur A M Wilde
- Heart Centre, Department of Cardiology, Amsterdam Universitair Medische
Centra, Amsterdam, location AMC, The Netherlands
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute,
University of Sydney, Sydney, Australia
| | - Manlio F Márquez
- Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de
México, Mexico
- Member of the Latin American Heart Rhythm Society (LAHRS)
| | | | - Michael J Ackerman
- Departments of Cardiovascular Medicine, Pediatric and Adolescent Medicine,
and Molecular Pharmacology & Experimental Therapeutics; Divisions of Heart Rhythm
Services and Pediatric Cardiology; Windland Smith Rice Genetic Heart Rhythm Clinic and
Windland Smith Rice Sudden Death Genomics Laboratory, Mayo
Clinic, Rochester, MN, USA
| | - Euan A Ashley
- Department of Cardiovascular Medicine, Stanford University,
Stanford, California, USA
| | - Eduardo Back Sternick
- Arrhythmia and Electrophysiology Unit, Biocor Institute,
Minas Gerais, Brazil; and
Member of the Latin American Heart Rhythm Society (LAHRS)
| | - Héctor Barajas-Martinez
- Cardiovascular Research, Lankenau Institute of Medical
Research, Wynnewood, PA, USA; and Member of the Latin American Heart Rhythm Society (LAHRS)
| | - Elijah R Behr
- Cardiovascular Clinical Academic Group, Institute of Molecular and Clinical
Sciences, St. George’s, University of London; St. George’s University Hospitals NHS
Foundation Trust, London, UK; Mayo Clinic Healthcare, London
| | - Connie R Bezzina
- Amsterdam UMC Heart Center, Department of Experimental
Cardiology, Amsterdam, The
Netherlands
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven,
Leuven, Belgium
| | - Philippe Charron
- Sorbonne Université, APHP, Centre de Référence des Maladies Cardiaques
Héréditaires, ICAN, Inserm UMR1166, Hôpital
Pitié-Salpêtrière, Paris, France
| | | | - Lia Crotti
- Center for Cardiac Arrhythmias of Genetic Origin,
Istituto Auxologico Italiano, IRCCS, Milan, Italy
- Cardiomyopathy Unit and Cardiac Rehabilitation Unit, San Luca Hospital,
Istituto Auxologico Italiano, IRCCS, Milan,
Italy
- Department of Medicine and Surgery, University of
Milano-Bicocca, Milan, Italy
| | - Michael H Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology,
University of Toronto, Toronto, ON, Canada
| | - Steven Lubitz
- Cardiac Arrhythmia Service, Massachusetts General Hospital and Harvard
Medical School, Boston, MA, USA
| | - Naomasa Makita
- National Cerebral and Cardiovascular Center, Research
Institute, Suita, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular
Center, Suita, Japan
| | - Martín Ortiz-Genga
- Clinical Department, Health in Code, A
Coruña, Spain; and Member of the Latin
American Heart Rhythm Society (LAHRS)
| | - Luciana Sacilotto
- Arrhythmia Unit, Instituto do Coracao, Hospital das Clinicas HCFMUSP,
Faculdade de Medicina, Universidade de Sao Paulo, Sao
Paulo, Brazil; and Member of the Latin
American Heart Rhythm Society (LAHRS)
| | - Eric Schulze-Bahr
- Institute for Genetics of Heart Diseases, University Hospital
Münster, Münster, Germany
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, Graduate School of Medicine, Nippon
Medical School, Bunkyo-ku, Tokyo, Japan
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of
Medicine, University of Washington, Seattle, WA,
USA
| | - Rafik Tadros
- Cardiovascular Genetics Center, Department of Medicine, Montreal Heart
Institute, Université de Montréal, Montreal,
Canada
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical
Sciences, Imperial College London, London,
UK
- Royal Brompton & Harefield Hospitals, Guy’s
and St. Thomas’ NHS Foundation Trust, London, UK
| | - David S Winlaw
- Cincinnati Children's Hospital Medical Centre, University of
Cincinnati, Cincinnati, OH, USA
| | - Elizabeth S Kaufman
- Metrohealth Medical Center, Case Western Reserve University,
Cleveland, OH, USA
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26
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Wilde AAM, Semsarian C, Márquez MF, Sepehri Shamloo A, Ackerman MJ, Ashley EA, Sternick Eduardo B, Barajas‐Martinez H, Behr ER, Bezzina CR, Breckpot J, Charron P, Chockalingam P, Crotti L, Gollob MH, Lubitz S, Makita N, Ohno S, Ortiz‐Genga M, Sacilotto L, Schulze‐Bahr E, Shimizu W, Sotoodehnia N, Tadros R, Ware JS, Winlaw DS, Kaufman ES, Aiba T, Bollmann A, Choi J, Dalal A, Darrieux F, Giudicessi J, Guerchicoff M, Hong K, Krahn AD, Mac Intyre C, Mackall JA, Mont L, Napolitano C, Ochoa Juan P, Peichl P, Pereira AC, Schwartz PJ, Skinner J, Stellbrink C, Tfelt‐Hansen J, Deneke T. European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the state of genetic testing for cardiac diseases. J Arrhythm 2022; 38:491-553. [PMID: 35936045 PMCID: PMC9347209 DOI: 10.1002/joa3.12717] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Arthur A. M. Wilde
- Heart Centre, Department of Cardiology, Amsterdam Universitair Medische CentraAmsterdamThe Netherlands
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary InstituteUniversity of SydneySydneyAustralia
| | - Manlio F. Márquez
- Instituto Nacional de Cardiología Ignacio ChávezCiudad de MéxicoMexico
| | | | - Michael J. Ackerman
- Departments of Cardiovascular Medicine, Pediatric and Adolescent Medicine, and Molecular Pharmacology & Experimental Therapeutics; Divisions of Heart Rhythm Services and Pediatric Cardiology; Windland Smith Rice Genetic Heart Rhythm Clinic and Windland Smith Rice Sudden Death Genomics Laboratory, Mayo ClinicRochesterMNUSA
| | - Euan A. Ashley
- Department of Cardiovascular MedicineStanford UniversityStanfordCAUSA
| | | | | | - Elijah R. Behr
- Cardiovascular Clinical Academic Group, Institute of Molecular and Clinical Sciences, St. George’sUniversity of London; St. George’s University Hospitals NHS Foundation TrustLondonUKMayo Clinic HealthcareLondon
| | - Connie R. Bezzina
- Amsterdam UMC Heart Center, Department of Experimental CardiologyAmsterdamThe Netherlands
| | - Jeroen Breckpot
- Center for Human GeneticsUniversity Hospitals LeuvenLeuvenBelgium
| | | | | | - Lia Crotti
- Center for Cardiac Arrhythmias of Genetic Origin, Istituto Auxologico Italiano, IRCCSMilanItaly
- Cardiomyopathy Unit and Cardiac Rehabilitation Unit, San Luca Hospital, Istituto Auxologico Italiano, IRCCSMilanItaly
- Department of Medicine and SurgeryUniversity of Milano‐BicoccaMilanItaly
| | - Michael H. Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of CardiologyUniversity of TorontoTorontoONCanada
| | - Steven Lubitz
- Cardiac Arrhythmia ServiceMassachusetts General Hospital and Harvard Medical SchoolBostonMAUSA
| | - Naomasa Makita
- National Cerebral and Cardiovascular CenterResearch InstituteSuitaJapan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular CenterSuitaJapan
| | | | - Luciana Sacilotto
- Arrhythmia Unit, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao PauloBrazil
| | - Eric Schulze‐Bahr
- Institute for Genetics of Heart DiseasesUniversity Hospital MünsterMünsterGermany
| | - Wataru Shimizu
- Department of Cardiovascular MedicineGraduate School of MedicineTokyoJapan
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of MedicineUniversity of WashingtonSeattleWAUSA
| | - Rafik Tadros
- Cardiovascular Genetics Center, Department of Medicine, Montreal Heart InstituteUniversité de MontréalMontrealCanada
| | - James S. Ware
- National Heart and Lung Institute and MRC London Institute of Medical SciencesImperial College LondonLondonUK
- Royal Brompton & Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation TrustLondonUK
| | - David S. Winlaw
- Cincinnati Children's Hospital Medical CentreUniversity of CincinnatiCincinnatiOHUSA
| | | | - Takeshi Aiba
- Department of Clinical Laboratory Medicine and Genetics, National Cerebral and Cardiovascular Center, SuitaOsakaJapan
| | - Andreas Bollmann
- Department of ElectrophysiologyHeart Center Leipzig at University of LeipzigLeipzigGermany
- Leipzig Heart InstituteLeipzigGermany
| | - Jong‐Il Choi
- Division of Cardiology, Department of Internal Medicine, Korea University Anam HospitalKorea University College of MedicineSeoulRepublic of Korea
| | - Aarti Dalal
- Department of Pediatrics, Division of CardiologyVanderbilt University School of MedicineNashvilleTNUSA
| | - Francisco Darrieux
- Arrhythmia Unit, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São PauloSão PauloBrazil
| | - John Giudicessi
- Department of Cardiovascular Medicine (Divisions of Heart Rhythm Services and Circulatory Failure and the Windland Smith Rice Genetic Heart Rhythm Clinic), Mayo ClinicRochesterMNUSA
| | - Mariana Guerchicoff
- Division of Pediatric Arrhythmia and Electrophysiology, Italian Hospital of Buenos AiresBuenos AiresArgentina
| | - Kui Hong
- Department of Cardiovascular MedicineThe Second Affiliated Hospital of Nanchang UniversityNanchangChina
| | - Andrew D. Krahn
- Division of CardiologyUniversity of British ColumbiaVancouverCanada
| | - Ciorsti Mac Intyre
- Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo ClinicRochesterMNUSA
| | - Judith A. Mackall
- Center for Cardiac Electrophysiology and Pacing, University Hospitals Cleveland Medical CenterCase Western Reserve University School of MedicineClevelandOHUSA
| | - Lluís Mont
- Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS). Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Cardiovasculares (CIBERCV), MadridSpain
| | - Carlo Napolitano
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri, IRCCSPaviaItaly
- Department of Molecular MedicineUniversity of PaviaPaviaItaly
| | - Pablo Ochoa Juan
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), MadridSpain
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de HierroMadridSpain
- Centro de Investigacion Biomedica en Red en Enfermedades Cariovasculares (CIBERCV), MadridSpain
| | - Petr Peichl
- Department of CardiologyInstitute for Clinical and Experimental MedicinePragueCzech Republic
| | - Alexandre C. Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart InstituteUniversity of São Paulo Medical SchoolSão PauloBrazil
- Hipercol Brasil ProgramSão PauloBrazil
| | - Peter J. Schwartz
- Center for Cardiac Arrhythmias of Genetic Origin, Istituto Auxologico Italiano, IRCCSMilanItaly
| | - Jon Skinner
- Sydney Childrens Hospital NetworkUniversity of SydneySydneyAustralia
| | - Christoph Stellbrink
- Department of Cardiology and Intensive Care MedicineUniversity Hospital Campus Klinikum BielefeldBielefeldGermany
| | - Jacob Tfelt‐Hansen
- The Department of Cardiology, the Heart Centre, Copenhagen University Hospital, Rigshopitalet, Copenhagen, Denmark; Section of genetics, Department of Forensic Medicine, Faculty of Medical SciencesUniversity of CopenhagenDenmark
| | - Thomas Deneke
- Heart Center Bad NeustadtBad Neustadt a.d. SaaleGermany
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27
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Smith E, Care M, Burke-Martindale C, Weissler-Snir A. Secondary Findings Using Broad Pan Cardiomyopathy and Arrhythmia Panels in Patients With a Personal or Family History of Inherited Cardiomyopathy or Arrhythmia Syndrome. Am J Cardiol 2022; 178:137-141. [PMID: 35835602 DOI: 10.1016/j.amjcard.2022.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022]
Abstract
With broad panels and whole exome or genome sequencing, there is the potential for secondary findings, which include pathogenic/likely pathogenic variants or variants of uncertain significance in genes that are unrelated to the primary clinical indication for the testing. No study examined the frequency and implications of secondary findings when using a broad panel for inherited cardiomyopathy or arrhythmia syndromes. We performed a retrospective review of the primary indications for genetic testing, tests performed, and genetic test results to identify secondary findings in patients seen in the Inherited Cardiovascular Disease Clinic for a personal or family history of (possible) inherited cardiomyopathy, inherited arrhythmia syndrome, previous cardiac arrest, or family history of sudden cardiac death. Of 325 probands and 20 family members who had genetic testing, with no-cost broad cardiomyopathy and arrhythmia panel, 4 probands (1.2%) and 4 family members (5%) had pathogenic/likely pathogenic variants in autosomal dominant genes, unrelated to the primary reason for testing. In conclusion, the prevalence of secondary findings using broad cardiomyopathy and arrhythmia panel in patients with personal or family history of inherited cardiomyopathy or arrhythmia was ∼2.2%. Our findings suggest that with appropriate genetic counseling, broad panels might be considered over disease-specific panels because of the relatively high prevalence of secondary findings that positively affect patient care and would not have been identified with more targeted testing.
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Affiliation(s)
- Emily Smith
- Hartford HealthCare, Heart and Vascular Institute, Hartford, Connecticut
| | - Melanie Care
- Division of Cardiology, Department of Medicine, Peter Munk Cardiac Center, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Adaya Weissler-Snir
- Hartford HealthCare, Heart and Vascular Institute, Hartford, Connecticut; Department of Medicine, University of Connecticut, Farmington, Connecticut.
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28
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Wilde AAM, Semsarian C, Márquez MF, Sepehri Shamloo A, Ackerman MJ, Ashley EA, Sternick EB, Barajas-Martinez H, Behr ER, Bezzina CR, Breckpot J, Charron P, Chockalingam P, Crotti L, Gollob MH, Lubitz S, Makita N, Ohno S, Ortiz-Genga M, Sacilotto L, Schulze-Bahr E, Shimizu W, Sotoodehnia N, Tadros R, Ware JS, Winlaw DS, Kaufman ES, Aiba T, Bollmann A, Choi JI, Dalal A, Darrieux F, Giudicessi J, Guerchicoff M, Hong K, Krahn AD, MacIntyre C, Mackall JA, Mont L, Napolitano C, Ochoa JP, Peichl P, Pereira AC, Schwartz PJ, Skinner J, Stellbrink C, Tfelt-Hansen J, Deneke T. European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the State of Genetic Testing for Cardiac Diseases. Heart Rhythm 2022; 19:e1-e60. [PMID: 35390533 DOI: 10.1016/j.hrthm.2022.03.1225] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Arthur A M Wilde
- Heart Centre, Department of Cardiology, Amsterdam Universitair Medische Centra, Amsterdam, location AMC, The Netherlands.
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia.
| | - Manlio F Márquez
- Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico; and Member of the Latin American Heart Rhythm Society (LAHRS).
| | | | - Michael J Ackerman
- Departments of Cardiovascular Medicine, Pediatric and Adolescent Medicine, and Molecular Pharmacology & Experimental Therapeutics; Divisions of Heart Rhythm Services and Pediatric Cardiology; Windland Smith Rice Genetic Heart Rhythm Clinic and Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Euan A Ashley
- Department of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| | - Eduardo Back Sternick
- Arrhythmia and Electrophysiology Unit, Biocor Institute, Minas Gerais, Brazil; and Member of the Latin American Heart Rhythm Society (LAHRS)
| | | | - Elijah R Behr
- Cardiovascular Clinical Academic Group, Institute of Molecular and Clinical Sciences, St. George's, University of London; St. George's University Hospitals NHS Foundation Trust, London, UK; Mayo Clinic Healthcare, London
| | - Connie R Bezzina
- Amsterdam UMC Heart Center, Department of Experimental Cardiology, Amsterdam, The Netherlands
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Charron
- Sorbonne Université, APHP, Centre de Référence des Maladies Cardiaques Héréditaires, ICAN, Inserm UMR1166, Hôpital Pitié-Salpêtrière, Paris, France
| | | | - Lia Crotti
- Center for Cardiac Arrhythmias of Genetic Origin, Istituto Auxologico Italiano, IRCCS, Milan, Italy; Cardiomyopathy Unit and Cardiac Rehabilitation Unit, San Luca Hospital, Istituto Auxologico Italiano, IRCCS, Milan, Italy; Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Michael H Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology, University of Toronto, Toronto, ON, Canada
| | - Steven Lubitz
- Cardiac Arrhythmia Service, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Naomasa Makita
- National Cerebral and Cardiovascular Center, Research Institute, Suita, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Martín Ortiz-Genga
- Clinical Department, Health in Code, A Coruña, Spain; and Member of the Latin American Heart Rhythm Society (LAHRS)
| | - Luciana Sacilotto
- Arrhythmia Unit, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil; and Member of the Latin American Heart Rhythm Society (LAHRS)
| | - Eric Schulze-Bahr
- Institute for Genetics of Heart Diseases, University Hospital Münster, Münster, Germany
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, Graduate School of Medicine, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Rafik Tadros
- Cardiovascular Genetics Center, Department of Medicine, Montreal Heart Institute, Université de Montréal, Montreal, Canada
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - David S Winlaw
- Cincinnati Children's Hospital Medical Centre, University of Cincinnati, Cincinnati, OH, USA
| | - Elizabeth S Kaufman
- Metrohealth Medical Center, Case Western Reserve University, Cleveland, OH, USA.
| | - Takeshi Aiba
- Department of Clinical Laboratory Medicine and Genetics, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Andreas Bollmann
- Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, Leipzig, Germany; Leipzig Heart Institute, Leipzig Heart Digital, Leipzig, Germany
| | - Jong-Il Choi
- Division of Cardiology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Aarti Dalal
- Department of Pediatrics, Division of Cardiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Francisco Darrieux
- Arrhythmia Unit, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - John Giudicessi
- Department of Cardiovascular Medicine (Divisions of Heart Rhythm Services and Circulatory Failure and the Windland Smith Rice Genetic Heart Rhythm Clinic), Mayo Clinic, Rochester, MN, USA
| | - Mariana Guerchicoff
- Division of Pediatric Arrhythmia and Electrophysiology, Italian Hospital of Buenos Aires, Buenos Aires, Argentina
| | - Kui Hong
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Andrew D Krahn
- Division of Cardiology, University of British Columbia, Vancouver, Canada
| | - Ciorsti MacIntyre
- Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, MN, USA
| | - Judith A Mackall
- Center for Cardiac Electrophysiology and Pacing, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Lluís Mont
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Carlo Napolitano
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri, IRCCS, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Juan Pablo Ochoa
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, Madrid, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Cariovasculares (CIBERCV), Madrid, Spain
| | - Petr Peichl
- Department of Cardiology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, São Paulo 05403-000, Brazil; Hipercol Brasil Program, São Paulo, Brazil
| | - Peter J Schwartz
- Center for Cardiac Arrhythmias of Genetic Origin, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Jon Skinner
- Sydney Childrens Hospital Network, University of Sydney, Sydney, Australia
| | - Christoph Stellbrink
- Department of Cardiology and Intensive Care Medicine, University Hospital Campus Klinikum Bielefeld, Bielefeld, Germany
| | - Jacob Tfelt-Hansen
- The Department of Cardiology, the Heart Centre, Copenhagen University Hospital, Rigshopitalet, Copenhagen, Denmark; Section of Genetics, Department of Forensic Medicine, Faculty of Medical Sciences, University of Copenhagen, Denmark
| | - Thomas Deneke
- Heart Center Bad Neustadt, Bad Neustadt a.d. Saale, Germany
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29
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Sanford Kobayashi EF, Dimmock DP. Better and faster is cheaper. Hum Mutat 2022; 43:1495-1506. [PMID: 35723630 DOI: 10.1002/humu.24422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022]
Abstract
The rapid pace of advancement in genomic sequencing technology has recently reached a new milestone, with a record-setting time to molecular diagnosis of a mere 8 h. The catalyst behind this achievement is the accumulation of evidence indicating that quicker results more often make an impact on patient care and lead to healthcare cost savings. Herein, we review the diagnostic and clinical utility of rapid whole genome and rapid whole exome sequencing, the associated reduction in healthcare costs, and the relationship between these outcome measures and time-to-diagnosis.
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Affiliation(s)
- Erica F Sanford Kobayashi
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
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30
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Torrado M, Maneiro E, Lamounier Junior A, Fernández-Burriel M, Sánchez Giralt S, Martínez-Carapeto A, Cazón L, Santiago E, Ochoa JP, McKenna WJ, Santomé L, Monserrat L. Identification of an elusive spliceogenic MYBPC3 variant in an otherwise genotype-negative hypertrophic cardiomyopathy pedigree. Sci Rep 2022; 12:7284. [PMID: 35508642 PMCID: PMC9068804 DOI: 10.1038/s41598-022-11159-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/13/2022] [Indexed: 11/10/2022] Open
Abstract
The finding of a genotype-negative hypertrophic cardiomyopathy (HCM) pedigree with several affected members indicating a familial origin of the disease has driven this study to discover causative gene variants. Genetic testing of the proband and subsequent family screening revealed the presence of a rare variant in the MYBPC3 gene, c.3331−26T>G in intron 30, with evidence supporting cosegregation with the disease in the family. An analysis of potential splice-altering activity using several splicing algorithms consistently yielded low scores. Minigene expression analysis at the mRNA and protein levels revealed that c.3331−26T>G is a spliceogenic variant with major splice-altering activity leading to undetectable levels of properly spliced transcripts or the corresponding protein. Minigene and patient mRNA analyses indicated that this variant induces complete and partial retention of intron 30, which was expected to lead to haploinsufficiency in carrier patients. As most spliceogenic MYBPC3 variants, c.3331−26T>G appears to be non-recurrent, since it was identified in only two additional unrelated probands in our large HCM cohort. In fact, the frequency analysis of 46 known splice-altering MYBPC3 intronic nucleotide substitutions in our HCM cohort revealed 9 recurrent and 16 non-recurrent variants present in a few probands (≤ 4), while 21 were not detected. The identification of non-recurrent elusive MYBPC3 spliceogenic variants that escape detection by in silico algorithms represents a challenge for genetic diagnosis of HCM and contributes to solving a fraction of genotype-negative HCM cases.
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Affiliation(s)
- Mario Torrado
- Cardiovascular Research Group, University of A Coruña, Campus de Oza, Building Fortín, 15006, A Coruña, Spain. .,Biomedical Research Institute of A Coruña, A Coruña, Spain.
| | - Emilia Maneiro
- Biomedical Research Institute of A Coruña, A Coruña, Spain. .,Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain.
| | - Arsonval Lamounier Junior
- Cardiovascular Research Group, University of A Coruña, Campus de Oza, Building Fortín, 15006, A Coruña, Spain.,Biomedical Research Institute of A Coruña, A Coruña, Spain.,Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain.,Medical School, Universidade Vale do Rio Doce, Governador Valadares, MG, Brazil
| | | | | | | | - Laura Cazón
- Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
| | - Elisa Santiago
- Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
| | - Juan Pablo Ochoa
- Biomedical Research Institute of A Coruña, A Coruña, Spain.,Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
| | - William J McKenna
- Cardiovascular Research Group, University of A Coruña, Campus de Oza, Building Fortín, 15006, A Coruña, Spain.,Biomedical Research Institute of A Coruña, A Coruña, Spain.,Institute of Cardiovascular Science, University College London, London, UK
| | - Luis Santomé
- Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
| | - Lorenzo Monserrat
- Biomedical Research Institute of A Coruña, A Coruña, Spain.,Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
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31
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Sepp R, Hategan L, Csányi B, Borbás J, Tringer A, Pálinkás ED, Nagy V, Takács H, Latinovics D, Nyolczas N, Pálinkás A, Faludi R, Rábai M, Szabó GT, Czuriga D, Balogh L, Halmosi R, Borbély A, Habon T, Hegedűs Z, Nagy I. The Genetic Architecture of Hypertrophic Cardiomyopathy in Hungary: Analysis of 242 Patients with a Panel of 98 Genes. Diagnostics (Basel) 2022; 12:diagnostics12051132. [PMID: 35626289 PMCID: PMC9139509 DOI: 10.3390/diagnostics12051132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/24/2022] [Accepted: 04/29/2022] [Indexed: 12/03/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a primary disease of the myocardium most commonly caused by mutations in sarcomeric genes. We aimed to perform a nationwide large-scale genetic analysis of a previously unreported, representative HCM cohort in Hungary. A total of 242 consecutive HCM index patients (127 men, 44 ± 11 years) were studied with next generation sequencing using a custom-designed gene-panel comprising 98 cardiomyopathy-related genes. A total of 90 patients (37%) carried pathogenic/likely pathogenic (P/LP) variants. The percentage of patients with P/LP variants in genes with definitive evidence for HCM association was 93%. Most of the patients with P/LP variants had mutations in MYBPC3 (55 pts, 61%) and in MYH7 (21 pts, 23%). Double P/LP variants were present in four patients (1.7%). P/LP variants in other genes could be detected in ≤3% of patients. Of the patients without P/LP variants, 46 patients (19%) carried a variant of unknown significance. Non-HCM P/LP variants were identified in six patients (2.5%), with two in RAF1 (p.Leu633Val, p.Ser257Leu) and one in DES (p.Arg406Trp), FHL1 (p.Glu96Ter), TTN (p.Lys23480fs), and in the mitochondrial genome (m.3243A>G). Frameshift, nonsense, and splice-variants made up 82% of all P/LP MYBPC3 variants. In all the other genes, missense mutations were the dominant form of variants. The MYBPC3 p.Gln1233Ter, the MYBPC3 p.Pro955ArgfsTer95, and the MYBPC3 p.Ser593ProfsTer11 variants were identified in 12, 7, and 13 patients, respectively. These three variants made up 36% of all patients with identified P/LP variants, raising the possibility of a possible founder effect for these mutations. Similar to other HCM populations, the MYBPC3 and the MYH7 genes seemed to be the most frequently affected genes in Hungarian HCM patients. The high prevalence of three MYBPC3 mutations raises the possibility of a founder effect in our HCM cohort.
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Affiliation(s)
- Róbert Sepp
- Division of Non-Invasive Cardiology, Department of Internal Medicine, Faculty of Medicine, University of Szeged, Semmelweis u. 8, H-6725 Szeged, Hungary; (L.H.); (B.C.); (J.B.); (A.T.); (E.D.P.); (V.N.); (H.T.)
- Correspondence: ; Tel.: +36-30-267-5845; Fax: +36-62-545-820
| | - Lidia Hategan
- Division of Non-Invasive Cardiology, Department of Internal Medicine, Faculty of Medicine, University of Szeged, Semmelweis u. 8, H-6725 Szeged, Hungary; (L.H.); (B.C.); (J.B.); (A.T.); (E.D.P.); (V.N.); (H.T.)
| | - Beáta Csányi
- Division of Non-Invasive Cardiology, Department of Internal Medicine, Faculty of Medicine, University of Szeged, Semmelweis u. 8, H-6725 Szeged, Hungary; (L.H.); (B.C.); (J.B.); (A.T.); (E.D.P.); (V.N.); (H.T.)
| | - János Borbás
- Division of Non-Invasive Cardiology, Department of Internal Medicine, Faculty of Medicine, University of Szeged, Semmelweis u. 8, H-6725 Szeged, Hungary; (L.H.); (B.C.); (J.B.); (A.T.); (E.D.P.); (V.N.); (H.T.)
| | - Annamária Tringer
- Division of Non-Invasive Cardiology, Department of Internal Medicine, Faculty of Medicine, University of Szeged, Semmelweis u. 8, H-6725 Szeged, Hungary; (L.H.); (B.C.); (J.B.); (A.T.); (E.D.P.); (V.N.); (H.T.)
| | - Eszter Dalma Pálinkás
- Division of Non-Invasive Cardiology, Department of Internal Medicine, Faculty of Medicine, University of Szeged, Semmelweis u. 8, H-6725 Szeged, Hungary; (L.H.); (B.C.); (J.B.); (A.T.); (E.D.P.); (V.N.); (H.T.)
| | - Viktória Nagy
- Division of Non-Invasive Cardiology, Department of Internal Medicine, Faculty of Medicine, University of Szeged, Semmelweis u. 8, H-6725 Szeged, Hungary; (L.H.); (B.C.); (J.B.); (A.T.); (E.D.P.); (V.N.); (H.T.)
| | - Hedvig Takács
- Division of Non-Invasive Cardiology, Department of Internal Medicine, Faculty of Medicine, University of Szeged, Semmelweis u. 8, H-6725 Szeged, Hungary; (L.H.); (B.C.); (J.B.); (A.T.); (E.D.P.); (V.N.); (H.T.)
| | - Dóra Latinovics
- SeqOmics Biotechnology Ltd., Vállalkozók útja 7, H-6782 Mórahalom, Hungary; (D.L.); (I.N.)
| | - Noémi Nyolczas
- Gottsegen National Cardiovascular Center, Haller u. 29, H-1096 Budapest, Hungary;
- Military Hospital-State Health Center, Róbert Károly körút 44, H-1134 Budapest, Hungary
| | - Attila Pálinkás
- Elisabeth Hospital, Dr. Imre József u. 9, H-6800 Hódmezővásárhely, Hungary;
| | - Réka Faludi
- Heart Institute, Medical School, University of Pécs, Ifjúság útja 13, H-7624 Pécs, Hungary;
| | - Miklós Rábai
- Division of Cardiology, First Department of Medicine, Medical School, University of Pécs, Ifjúság útja 13, H-7624 Pécs, Hungary; (M.R.); (R.H.); (T.H.)
| | - Gábor Tamás Szabó
- Division of Cardiology and Division of Clinical Physiology, Department of Cardiology, University of Debrecen, Móricz Zsigmond körút 22, H-4032 Debrecen, Hungary; (G.T.S.); (D.C.); (L.B.); (A.B.)
| | - Dániel Czuriga
- Division of Cardiology and Division of Clinical Physiology, Department of Cardiology, University of Debrecen, Móricz Zsigmond körút 22, H-4032 Debrecen, Hungary; (G.T.S.); (D.C.); (L.B.); (A.B.)
| | - László Balogh
- Division of Cardiology and Division of Clinical Physiology, Department of Cardiology, University of Debrecen, Móricz Zsigmond körút 22, H-4032 Debrecen, Hungary; (G.T.S.); (D.C.); (L.B.); (A.B.)
| | - Róbert Halmosi
- Division of Cardiology, First Department of Medicine, Medical School, University of Pécs, Ifjúság útja 13, H-7624 Pécs, Hungary; (M.R.); (R.H.); (T.H.)
- Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - Attila Borbély
- Division of Cardiology and Division of Clinical Physiology, Department of Cardiology, University of Debrecen, Móricz Zsigmond körút 22, H-4032 Debrecen, Hungary; (G.T.S.); (D.C.); (L.B.); (A.B.)
| | - Tamás Habon
- Division of Cardiology, First Department of Medicine, Medical School, University of Pécs, Ifjúság útja 13, H-7624 Pécs, Hungary; (M.R.); (R.H.); (T.H.)
| | - Zoltán Hegedűs
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Temesvári krt. 62, H-6726 Szeged, Hungary;
- Department of Biochemistry and Medical Chemistry, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd., Vállalkozók útja 7, H-6782 Mórahalom, Hungary; (D.L.); (I.N.)
- Institute of Biochemistry, Biological Research Center, Eötvös Loránd Research Network, Temesvári krt. 62, H-6726 Szeged, Hungary
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32
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Toste A. Advances in hypertrophic cardiomyopathy: What the cardiologist needs to know. Rev Port Cardiol 2022; 41:499-509. [DOI: 10.1016/j.repc.2021.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/19/2021] [Accepted: 05/10/2021] [Indexed: 10/18/2022] Open
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Christian S, Cirino A, Hansen B, Harris S, Murad AM, Natoli JL, Malinowski J, Kelly MA. Diagnostic validity and clinical utility of genetic testing for hypertrophic cardiomyopathy: a systematic review and meta-analysis. Open Heart 2022; 9:openhrt-2021-001815. [PMID: 35387861 PMCID: PMC8987756 DOI: 10.1136/openhrt-2021-001815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/28/2022] [Indexed: 11/23/2022] Open
Abstract
Objective This study summarises the diagnostic validity and clinical utility of genetic testing for patients with hypertrophic cardiomyopathy (HCM) and their at-risk relatives. Methods A systematic search was performed in PubMed (MEDLINE), Embase, CINAHL and Cochrane Central Library databases from inception through 2 March 2020. Subgroup and sensitivity analyses were prespecified for individual sarcomere genes, presence/absence of pathogenic variants, paediatric and adult cohorts, family history, inclusion of probands, and variant classification method. Study quality was assessed using the Newcastle-Ottawa tool. Results A total of 132 articles met inclusion criteria. The detection rate based on pathogenic and likely pathogenic variants was significantly higher in paediatric cohorts compared with adults (56% vs 42%; p=0.01) and in adults with a family history compared with sporadic cases (59% vs 33%; p=0.005). When studies applied current, improved, variant interpretation standards, the adult detection rate significantly decreased from 42% to 33% (p=0.0001) because less variants met criteria to be considered pathogenic. The mean difference in age-of-onset in adults was significantly earlier for genotype-positive versus genotype-negative cohorts (8.3 years; p<0.0001), MYH7 versus MYBPC3 cohorts (8.2 years; p<0.0001) and individuals with multiple versus single variants (7.0 years; p<0.0002). Overall, disease penetrance in adult cohorts was 62%, but differed significantly depending on if probands were included or excluded (73% vs 55%; p=0.003). Conclusions This systematic review and meta-analysis is the first, to our knowledge, to collectively quantify historical understandings of detection rate, genotype-phenotype associations and disease penetrance for HCM, while providing the answers to important routine clinical questions and highlighting key areas for future study.
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Affiliation(s)
- Susan Christian
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Allison Cirino
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,MGH Institute of Health Professions, Boston, Massachusetts, USA
| | - Brittany Hansen
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio, USA
| | - Stephanie Harris
- Cardiology Division, Cardiovascular Genetics Program, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Andrea M Murad
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Hospitals and Health Centers, Ann Arbor, Michigan, USA
| | - Jaime L Natoli
- Kaiser Permanente, Southern California Permanente Medical Group, Pasadena, California, USA
| | | | - Melissa A Kelly
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, USA
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34
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Circulating miR-499a-5p Is a Potential Biomarker of MYH7-Associated Hypertrophic Cardiomyopathy. Int J Mol Sci 2022; 23:ijms23073791. [PMID: 35409153 PMCID: PMC8998764 DOI: 10.3390/ijms23073791] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited myocardial disease with significant genetic and phenotypic heterogeneity. To search for novel biomarkers, which could increase the accuracy of HCM diagnosis and improve understanding of its phenotype formation, we analyzed the levels of circulating miRNAs—stable non-coding RNAs involved in post-transcriptional gene regulation. Performed high throughput sequencing of miRNAs in plasma of HCM patients and controls pinpointed miR-499a-5p as one of 35 miRNAs dysregulated in HCM. Further investigation on enlarged groups of individuals showed that its level was higher in carriers of pathogenic/likely pathogenic (P/LP) variants in MYH7 gene compared to controls (fold change, FC = 8.9; p < 0.0001). Just as important, carriers of variants in MYH7 gene were defined with higher miRNA levels than carriers of variants in the MYBPC3 gene (FC = 14.1; p = 0.0003) and other patients (FC = 4.1; p = 0.0008). The receiver operating characteristic analysis analysis showed the ability of miR-499a-5p to identify MYH7 variant carriers with the HCM phenotype with area under the curve value of 0.95 (95% confidence interval: 0.88−1.03, p = 0.0004); sensitivity and specificity were 0.86 and 0.91 (cut-off = 0.0014). Therefore, miR-499a-5p could serve as a circulating biomarker of HCM, caused by P/LP variants in MYH7 gene.
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Lesurf R, Said A, Akinrinade O, Breckpot J, Delfosse K, Liu T, Yao R, Persad G, McKenna F, Noche RR, Oliveros W, Mattioli K, Shah S, Miron A, Yang Q, Meng G, Yue MCS, Sung WWL, Thiruvahindrapuram B, Lougheed J, Oechslin E, Mondal T, Bergin L, Smythe J, Jayappa S, Rao VJ, Shenthar J, Dhandapany PS, Semsarian C, Weintraub RG, Bagnall RD, Ingles J, Melé M, Maass PG, Ellis J, Scherer SW, Mital S. Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. NPJ Genom Med 2022; 7:18. [PMID: 35288587 PMCID: PMC8921194 DOI: 10.1038/s41525-022-00288-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/04/2022] [Indexed: 11/08/2022] Open
Abstract
Cardiomyopathy (CMP) is a heritable disorder. Over 50% of cases are gene-elusive on clinical gene panel testing. The contribution of variants in non-coding DNA elements that result in cryptic splicing and regulate gene expression has not been explored. We analyzed whole-genome sequencing (WGS) data in a discovery cohort of 209 pediatric CMP patients and 1953 independent replication genomes and exomes. We searched for protein-coding variants, and non-coding variants predicted to affect the function or expression of genes. Thirty-nine percent of cases harbored pathogenic coding variants in known CMP genes, and 5% harbored high-risk loss-of-function (LoF) variants in additional candidate CMP genes. Fifteen percent harbored high-risk regulatory variants in promoters and enhancers of CMP genes (odds ratio 2.25, p = 6.70 × 10-7 versus controls). Genes involved in α-dystroglycan glycosylation (FKTN, DTNA) and desmosomal signaling (DSC2, DSG2) were most highly enriched for regulatory variants (odds ratio 6.7-58.1). Functional effects were confirmed in patient myocardium and reporter assays in human cardiomyocytes, and in zebrafish CRISPR knockouts. We provide strong evidence for the genomic contribution of functionally active variants in new genes and in regulatory elements of known CMP genes to early onset CMP.
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Affiliation(s)
- Robert Lesurf
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Abdelrahman Said
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Oyediran Akinrinade
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- St. George's University School of Medicine, Grenada, Grenada
| | | | - Kathleen Delfosse
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ting Liu
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Roderick Yao
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gabrielle Persad
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Fintan McKenna
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ramil R Noche
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Zebrafish Genetics and Disease Models Core, The Hospital for Sick Children, Toronto, ON, Canada
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shreya Shah
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anastasia Miron
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Qian Yang
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Guoliang Meng
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jane Lougheed
- Division of Cardiology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Erwin Oechslin
- Peter Munk Cardiac Centre, Division of Cardiology, Toronto General Hospital, University of Toronto, Toronto, ON, Canada
| | - Tapas Mondal
- Department of Pediatrics, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Lynn Bergin
- Division of Cardiology, London Health Sciences Centre, London, ON, Canada
| | - John Smythe
- Department of Pediatrics, Kingston General Hospital, Kingston, ON, Canada
| | - Shashank Jayappa
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Vinay J Rao
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Jayaprakash Shenthar
- Department of Cardiology, Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bengaluru, India
| | - Perundurai S Dhandapany
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Robert G Weintraub
- Cardiology Department, Royal Children's Hospital, Melbourne, Australia
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard D Bagnall
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Cardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Philipp G Maass
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Seema Mital
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.
- Ted Rogers Centre for Heart Research, Toronto, ON, Canada.
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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Tobert KE, Tester DJ, Zhou W, Haglund-Turnquist CM, Giudicessi JR, Ackerman MJ. Genome Sequencing in a Genetically Elusive Multi-Generational Long QT Syndrome Pedigree Identifies a Novel LQT2-Causative Deeply Intronic KCNH2 Variant. Heart Rhythm 2022; 19:998-1007. [PMID: 35144019 DOI: 10.1016/j.hrthm.2022.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Most of long QT syndrome (LQTS) stems from pathogenic variants in KCNQ1, KCNH2, or SCN5A. However, ∼10-20% of LQTS index cases remain genotype-negative. OBJECTIVE Here, we identified and characterized functionally a novel LQTS genetic substrate in a multi-generational, "genotype-negative" LQTS pedigree. METHODS The patient was a 40-year-old female with a history of syncope, seizures, ventricular fibrillation, and a family history of LQTS and sudden death. Commercial genetic testing of all LQTS-causative genes was negative. Genome sequencing was performed on 6 affected family members. Patient-specific and CRISPR/Cas9 "gene-corrected" isogenic control induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) were generated. RESULTS No ultra-rare, nonsynonymous heterozygous variants co-segregated among the 6 LQTS phenotype-positive individuals. Instead, a deep intronic KCNH2 variant (c.3331-316G>T) was present in all affected individuals. RT-PCR analysis of patient-specific iPSC-CM-derived RNA revealed that c.3331-316G>T creates a novel 89 base-pair exon that results in a frame-shift variant (p.S1112Pfs*171). The action potential duration (APD90) was significantly longer in p.S1112Pfs*171-iPSC-CMs (602.4 ± 12.2 ms, n=70) compared to isogenic control iPSC-CMs (425.7 ± 9.3 ms, n=61, p<0.0001). Further, the field potential duration (FPD) was significantly longer in p.S1112Pfs*171-iPSC-CMs (358.9 ± 7.7 ms, n=65) compared to isogenic control iPSC-CMs (282.2 ± 10.8 ms, n=51, p<0.0001). CONCLUSIONS A novel deep intronic KCNH2 variant was identified in a multi-generational, genetically elusive LQTS pedigree. The iPSC-CMs establish that the variant is the monogenetic cause for this family's LQTS. Deep intronic variants within the two most common LQTS-susceptibility genes should be considered in patients with seemingly, genetically elusive LQTS.
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Affiliation(s)
- Kathryn E Tobert
- Departments of Cardiovascular Medicine (Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic), Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - David J Tester
- Departments of Cardiovascular Medicine (Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic), Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - Wei Zhou
- Departments of Cardiovascular Medicine (Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic), Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - Carla M Haglund-Turnquist
- Departments of Cardiovascular Medicine (Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic), Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - John R Giudicessi
- Departments of Cardiovascular Medicine (Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic), Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN; Departments of Cardiovascular Medicine (Clinician-Investigator Training Program), Mayo Clinic, Rochester, MN
| | - Michael J Ackerman
- Departments of Cardiovascular Medicine (Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic), Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), and Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN.
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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Zhu Y, Jackson D, Hunter B, Beattie L, Turner L, Hambly BD, Jeremy RW, Malecki C, Robertson EN, Li A, Remedios C, Richmond D, Semsarian C, O'Sullivan JF, Bannon PG, Lal S. Models of cardiovascular surgery biobanking to facilitate translational research and precision medicine. ESC Heart Fail 2021; 9:21-30. [PMID: 34931483 PMCID: PMC8787984 DOI: 10.1002/ehf2.13768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 11/07/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Biobanking in health care has evolved over the last few decades from simple biological sample repositories to complex and dynamic units with multi‐organizational infrastructure networks and has become an essential tool for modern medical research. Cardiovascular tissue biobanking provides a unique opportunity to utilize cardiac and vascular samples for translational research into heart failure and other related pathologies. Current techniques for diagnosis, classification, and treatment monitoring of cardiac disease relies primarily on interpretation of clinical signs, imaging, and blood biomarkers. Further research at the disease source (i.e. myocardium and blood vessels) has been limited by a relative lack of access to quality human cardiac tissue and the inherent shortcomings of most animal models of heart disease. In this review, we describe a model for cardiovascular tissue biobanking and databasing, and its potential to facilitate basic and translational research. We share techniques to procure endocardial samples from patients with hypertrophic cardiomyopathy, heart failure with reduced ejection fraction, and heart failure with preserved ejection fraction, in addition to aortic disease samples. We discuss some of the issues with respect to data collection, privacy, biobank consent, and the governance of tissue biobanking. The development of tissue biobanks as described here has significant scope to improve and facilitate translational research in multi‐omic fields such as genomics, transcriptomics, proteomics, and metabolomics. This research heralds an era of precision medicine, in which patients with cardiovascular pathology can be provided with optimized and personalized medical care for the treatment of their individual phenotype.
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Affiliation(s)
- YingYan Zhu
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Dan Jackson
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Benjamin Hunter
- Cardiovascular Precision Laboratory The University of Sydney Sydney New South Wales 2006 Australia
- Charles Perkins Centre The University of Sydney Sydney New South Wales Australia
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - Lorna Beattie
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
| | - Lisa Turner
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
| | - Brett D. Hambly
- Charles Perkins Centre The University of Sydney Sydney New South Wales Australia
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - Richmond W. Jeremy
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Cassandra Malecki
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - Elizabeth N. Robertson
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Amy Li
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Department of Pharmacy & Biomedical Sciences La Trobe University Melbourne Victoria Australia
| | - Cris Remedios
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - David Richmond
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Christopher Semsarian
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
- Agnes Ginges Centre for Molecular Cardiology Centenary Institute Sydney New South Wales Australia
| | - John F. O'Sullivan
- Cardiovascular Precision Laboratory The University of Sydney Sydney New South Wales 2006 Australia
- Charles Perkins Centre The University of Sydney Sydney New South Wales Australia
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
- Heart Research Institute The University of Sydney Sydney New South Wales Australia
| | - Paul G. Bannon
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
- Charles Perkins Centre The University of Sydney Sydney New South Wales Australia
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
- RPA Institute of Academic Surgery (IAS) Royal Prince Alfred Hospital and the University of Sydney Sydney New South Wales Australia
| | - Sean Lal
- Cardiovascular Precision Laboratory The University of Sydney Sydney New South Wales 2006 Australia
- Charles Perkins Centre The University of Sydney Sydney New South Wales Australia
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
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Parker LE, Landstrom AP. The clinical utility of pediatric cardiomyopathy genetic testing: From diagnosis to a precision medicine-based approach to care. PROGRESS IN PEDIATRIC CARDIOLOGY 2021; 62. [PMID: 34776723 DOI: 10.1016/j.ppedcard.2021.101413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Pediatric-onset cardiomyopathies are rare yet cause significant morbidity and mortality in affected children. Genetic testing has a major role in the clinical evaluation of pediatric-onset cardiomyopathies, and identification of a variant in an associated gene can be used to confirm the clinical diagnosis and exclude syndromic causes that may warrant different treatment strategies. Further, risk-predictive testing of first-degree relatives can assess who is at-risk of disease and requires continued clinical follow-up. Aim of Review In this review, we seek to describe the current role of genetic testing in the clinical diagnosis and management of patients and families with the five major cardiomyopathies. Further, we highlight the ongoing development of precision-based approaches to diagnosis, prognosis, and treatment. Key Scientific Concepts of Review Emerging application of genotype-phenotype correlations opens the door for genetics to guide a precision medicine-based approach to prognosis and potentially for therapies. Despite advances in our understanding of the genetic etiology of cardiomyopathy and increased accessibility of clinical genetic testing, not all pediatric cardiomyopathy patients have a clear genetic explanation for their disease. Expanded genomic studies are needed to understand the cause of disease in these patients, improve variant classification and genotype-driven prognostic predictions, and ultimately develop truly disease preventing treatment.
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Affiliation(s)
- Lauren E Parker
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, NC, United States
| | - Andrew P Landstrom
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, NC, United States.,Department of Cell Biology, Duke University School of Medicine, Durham, NC, United States
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He M, Qiu J, Bai Y, Wang Y, Hu M, Chen G. Non-pharmaceutical Interventions for Hypertrophic Cardiomyopathy: A Mini Review. Front Cardiovasc Med 2021; 8:695247. [PMID: 34722651 PMCID: PMC8553933 DOI: 10.3389/fcvm.2021.695247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Hypertrophic cardiomyopathy is an inherited cardiovascular disease, and 70% of patients have left ventricular outflow tract obstruction. Ventricular septal myectomy has been the gold standard treatment for most patients with refractory symptoms. Due to higher mortality associated with medical facilities with less experience, alcohol septal ablation has been accepted as an alternative to conventional surgical myectomy. It offers lower all-cause in-hospital complications and mortality, which could be potentially more preferable for patients with serious comorbidities. In recent years, radiofrequency ablation, providing another option with reproducibility and a low risk of permanent atrioventricular block, has become an effective invasive treatment to relieve left ventricular outflow tract obstruction. Moreover, substantial progress has been made in gene therapy for hypertrophic cardiomyopathy. The principal objective of this review is to present recent advances in non-pharmaceutical interventions in hypertrophic cardiomyopathy.
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Affiliation(s)
- Miaomiao He
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Qiu
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Bai
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Hu
- Health Management Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guangzhi Chen
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Keegan NP, Fletcher S. A spotter's guide to SNPtic exons: The common splice variants underlying some SNP-phenotype correlations. Mol Genet Genomic Med 2021; 10:e1840. [PMID: 34708937 PMCID: PMC8801146 DOI: 10.1002/mgg3.1840] [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: 07/12/2021] [Accepted: 10/12/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cryptic exons are typically characterised as deleterious splicing aberrations caused by deep intronic mutations. However, low-level splicing of cryptic exons is sometimes observed in the absence of any pathogenic mutation. Five recent reports have described how low-level splicing of cryptic exons can be modulated by common single-nucleotide polymorphisms (SNPs), resulting in phenotypic differences amongst different genotypes. METHODS We sought to investigate whether additional 'SNPtic' exons may exist, and whether these could provide an explanatory mechanism for some of the genotype-phenotype correlations revealed by genome-wide association studies. We thoroughly searched the literature for reported cryptic exons, cross-referenced their genomic coordinates against the dbSNP database of common SNPs, then screened out SNPs with no reported phenotype associations. RESULTS This method discovered five probable SNPtic exons in the genes APC, FGB, GHRL, MYPBC3 and OTC. For four of these five exons, we observed that the phenotype associated with the SNP was compatible with the predicted splicing effect of the nucleotide change, whilst the fifth (in GHRL) likely had a more complex splice-switching effect. CONCLUSION Application of our search methods could augment the knowledge value of future cryptic exon reports and aid in generating better hypotheses for genome-wide association studies.
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Affiliation(s)
- Niall Patrick Keegan
- Murdoch University, Murdoch, Western Australia, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Perth, Western Australia, Australia.,Perron Institute, Perth, Western Australia, Australia
| | - Sue Fletcher
- Murdoch University, Murdoch, Western Australia, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Perth, Western Australia, Australia.,University of Western Australia, Perth, Western Australia, Australia
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Yang Y, Zhang J, Li LT, Qiu YL, Gong JY, Zhang MH, Li CH, Wang JS. Whole-Genome Sequencing Reveals Large ATP8B1 Deletion/Duplications as Second Mutations Missed by Exome-Based Sequencing. J Mol Diagn 2021; 23:1491-1499. [PMID: 34543749 DOI: 10.1016/j.jmoldx.2021.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/15/2022] Open
Abstract
Progressive familial intrahepatic cholestasis type 1 (PFIC1) results from biallelic pathogenic variants in ATP8B1. This study sought second pathogenic variants in ATP8B1 by whole-genome sequencing (WGS) in four unrelated low γ-glutamyl transpeptidase cholestasis patients in whom clinical suspicion of PFIC1 was high and gene-panel or Sanger sequencing had identified only one pathogenic variant in ATP8B1. Sanger sequencing confirmed WGS findings and determined the origin of each variant. Novel nonrecurrent structural variants in three patients (patient 1 to patient 3) were identified in trans: g.55396652_55403080del (6427-bp deletion), g.55335906_55346620dup (10,715-bp duplication), and g.55362063_55364293dup (2231-bp duplication). One synonymous variant in patient 4 was recognized in trans (c.1029G>A, p. Thr343Thr) and demonstrated as deleterious. In conclusion, WGS improves genetic diagnostic yield in PFIC1. These findings expand the gene-variant spectrum associated with familiar intrahepatic cholestasis 1 (FIC1) disease and for the first time report tandem duplication in ATP8B1 associated with cholestasis.
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Affiliation(s)
- Ye Yang
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jing Zhang
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Li-Ting Li
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yi-Ling Qiu
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China; Department of Pediatrics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jing-Yu Gong
- Department of Pediatrics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Mei-Hong Zhang
- Department of Pediatrics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Cai-Hua Li
- Genesky Biotechnologies, Shanghai, China
| | - Jian-She Wang
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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43
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Park J, Packard EA, Levin MG, Judy RL, Damrauer SM, Day SM, Ritchie MD, Rader DJ. A genome-first approach to rare variants in hypertrophic cardiomyopathy genes MYBPC3 and MYH7 in a medical biobank. Hum Mol Genet 2021; 31:827-837. [PMID: 34542152 DOI: 10.1093/hmg/ddab249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/24/2021] [Accepted: 08/19/2021] [Indexed: 11/14/2022] Open
Abstract
'Genome-first' approaches to analyzing rare variants can reveal new insights into human biology and disease. Because pathogenic variants are often rare, new discovery requires aggregating rare coding variants into 'gene burdens' for sufficient power. However, a major challenge is deciding which variants to include in gene burden tests. Pathogenic variants in MYBPC3 and MYH7 are well-known causes of hypertrophic cardiomyopathy (HCM), and focusing on these 'positive control' genes in a genome-first approach could help inform variant selection methods and gene burdening strategies for other genes and diseases. Integrating exome sequences with electronic health records among 41 759 participants in the Penn Medicine BioBank, we evaluated the performance of aggregating predicted loss-of-function (pLOF) and/or predicted deleterious missense (pDM) variants in MYBPC3 and MYH7 for gene burden phenome-wide association studies (PheWAS). The approach to grouping rare variants for these two genes produced very different results: pLOFs but not pDM variants in MYBPC3 were strongly associated with HCM, whereas the opposite was true for MYH7. Detailed review of clinical charts revealed that only 38.5% of patients with HCM diagnoses carrying an HCM-associated variant in MYBPC3 or MYH7 had a clinical genetic test result. Additionally, 26.7% of MYBPC3 pLOF carriers without HCM diagnoses had clear evidence of left atrial enlargement and/or septal/LV hypertrophy on echocardiography. Our study shows the importance of evaluating both pLOF and pDM variants for gene burden testing in future studies to uncover novel gene-disease relationships and identify new pathogenic loss-of-function variants across the human genome through genome-first analyses of healthcare-based populations.
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Affiliation(s)
- Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elizabeth A Packard
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael G Levin
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Renae L Judy
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sharlene M Day
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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44
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Kim KH, Pereira NL. Genetics of Cardiomyopathy: Clinical and Mechanistic Implications for Heart Failure. Korean Circ J 2021; 51:797-836. [PMID: 34327881 PMCID: PMC8484993 DOI: 10.4070/kcj.2021.0154] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 11/11/2022] Open
Abstract
Genetic cardiomyopathies are an important cause of sudden cardiac death across all age groups. Genetic testing in heart failure clinics is useful for family screening and providing individual prognostic insight. Obtaining a family history of at least three generations, including the creation of a pedigree, is recommended for all patients with primary cardiomyopathy. Additionally, when appropriate, consultation with a genetic counsellor can aid in the success of a genetic evaluation. Clinical screening should be performed on all first-degree relatives of patients with genetic cardiomyopathy. Genetics has played an important role in the understanding of different cardiomyopathies, and the field of heart failure (HF) genetics is progressing rapidly. Much research has also focused on distinguishing markers of risk in patients with cardiomyopathy using genetic testing. While these efforts currently remain incomplete, new genomic technologies and analytical strategies provide promising opportunities to further explore the genetic architecture of cardiomyopathies, afford insight into the early manifestations of cardiomyopathy, and help define the molecular pathophysiological basis for cardiac remodeling. Cardiovascular physicians should be fully aware of the utility and potential pitfalls of incorporating genetic test results into pre-emptive treatment strategies for patients in the preliminary stages of HF. Future work will need to be directed towards elucidating the biological mechanisms of both rare and common gene variants and environmental determinants of plasticity in the genotype-phenotype relationship. This future research should aim to further our ability to identify, diagnose, and treat disorders that cause HF and sudden cardiac death in young patients, as well as prioritize improving our ability to stratify the risk for these patients prior to the onset of the more severe consequences of their disease.
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Affiliation(s)
- Kyung Hee Kim
- Division of Cardiology, Incheon Sejong General Hospital, Incheon, Korea.
| | - Naveen L Pereira
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
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45
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Suay-Corredera C, Pricolo MR, Herrero-Galán E, Velázquez-Carreras D, Sánchez-Ortiz D, García-Giustiniani D, Delgado J, Galano-Frutos JJ, García-Cebollada H, Vilches S, Domínguez F, Molina MS, Barriales-Villa R, Frisso G, Sancho J, Serrano L, García-Pavía P, Monserrat L, Alegre-Cebollada J. Protein haploinsufficiency drivers identify MYBPC3 variants that cause hypertrophic cardiomyopathy. J Biol Chem 2021; 297:100854. [PMID: 34097875 PMCID: PMC8260873 DOI: 10.1016/j.jbc.2021.100854] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/21/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease. Variants in MYBPC3, the gene encoding cardiac myosin-binding protein C (cMyBP-C), are the leading cause of HCM. However, the pathogenicity status of hundreds of MYBPC3 variants found in patients remains unknown, as a consequence of our incomplete understanding of the pathomechanisms triggered by HCM-causing variants. Here, we examined 44 nontruncating MYBPC3 variants that we classified as HCM-linked or nonpathogenic according to cosegregation and population genetics criteria. We found that around half of the HCM-linked variants showed alterations in RNA splicing or protein stability, both of which can lead to cMyBP-C haploinsufficiency. These protein haploinsufficiency drivers associated with HCM pathogenicity with 100% and 94% specificity, respectively. Furthermore, we uncovered that 11% of nontruncating MYBPC3 variants currently classified as of uncertain significance in ClinVar induced one of these molecular phenotypes. Our strategy, which can be applied to other conditions induced by protein loss of function, supports the idea that cMyBP-C haploinsufficiency is a fundamental pathomechanism in HCM.
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Affiliation(s)
| | - Maria Rosaria Pricolo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | | | | | | | | | - Javier Delgado
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Juan José Galano-Frutos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Helena García-Cebollada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Silvia Vilches
- Heart Failure and Inherited Cardiac Diseases Unit. Department of Cardiology. Hospital Universitario Puerta de Hierro, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART), Madrid, Spain
| | - Fernando Domínguez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit. Department of Cardiology. Hospital Universitario Puerta de Hierro, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - María Sabater Molina
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART), Madrid, Spain; Hospital C. Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain
| | - Roberto Barriales-Villa
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Unidad de Cardiopatías Familiares, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña, Servizo Galego de Saúde (SERGAS), Universidade da Coruña, A Coruña, Spain
| | - Giulia Frisso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; CEINGE Biotecnologie Avanzate, scarl, Naples, Italy
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain; Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Pablo García-Pavía
- Heart Failure and Inherited Cardiac Diseases Unit. Department of Cardiology. Hospital Universitario Puerta de Hierro, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, Madrid, Spain
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46
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Ommen SR, Mital S, Burke MA, Day SM, Deswal A, Elliott P, Evanovich LL, Hung J, Joglar JA, Kantor P, Kimmelstiel C, Kittleson M, Link MS, Maron MS, Martinez MW, Miyake CY, Schaff HV, Semsarian C, Sorajja P, O'Gara PT, Beckman JA, Levine GN, Al-Khatib SM, Armbruster A, Birtcher KK, Ciggaroa J, Dixon DL, de Las Fuentes L, Deswal A, Fleisher LA, Gentile F, Goldberger ZD, Gorenek B, Haynes N, Hernandez AF, Hlatky MA, Joglar JA, Jones WS, Marine JE, Mark D, Palaniappan L, Piano MR, Tamis-Holland J, Wijeysundera DN, Woo YJ. 2020 AHA/ACC guideline for the diagnosis and treatment of patients with hypertrophic cardiomyopathy: A report of the American College of Cardiology/American Heart Association Joint Committee on Clinical Practice Guidelines. J Thorac Cardiovasc Surg 2021; 162:e23-e106. [PMID: 33926766 DOI: 10.1016/j.jtcvs.2021.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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Ma A, Grigg JR, Flaherty M, Smith J, Minoche AE, Cowley MJ, Nash BM, Ho G, Gayagay T, Lai T, Farnsworth E, Hackett EL, Slater K, Wong K, Holman KJ, Jenkins G, Cheng A, Martin F, Brown NJ, Leighton SE, Amor DJ, Goel H, Dinger ME, Bennetts B, Jamieson RV. Genome sequencing in congenital cataracts improves diagnostic yield. Hum Mutat 2021; 42:1173-1183. [PMID: 34101287 DOI: 10.1002/humu.24240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 01/11/2023]
Abstract
Congenital cataracts are one of the major causes of childhood-onset blindness around the world. Genetic diagnosis provides benefits through avoidance of unnecessary tests, surveillance of extraocular features, and genetic family information. In this study, we demonstrate the value of genome sequencing in improving diagnostic yield in congenital cataract patients and families. We applied genome sequencing to investigate 20 probands with congenital cataracts. We examined the added value of genome sequencing across a total cohort of 52 probands, including 14 unable to be diagnosed using previous microarray and exome or panel-based approaches. Although exome or genome sequencing would have detected the variants in 35/52 (67%) of the cases, specific advantages of genome sequencing led to additional diagnoses in 10% (5/52) of the overall cohort, and we achieved an overall diagnostic rate of 77% (40/52). Specific benefits of genome sequencing were due to detection of small copy number variants (2), indels in repetitive regions (2) or single-nucleotide variants (SNVs) in GC-rich regions (1), not detectable on the previous microarray, exome sequencing, or panel-based approaches. In other cases, SNVs were identified in cataract disease genes, including those newly identified since our previous study. This study highlights the additional yield of genome sequencing in congenital cataracts.
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Affiliation(s)
- Alan Ma
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - John R Grigg
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia.,Save Sight Institute, Sydney Eye Hospital, Sydney, New South Wales, Australia
| | - Maree Flaherty
- Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - James Smith
- Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - Andre E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales, Australia
| | - Benjamin M Nash
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Gladys Ho
- Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Thet Gayagay
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Tiffany Lai
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Elizabeth Farnsworth
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Emma L Hackett
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Katrina Slater
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Karen Wong
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Katherine J Holman
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Gemma Jenkins
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Anson Cheng
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Frank Martin
- Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialty of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - Natasha J Brown
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | | | - David J Amor
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Himanshu Goel
- Hunter Genetics, Newcastle, New South Wales, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, New South Wales, Australia
| | - Bruce Bennetts
- Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Specialties of Genomic Medicine & Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
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48
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Pathogenic Intronic Splice-Affecting Variants in MYBPC3 in Three Patients with Hypertrophic Cardiomyopathy. CARDIOGENETICS 2021. [DOI: 10.3390/cardiogenetics11020009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Genetic variants in MYBPC3 are one of the most common causes of hypertrophic cardiomyopathy (HCM). While variants in MYBPC3 affecting canonical splice site dinucleotides are a well-characterised cause of HCM, only recently has work begun to investigate the pathogenicity of more deeply intronic variants. Here, we present three patients with HCM and intronic splice-affecting MYBPC3 variants and analyse the impact of variants on splicing using in vitro minigene assays. We show that the three variants, a novel c.927-8G>A variant and the previously reported c.1624+4A>T and c.3815-10T>G variants, result in MYBPC3 splicing errors. Analysis of blood-derived patient RNA for the c.3815-10T>G variant revealed only wild type spliced product, indicating that mis-spliced transcripts from the mutant allele are degraded. These data indicate that the c.927-8G>A variant of uncertain significance and likely benign c.3815-10T>G should be reclassified as likely pathogenic. Furthermore, we find shortcomings in commonly applied bioinformatics strategies to prioritise variants impacting MYBPC3 splicing and re-emphasise the need for functional assessment of variants of uncertain significance in diagnostic testing.
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49
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Genetic Diagnosis in Sudden Cardiac Death: The Crucial Role of Multidisciplinary Care. CARDIOGENETICS 2021. [DOI: 10.3390/cardiogenetics11020008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sudden death, especially at a young age, may be caused by an underlying genetic cause. Hereditary conditions with an increased risk of sudden death at a young age include cardiomyopathies, arrhythmia syndromes, and hereditary thoracic aortic aneurysms and dissections. The identification of a genetic cause allows for genetic testing and cardiological surveillance in at-risk relatives. Three sudden death cases from our hospital illustrate the value of autopsy, genetic, and cardiological screening in relatives following a sudden death. On autopsy, histology consistent with hereditary cardiomyopathy is a reason for the referral of relatives. In addition, in the absence of an identifiable cause of death by autopsy in young sudden death patients, arrhythmia syndrome should be considered as a potential genetic cause.
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50
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Lopes LR, Murphy D, Bugiardini E, Salem R, Jager J, Futema M, Majid Akhtar M, Savvatis K, Woodward C, Pittman AM, Hanna MG, Syrris P, Pitceathly RDS, Elliott PM. Iterative Reanalysis of Hypertrophic Cardiomyopathy Exome Data Reveals Causative Pathogenic Mitochondrial DNA Variants. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003388. [PMID: 33970670 DOI: 10.1161/circgen.121.003388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Luis R Lopes
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science (L.R.L., J.J., M.F., M.M.A., K.S., P.S., P.M.E.), University College London.,Barts Heart Centre, St. Bartholomew's Hospital, Barts Health National Health Service Trust (L.R.L., M.M.A., K.S., P.M.E.)
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology (D.M.), University College London
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery (E.B., M.G.H., R.D.S.P.)
| | - Reem Salem
- UCL Division of Biosciences (R.S.), University College London
| | - Joanna Jager
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science (L.R.L., J.J., M.F., M.M.A., K.S., P.S., P.M.E.), University College London
| | - Marta Futema
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science (L.R.L., J.J., M.F., M.M.A., K.S., P.S., P.M.E.), University College London
| | - Mohammed Majid Akhtar
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science (L.R.L., J.J., M.F., M.M.A., K.S., P.S., P.M.E.), University College London.,Barts Heart Centre, St. Bartholomew's Hospital, Barts Health National Health Service Trust (L.R.L., M.M.A., K.S., P.M.E.)
| | - Konstantinos Savvatis
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science (L.R.L., J.J., M.F., M.M.A., K.S., P.S., P.M.E.), University College London.,Barts Heart Centre, St. Bartholomew's Hospital, Barts Health National Health Service Trust (L.R.L., M.M.A., K.S., P.M.E.).,William Harvey Research Institute, Queen Mary University London (K.S.)
| | - Cathy Woodward
- Neurogenetics Unit, The National Hospital for Neurology and Neurosurgery (C.W.)
| | - Alan M Pittman
- Genetics Research Centre, Molecular and Clinical Sciences, St. Georges University of London, United Kingdom (A.M.P.)
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery (E.B., M.G.H., R.D.S.P.)
| | - Petros Syrris
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science (L.R.L., J.J., M.F., M.M.A., K.S., P.S., P.M.E.), University College London
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery (E.B., M.G.H., R.D.S.P.)
| | - Perry M Elliott
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science (L.R.L., J.J., M.F., M.M.A., K.S., P.S., P.M.E.), University College London.,Barts Heart Centre, St. Bartholomew's Hospital, Barts Health National Health Service Trust (L.R.L., M.M.A., K.S., P.M.E.)
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