1
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Nafissi NA, Abdulrahim JW, Kwee LC, Coniglio AC, Kraus WE, Piccini JP, Daubert JP, Sun AY, Shah SH. Prevalence and Phenotypic Burden of Monogenic Arrhythmias Using Integration of Electronic Health Records With Genetics. Circ Genom Precis Med 2022; 15:e003675. [PMID: 36136372 PMCID: PMC9588708 DOI: 10.1161/circgen.121.003675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Inherited primary arrhythmia syndromes and arrhythmogenic cardiomyopathies can lead to sudden cardiac arrest in otherwise healthy individuals. The burden and expression of these diseases in a real-world, well-phenotyped cardiovascular population is not well understood. METHODS Whole exome sequencing was performed on 8574 individuals from the CATHGEN cohort (Catheterization Genetics). Variants in 55 arrhythmia-related genes (associated with 8 disorders) were identified and assessed for pathogenicity based on American College of Genetics and Genomics/Association for Molecular Pathology criteria. Individuals carrying pathogenic/likely pathogenic (P/LP) variants were grouped by arrhythmogenic disorder and matched 1:5 to noncarrier controls based on age, sex, and genetic ancestry. Long-term phenotypic data were annotated through deep electronic health record review. RESULTS Fifty-eight P/LP variants were found in 79 individuals in 12 genes associated with 5 arrhythmogenic disorders (arrhythmogenic right ventricular cardiomyopathy, Brugada syndrome, hypertrophic cardiomyopathy, LMNA-related cardiomyopathy, and long QT syndrome). The penetrance of these P/LP variants in this cardiovascular cohort was 33%, 0%, 28%, 83%, and 4%, respectively. Carriers of P/LP variants associated with arrhythmogenic disorders showed significant differences in ECG, imaging, and clinical phenotypes compared with noncarriers, but displayed no difference in survival. Carriers of novel truncating variants in FLNC, MYBPC3, and MYH7 also developed relevant arrhythmogenic cardiomyopathy phenotypes. CONCLUSIONS In a real-world cardiovascular cohort, P/LP variants in arrhythmia-related genes were relatively common (1:108 prevalence) and most penetrant in LMNA. While hypertrophic cardiomyopathy P/LP variant carriers showed significant differences in clinical outcomes compared with noncarriers, carriers of P/LP variants associated with other arrhythmogenic disorders displayed only ECG differences.
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Affiliation(s)
- Navid A. Nafissi
- Division of Cardiology, Dept of Medicine, Duke University School of Medicine, Durham, NC
| | | | - Lydia Coulter Kwee
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC
| | - Amanda C. Coniglio
- Division of Cardiology, Dept of Medicine, Duke University School of Medicine, Durham, NC
| | - William E. Kraus
- Division of Cardiology, Dept of Medicine, Duke University School of Medicine, Durham, NC
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC
| | - Jonathan P. Piccini
- Division of Cardiology, Dept of Medicine, Duke University School of Medicine, Durham, NC
- Duke Clinical Research Institute, Durham, NC
| | - James P. Daubert
- Division of Cardiology, Dept of Medicine, Duke University School of Medicine, Durham, NC
| | - Albert Y. Sun
- Division of Cardiology, Dept of Medicine, Duke University School of Medicine, Durham, NC
| | - Svati H. Shah
- Division of Cardiology, Dept of Medicine, Duke University School of Medicine, Durham, NC
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC
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2
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Abstract
Brugada syndrome is a heritable channelopathy characterized by a peculiar electrocardiogram (ECG) pattern and increased risk of cardiac arrhythmias and sudden death. The arrhythmias originate because of an imbalance between the repolarizing and depolarizing currents that modulate the cardiac action potential. Even if an overt structural cardiomyopathy is not typical of Brugada syndrome, fibrosis and structural changes in the right ventricle contribute to a conduction slowing, which ultimately facilitates ventricular arrhythmias. Currently, Mendelian autosomal dominant transmission is detected in less than 25% of all clinical confirmed cases. Although 23 genes have been associated with the condition, only SCN5A, encoding the cardiac sodium channel, is considered clinically actionable and disease causing. The limited monogenic inheritance has pointed toward new perspectives on the possible complex genetic architecture of the disease, involving polygenic inheritance and a polygenic risk score that can influence penetrance and risk stratification. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Marina Cerrone
- Leon H. Charney Division of Cardiology, Grossman School of Medicine, New York University, New York, NY, USA;
| | - Sarah Costa
- Department of Internal Medicine, Kantonsspital Baden, Baden, Switzerland
| | - Mario Delmar
- Leon H. Charney Division of Cardiology, Grossman School of Medicine, New York University, New York, NY, USA;
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3
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Vad OB, Yan Y, Denti F, Ahlberg G, Refsgaard L, Bomholtz SH, Santos JL, Rasmussen S, Haunsø S, Svendsen JH, Christophersen IE, Schmitt N, Olesen MS, Bentzen BH. Whole-Exome Sequencing Implicates Neuronal Calcium Channel with Familial Atrial Fibrillation. Front Genet 2022; 13:806429. [PMID: 35154276 PMCID: PMC8832975 DOI: 10.3389/fgene.2022.806429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Atrial Fibrillation (AF) is the most prevalent sustained cardiac arrhythmia, responsible for considerable morbidity and mortality. The heterogenic and complex pathogenesis of AF remains poorly understood, which contributes to the current limitation in effective treatments. We aimed to identify rare genetic variants associated with AF in patients with familial AF. Methods and results: We performed whole exome sequencing in a large family with familial AF and identified a rare variant in the gene CACNA1A c.5053G > A which co-segregated with AF. The gene encodes for the protein variants CaV2.1-V1686M, and is important in neuronal function. Functional characterization of the CACNA1A, using patch-clamp recordings on transiently transfected mammalian cells, revealed a modest loss-of-function of CaV2.1-V1686M. Conclusion: We identified a rare loss-of-function variant associated with AF in a gene previously linked with neuronal function. The results allude to a novel link between dysfunction of an ion channel previously associated with neuronal functions and increased risk of developing AF.
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Affiliation(s)
- Oliver Bundgaard Vad
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Yannan Yan
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Federico Denti
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gustav Ahlberg
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lena Refsgaard
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sofia Hammami Bomholtz
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joana Larupa Santos
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Disease Systems Biology Program, University of Copenhagen, Copenhagen, Denmark
| | - Stig Haunsø
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jesper Hastrup Svendsen
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ingrid Elizabeth Christophersen
- The Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway
| | - Nicole Schmitt
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Salling Olesen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular-, Pulmonary and Infectious Diseases, Righospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- *Correspondence: Morten Salling Olesen,
| | - Bo Hjorth Bentzen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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4
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Man JCK, Bosada FM, Scholman KT, Offerhaus JA, Walsh R, van Duijvenboden K, van Eif VWW, Bezzina CR, Verkerk AO, Boukens BJ, Barnett P, Christoffels VM. Variant Intronic Enhancer Controls SCN10A-short Expression and Heart Conduction. Circulation 2021; 144:229-242. [PMID: 33910361 DOI: 10.1161/circulationaha.121.054083] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Genetic variants in SCN10A, encoding the neuronal voltage-gated sodium channel NaV1.8, are strongly associated with atrial fibrillation, Brugada syndrome, cardiac conduction velocities, and heart rate. The cardiac function of SCN10A has not been resolved, however, and diverging mechanisms have been proposed. Here, we investigated the cardiac expression of SCN10A and the function of a variant-sensitive intronic enhancer previously linked to the regulation of SCN5A, encoding the major essential cardiac sodium channel NaV1.5. METHODS The expression of SCN10A was investigated in mouse and human hearts. With the use of CRISPR/Cas9 genome editing, the mouse intronic enhancer was disrupted, and mutant mice were characterized by transcriptomic and electrophysiological analyses. The association of genetic variants at SCN5A-SCN10A enhancer regions and gene expression were evaluated by genome-wide association studies single-nucleotide polymorphism mapping and expression quantitative trait loci analysis. RESULTS We found that cardiomyocytes of the atria, sinoatrial node, and ventricular conduction system express a short transcript comprising the last 7 exons of the gene (Scn10a-short). Transcription occurs from an intronic enhancer-promoter complex, whereas full-length Scn10a transcript was undetectable in the human and mouse heart. Expression quantitative trait loci analysis revealed that the genetic variants in linkage disequilibrium with genetic variant rs6801957 in the intronic enhancer associate with SCN10A transcript levels in the heart. Genetic modification of the enhancer in the mouse genome led to reduced cardiac Scn10a-short expression in atria and ventricles, reduced cardiac sodium current in atrial cardiomyocytes, atrial conduction slowing and arrhythmia, whereas the expression of Scn5a, the presumed enhancer target gene, remained unaffected. In patch-clamp transfection experiments, expression of Scn10a-short-encoded NaV1.8-short increased NaV1.5-mediated sodium current. We propose that noncoding genetic variation modulates transcriptional regulation of Scn10a-short in cardiomyocytes that impacts NaV1.5-mediated sodium current and heart rhythm. CONCLUSIONS Genetic variants in and around SCN10A modulate enhancer function and expression of a cardiac-specific SCN10A-short transcript. We propose that noncoding genetic variation modulates transcriptional regulation of a functional C-terminal portion of NaV1.8 in cardiomyocytes that impacts on NaV1.5 function, cardiac conduction velocities, and arrhythmia susceptibility.
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Affiliation(s)
- Joyce C K Man
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Fernanda M Bosada
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Koen T Scholman
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Joost A Offerhaus
- Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Roddy Walsh
- Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Karel van Duijvenboden
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Vincent W W van Eif
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Connie R Bezzina
- Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Arie O Verkerk
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Bastiaan J Boukens
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Phil Barnett
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
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Al Alawi I, Al Riyami M, Barroso-Gil M, Powell L, Olinger E, Al Salmi I, Sayer JA. The diagnostic yield of whole exome sequencing as a first approach in consanguineous Omani renal ciliopathy syndrome patients. F1000Res 2021; 10:207. [PMID: 34354814 PMCID: PMC8290205 DOI: 10.12688/f1000research.40338.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice. In the investigation of inherited cystic kidney disease and renal ciliopathy syndromes, WES has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. The yield of WES critically depends on the characteristics of the patient population. Methods: In this study, we selected 8 unrelated Omani children, presenting with renal ciliopathy syndromes with a positive family history and originating from consanguineous families. We performed WES in affected children to determine the genetic cause of disease and to test the yield of this approach, coupled with homozygosity mapping, in this highly selected population. DNA library construction and WES was carried out using SureSelect Human All Exon V6 Enrichment Kit and Illumina HiSeq platform. For variants filtering and annotation Qiagen Variant Ingenuity tool was used. Nexus copy number software from BioDiscovery was used for evaluation of copy number variants and whole gene deletions. Patient and parental DNA was used to confirm mutations and the segregation of alleles using Sanger sequencing. Results: Genetic analysis identified 4 potential causative homozygous variants each confirmed by Sanger sequencing in 4 clinically relevant ciliopathy syndrome genes, ( TMEM231, TMEM138, WDR19 and BBS9), leading to an overall diagnostic yield of 50%. Conclusions: WES coupled with homozygosity mapping provided a diagnostic yield of 50% in this selected population. This genetic approach needs to be embedded into clinical practise to allow confirmation of clinical diagnosis, to inform genetic screening as well as family planning decisions. Half of the patients remain without diagnosis highlighting the technical and interpretational hurdles that need to be overcome in the future.
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Affiliation(s)
- Intisar Al Alawi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Mohammed Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Laura Powell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Issa Al Salmi
- Renal Medicine Department, Royal Hospital, Ministry of Health, Muscat, Oman
- Oman Medical Speciality Board, Muscat, Oman
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- Oman Medical Speciality Board, Muscat, Oman
- Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne, Tyne and Wear, NE45PL, UK
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6
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Al Alawi I, Al Riyami M, Barroso-Gil M, Powell L, Olinger E, Al Salmi I, Sayer JA. The diagnostic yield of whole exome sequencing as a first approach in consanguineous Omani renal ciliopathy syndrome patients. F1000Res 2021; 10:207. [PMID: 34354814 PMCID: PMC8290205 DOI: 10.12688/f1000research.40338.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice. In the investigation of inherited cystic kidney disease and renal ciliopathy syndromes, WES has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. The yield of WES critically depends on the characteristics of the patient population. Methods: In this study, we selected 8 unrelated Omani children, presenting with renal ciliopathy syndromes with a positive family history and originating from consanguineous families. We performed WES in affected children to determine the genetic cause of disease and to test the yield of this approach, coupled with homozygosity mapping, in this highly selected population. DNA library construction and WES was carried out using SureSelect Human All Exon V6 Enrichment Kit and Illumina HiSeq platform. For variants filtering and annotation Qiagen Variant Ingenuity tool was used. Nexus copy number software from BioDiscovery was used for evaluation of copy number variants and whole gene deletions. Patient and parental DNA was used to confirm mutations and the segregation of alleles using Sanger sequencing. Results: Genetic analysis identified 4 potential causative homozygous variants each confirmed by Sanger sequencing in 4 clinically relevant ciliopathy syndrome genes, ( TMEM231, TMEM138, WDR19 and BBS9), leading to an overall diagnostic yield of 50%. Conclusions: WES coupled with homozygosity mapping provided a diagnostic yield of 50% in this selected population. This genetic approach needs to be embedded into clinical practise to allow confirmation of clinical diagnosis, to inform genetic screening as well as family planning decisions. Half of the patients remain without diagnosis highlighting the technical and interpretational hurdles that need to be overcome in the future.
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Affiliation(s)
- Intisar Al Alawi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Mohammed Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Laura Powell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Issa Al Salmi
- Renal Medicine Department, Royal Hospital, Ministry of Health, Muscat, Oman
- Oman Medical Speciality Board, Muscat, Oman
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- Oman Medical Speciality Board, Muscat, Oman
- Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne, Tyne and Wear, NE45PL, UK
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7
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Park KJ, Lee W, Chun S, Min WK. The Frequency of Discordant Variant Classification in the Human Gene Mutation Database: A Comparison of the American College of Medical Genetics and Genomics Guidelines and ClinVar. Lab Med 2020; 52:250-259. [PMID: 32926152 DOI: 10.1093/labmed/lmaa072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE Discordant variant classifications among public databases is one of the well-documented limitations when interpreting the pathogenicity of variants. The aim of this study is to investigate the level of germline variant misannotation from the Human Gene Mutation Database (HGMD) and the annotation concordance between databases. METHODS We used a total of 188,106 classified variants (disease-causing mutations [n = 179,454] and polymorphisms [n = 8652]) in 6466 genes from the HGMD. All variants were reanalyzed based on the American College of Medical Genetics and Genomics (ACMG) guidelines and compared to ClinVar database variants. RESULTS When variants were classified based on the ACMG guidelines, misclassification was observed in 3.47% (2289/65,896) of variants. The overall concordance between HGMD and ClinVar was 97.62% (52,499/53,780) of variants studied. CONCLUSION Variants in databases must be used with caution when variant pathogenicity is interpreted. This study reveals the frequency of misannotation of the HGMD variants and annotation concordance between databases in depth.
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Affiliation(s)
- Kyoung-Jin Park
- Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang-Si, Gyeonggi-Do, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sail Chun
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Won-Ki Min
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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8
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Monasky MM, Micaglio E, Ciconte G, Pappone C. Brugada Syndrome: Oligogenic or Mendelian Disease? Int J Mol Sci 2020; 21:ijms21051687. [PMID: 32121523 PMCID: PMC7084676 DOI: 10.3390/ijms21051687] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 02/06/2023] Open
Abstract
Brugada syndrome (BrS) is diagnosed by a coved-type ST-segment elevation in the right precordial leads on the electrocardiogram (ECG), and it is associated with an increased risk of sudden cardiac death (SCD) compared to the general population. Although BrS is considered a genetic disease, its molecular mechanism remains elusive in about 70-85% of clinically-confirmed cases. Variants occurring in at least 26 different genes have been previously considered causative, although the causative effect of all but the SCN5A gene has been recently challenged, due to the lack of systematic, evidence-based evaluations, such as a variant's frequency among the general population, family segregation analyses, and functional studies. Also, variants within a particular gene can be associated with an array of different phenotypes, even within the same family, preventing a clear genotype-phenotype correlation. Moreover, an emerging concept is that a single mutation may not be enough to cause the BrS phenotype, due to the increasing number of common variants now thought to be clinically relevant. Thus, not only the complete list of genes causative of the BrS phenotype remains to be determined, but also the interplay between rare and common multiple variants. This is particularly true for some common polymorphisms whose roles have been recently re-evaluated by outstanding works, including considering for the first time ever a polygenic risk score derived from the heterozygous state for both common and rare variants. The more common a certain variant is, the less impact this variant might have on heart function. We are aware that further studies are warranted to validate a polygenic risk score, because there is no mutated gene that connects all, or even a majority, of BrS cases. For the same reason, it is currently impossible to create animal and cell line genetic models that represent all BrS cases, which would enable the expansion of studies of this syndrome. Thus, the best model at this point is the human patient population. Further studies should first aim to uncover genetic variants within individuals, as well as to collect family segregation data to identify potential genetic causes of BrS.
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Affiliation(s)
| | | | | | - Carlo Pappone
- Correspondence: ; Tel.: +39-0252-774260; Fax: +39-0252-774306
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9
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Paludan-Müller C, Ghouse J, Vad OB, Herfelt CB, Lundegaard P, Ahlberg G, Schmitt N, Svendsen JH, Haunsø S, Bundgaard H, Hansen T, Kanters JK, Olesen MS. Reappraisal of variants previously linked with sudden infant death syndrome: results from three population-based cohorts. Eur J Hum Genet 2019; 27:1427-1435. [PMID: 31043699 PMCID: PMC6777469 DOI: 10.1038/s41431-019-0416-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/21/2019] [Accepted: 04/06/2019] [Indexed: 12/23/2022] Open
Abstract
We aimed to investigate the pathogenicity of cardiac ion channel variants previously associated with SIDS. We reviewed SIDS-associated variants previously reported in databases and the literature in three large population-based cohorts; The ExAC database, the Inter99 study, and the UK Biobank (UKBB). Variants were classified according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Of the 92 SIDS-associated variants, 59 (64%) were present in ExAC, 18 (20%) in Inter99, and 24 (26%) in UKBB. Using the Inter99 cohort, we found no difference in J-point amplitude and QTc-interval between carriers and non-carriers for 14/18 variants. There was no difference in the risk of syncope (P = 0.32), malignant ventricular arrhythmia (P = 0.96), and all-cause mortality (P = 0.59) between carriers and non-carriers. The ACMG guidelines reclassified 75% of all variants as variant-of-uncertain significance, likely benign, and benign. We identified ~2/3 of variants previously associated with SIDS and found no significant associations with electrocardiographic traits, syncope, malignant ventricular arrhythmia, or all-cause mortality. These data indicate that many of these variants are not highly penetrant, monogenic causes of SIDS and underline the importance of frequent reappraisal of genetic variants to avoid future misdiagnosis.
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Affiliation(s)
- Christian Paludan-Müller
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Ghouse
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oliver B Vad
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie B Herfelt
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pia Lundegaard
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gustav Ahlberg
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicole Schmitt
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper H Svendsen
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stig Haunsø
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Unit for Inherited Cardiac Diseases, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Herlev and Gentofte University Hospitals, Copenhagen, Denmark
| | - Morten S Olesen
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Abstract
Brugada syndrome (BrS) is one of the most common causes of sudden cardiac death in normal structural heart individuals. First characterised in 1992, the global prevalence of BrS is unclear, with estimates placing it at around 0.05% and presenting most frequently in southeast Asian countries. This review aims to summarise the development in the understanding of BrS and, importantly, progress in its management, underpinned by knowledge regarding its genetics and molecular mechanisms. It also provides update on risk stratification and promising new therapies for BrS, including epicardial ablation. Future studies are required to increase understanding of the pathogenesis of this disease and to guide clinical practice.
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Affiliation(s)
- Jorge Romero
- Montefiore Medical Center, Albert Einstein College of Medicine Bronx, NY, US
| | - Dan L Li
- Montefiore Medical Center, Albert Einstein College of Medicine Bronx, NY, US.,Cardiovascular Division, Department of Medicine, Vanderbilt University Medical Center Nashville, TN, US
| | - Ricardo Avendano
- Montefiore Medical Center, Albert Einstein College of Medicine Bronx, NY, US.,Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine New Haven, CT, US
| | - Juan Carlos Diaz
- Montefiore Medical Center, Albert Einstein College of Medicine Bronx, NY, US
| | - Roderick Tung
- University of Chicago, School of Medicine Chicago, IL, US
| | - Luigi Di Biase
- Montefiore Medical Center, Albert Einstein College of Medicine Bronx, NY, US
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Ghorayeb N, Stein R, Daher DJ, Silveira ADD, Ritt LEF, Santos DFPD, Sierra APR, Herdy AH, Araújo CGSD, Colombo CSSDS, Kopiler DA, Lacerda FFRD, Lazzoli JK, Matos LDNJD, Leitão MB, Francisco RC, Alô ROB, Timerman S, Carvalho TD, Garcia TG. The Brazilian Society of Cardiology and Brazilian Society of Exercise and Sports Medicine Updated Guidelines for Sports and Exercise Cardiology - 2019. Arq Bras Cardiol 2019; 112:326-368. [PMID: 30916199 PMCID: PMC6424031 DOI: 10.5935/abc.20190048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Nabil Ghorayeb
- Instituto Dante Pazzanese de Cardiologia, São Paulo, SP - Brazil
- Hospital do Coração (HCor), Associação do Sanatório Sírio, São Paulo, SP - Brazil
- Programa de Pós-Graduação em Medicina do Esporte da Universidade Federal de São Paulo (UNIFESP), São Paulo, SP - Brazil
- Instituto de Assistência Médica ao Servidor Público Estadual (IAMSPE), São Paulo, SP - Brazil
| | - Ricardo Stein
- Programa de Pós-Graduação em Cardiologia e Ciências Cardiovasculares da Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS - Brazil
- Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul (HCPA/UFRGS), Porto Alegre, RS - Brazil
- Vitta Centro de Bem Estar Físico, Porto Alegre, RS - Brazil
| | - Daniel Jogaib Daher
- Hospital do Coração (HCor), Associação do Sanatório Sírio, São Paulo, SP - Brazil
| | - Anderson Donelli da Silveira
- Programa de Pós-Graduação em Cardiologia e Ciências Cardiovasculares da Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS - Brazil
- Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul (HCPA/UFRGS), Porto Alegre, RS - Brazil
- Vitta Centro de Bem Estar Físico, Porto Alegre, RS - Brazil
| | - Luiz Eduardo Fonteles Ritt
- Hospital Cárdio Pulmonar, Salvador, BA - Brazil
- Escola Bahiana de Medicina e Saúde Pública, Salvador, BA - Brazil
| | | | | | - Artur Haddad Herdy
- Instituto de Cardiologia de Santa Catarina, Florianópolis, SC - Brazil
- Clínica Cardiosport de Prevenção e Reabilitação, Florianópolis, SC - Brazil
| | | | - Cléa Simone Sabino de Souza Colombo
- Hospital do Coração (HCor), Associação do Sanatório Sírio, São Paulo, SP - Brazil
- Sports Cardiology, Cardiology Clinical Academic Group - St George's University of London,14 London - UK
| | - Daniel Arkader Kopiler
- Sociedade Brasileira de Medicina do Esporte e do Exercício (SBMEE), São Paulo, SP - Brazil
- Instituto Nacional de Cardiologia (INC), Rio de Janeiro, RJ - Brazil
| | - Filipe Ferrari Ribeiro de Lacerda
- Programa de Pós-Graduação em Cardiologia e Ciências Cardiovasculares da Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS - Brazil
| | - José Kawazoe Lazzoli
- Sociedade Brasileira de Medicina do Esporte e do Exercício (SBMEE), São Paulo, SP - Brazil
- Federação Internacional de Medicina do Esporte (FIMS), Lausanne - Switzerland
| | | | - Marcelo Bichels Leitão
- Sociedade Brasileira de Medicina do Esporte e do Exercício (SBMEE), São Paulo, SP - Brazil
| | - Ricardo Contesini Francisco
- Instituto Dante Pazzanese de Cardiologia, São Paulo, SP - Brazil
- Hospital do Coração (HCor), Associação do Sanatório Sírio, São Paulo, SP - Brazil
| | - Rodrigo Otávio Bougleux Alô
- Instituto Dante Pazzanese de Cardiologia, São Paulo, SP - Brazil
- Hospital Geral de São Mateus, São Paulo, SP - Brazil
| | - Sérgio Timerman
- Instituto do Coração da Faculdade de Medicina da Universidade de São Paulo (InCor-FMUSP), São Paulo, SP - Brazil
- Universidade Anhembi Morumbi, Laureate International Universities, São Paulo, SP - Brazil
| | - Tales de Carvalho
- Clínica Cardiosport de Prevenção e Reabilitação, Florianópolis, SC - Brazil
- Departamento de Ergometria e Reabilitação Cardiovascular da Sociedade Brasileira de Cardiologia (DERC/SBC), Rio de Janeiro, RJ - Brazil
- Universidade do Estado de Santa Catarina (UDESC), Florianópolis, SC - Brazil
| | - Thiago Ghorayeb Garcia
- Instituto Dante Pazzanese de Cardiologia, São Paulo, SP - Brazil
- Hospital do Coração (HCor), Associação do Sanatório Sírio, São Paulo, SP - Brazil
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12
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Yang Y, Hu D, Sacher F, Kusano KF, Li X, Barajas-Martinez H, Hocini M, Li Y, Gao Y, Shang H, Xing Y. Meta-Analysis of Risk Stratification of SCN5A With Brugada Syndrome: Is SCN5A Always a Marker of Low Risk? Front Physiol 2019; 10:103. [PMID: 30837887 PMCID: PMC6389868 DOI: 10.3389/fphys.2019.00103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/28/2019] [Indexed: 12/17/2022] Open
Abstract
Background: SCN5A with Brugada syndrome (BrS) is not commonly considered as an independent risk marker for subsequent cardiac events. However, the risk of SCN5A combined with other clinical characteristics has not been fully investigated. Objectives: The aim of this study is to investigate and evaluate risk stratification and related risk factors of SCN5A in BrS. Methods: The databases of PubMed, EMBASE, Cochrane Library, MEDLINE, Chinese National Knowledge Infrastructure (CNKI) and Wanfang Data were searched for related studies published from January 2002 to May 2018 followed by meta-analysis. The BrS patients who underwent SCN5A gene tests were included. The prognosis and risk stratification of SCN5A combined with symptoms and asymptoms diagnosis in BrS, electrophysiology study (EPS) were then investigated and evaluated. Outcomes were defined as ventricular tachycardia/fibrillation (VT/VF), sudden cardiac death (SCD). Results: Eleven suitable studies involving 1892 BrS patients who underwent SCN5A gene tests were identified. SCN5A (+) was not considered to be a significant predictor of future cardiac events (95% CI: 0.89-2.11; P = 0.15; I 2 = 0%). However, SCN5A (+) patients with symptoms at diagnosis revealed a higher prevalence of future VT/VF, SCD compared to SCN5A (-) patients with symptoms at diagnosis. (95% CI: 1.06-3.70; P = 0.03 I 2 = 0%) Among asymptomatic patients, the risk did not significantly differ between SCN5A (+) patients and SCN5A (-) patients. (95% CI: 0.51-4.72; P = 0.45 I 2 = 0 %). In an investigation involving patients in EPS (-) BrS electrocardiogram (ECG), the risk of SCN5A (+) is higher than that of SCN5A (-) (P < 0.001). Conclusions: In BrS patients with symptoms at diagnosis or EPS (-), the meta-analysis suggests that SCN5A (+) are at a higher risk of arrhythmic events than SCN5A (-).
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Affiliation(s)
- Yihan Yang
- Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, Beijing, China
- Beijing University of Chinese Medicine, Beijing, China
| | - Dan Hu
- Department of Cardiology and Cardiovascular Research Institution, Renmin Hospital of Wuhan University, Wuhan, China
| | - Frederic Sacher
- Hôpital Cardiologique Haut Lévêque, Lyric institute, Université de Bordeaux, Bordeaux-Pessac, France
| | - Kengo F. Kusano
- Division of Arrhythmia and Electrophysiology, Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Xinye Li
- Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, Beijing, China
- Beijing University of Chinese Medicine, Beijing, China
| | | | - Mélèze Hocini
- Hôpital Cardiologique Haut Lévêque, Lyric institute, Université de Bordeaux, Bordeaux-Pessac, France
| | - Yanda Li
- Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, Beijing, China
| | - Yonghong Gao
- Key Laboratory of Chinese Internal Medicine of the Ministry of Education, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - Hongcai Shang
- Key Laboratory of Chinese Internal Medicine of the Ministry of Education, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - Yanwei Xing
- Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, Beijing, China
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Andreasen L, Ghouse J, Skov MW, Have CT, Ahlberg G, Rasmussen PV, Linneberg A, Pedersen O, Platonov PG, Haunsø S, Svendsen JH, Hansen T, Kanters JK, Olesen MS. Brugada Syndrome-Associated Genetic Loci Are Associated With J-Point Elevation and an Increased Risk of Cardiac Arrest. Front Physiol 2018; 9:894. [PMID: 30042696 PMCID: PMC6048413 DOI: 10.3389/fphys.2018.00894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 06/21/2018] [Indexed: 12/19/2022] Open
Abstract
Introduction: A previous genome-wide association study found three genetic loci, rs9388451, rs10428132, and rs11708996, to increase the risk of Brugada Syndrome (BrS). Since the effect of these loci in the general population is unknown, we aimed to investigate the effect on electrocardiogram (ECG) parameters and outcomes in the general population. Materials and Methods: A cohort of 6,161 individuals (median age 45 [interquartile range (IQR) 40–50] years, 49% males), with available digital ECGs, was genotyped and subsequently followed for a median period of 13 [IQR 12.6–13.4] years. Data on outcomes were collected from Danish administrative healthcare registries. Furthermore, ~400,000 persons from UK Biobank were investigated for associations between the three loci and cardiac arrest/ventricular fibrillation (VF). Results: Homozygote carriers of the C allele in rs6800541 intronic to SCN10A had a significantly larger J-point elevation (JPE) compared with wildtype carriers (11 vs. 6 μV, P < 0.001). There was an additive effect of carrying multiple BrS-associated risk alleles with an increased JPE in lead V1. None of the BrS-associated genetic loci predisposed to syncope, atrial fibrillation, or total mortality in the general Danish population. The rs9388451 genetic locus adjacent to the HEY2 gene was associated with cardiac arrest/VF in an analysis using the UK Biobank study (odds ratio = 1.13 (95% confidence interval: 1.08–1.18), P = 0.006). Conclusions: BrS-associated risk alleles increase the JPE in lead V1 in an additive manner, but was not associated with increased mortality or syncope in the general population of Denmark. However, the HEY2 risk allele increased the risk of cardiac arrest/VF in the larger population study of UK Biobank indicating an important role of this common genetic locus.
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Affiliation(s)
- Laura Andreasen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jonas Ghouse
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten W Skov
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christian T Have
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Gustav Ahlberg
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peter V Rasmussen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Allan Linneberg
- Research Centre for Prevention and Health, Copenhagen, Denmark.,Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Pyotr G Platonov
- Center for Integrative Electrocardiology at Lund University, Arrhythmia Clinic, Skåne University Hospital, Lund, Sweden
| | - Stig Haunsø
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Medicine and Surgery, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper H Svendsen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Medicine and Surgery, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten S Olesen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark.,Laboratory for Molecular Cardiology, Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Abstract
The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.
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15
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Paludan-Müller C, Ahlberg G, Ghouse J, Svendsen JH, Haunsø S, Olesen MS. Analysis of 60 706 Exomes Questions the Role of De Novo Variants Previously Implicated in Cardiac Disease. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.117.001878. [DOI: 10.1161/circgenetics.117.001878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/20/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Christian Paludan-Müller
- From the Laboratory for Molecular Cardiology, Institute for Biomedical Sciences, University of Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Laboratory for Molecular Cardiology, Department of Cardiology, Heart Centre at Rigshospitalet, Copenhagen University Hospital, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); and Department of Clinical
| | - Gustav Ahlberg
- From the Laboratory for Molecular Cardiology, Institute for Biomedical Sciences, University of Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Laboratory for Molecular Cardiology, Department of Cardiology, Heart Centre at Rigshospitalet, Copenhagen University Hospital, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); and Department of Clinical
| | - Jonas Ghouse
- From the Laboratory for Molecular Cardiology, Institute for Biomedical Sciences, University of Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Laboratory for Molecular Cardiology, Department of Cardiology, Heart Centre at Rigshospitalet, Copenhagen University Hospital, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); and Department of Clinical
| | - Jesper H. Svendsen
- From the Laboratory for Molecular Cardiology, Institute for Biomedical Sciences, University of Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Laboratory for Molecular Cardiology, Department of Cardiology, Heart Centre at Rigshospitalet, Copenhagen University Hospital, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); and Department of Clinical
| | - Stig Haunsø
- From the Laboratory for Molecular Cardiology, Institute for Biomedical Sciences, University of Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Laboratory for Molecular Cardiology, Department of Cardiology, Heart Centre at Rigshospitalet, Copenhagen University Hospital, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); and Department of Clinical
| | - Morten S. Olesen
- From the Laboratory for Molecular Cardiology, Institute for Biomedical Sciences, University of Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Laboratory for Molecular Cardiology, Department of Cardiology, Heart Centre at Rigshospitalet, Copenhagen University Hospital, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark (C.P.-M., G.A., J.G., J.H.S., S.H., M.S.O.); and Department of Clinical
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16
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Abstract
The Brugada syndrome is an inherited channelopathy associated with increased risk of ventricular arrhythmias and sudden death, often occurring during sleep or resting conditions. Although this entity has been described more than 20 years ago, it remains one of the most debated among channelopathies, with several open questions on its genetic substrate, arrhythmia mechanisms, and clinical management. Studies on the genetics and physiopathology bases of the Brugada syndrome have opened novel investigative pathways and concepts that are now entering the field of cardiovascular genetics and are applied to other inherited arrhythmias. In this perspective, Brugada syndrome can be seen as an example on how basic science discoveries have influenced clinical management and led to novel therapeutic approaches.
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Affiliation(s)
- Marina Cerrone
- Cardiovascular Genetics Program, Leon H. Charney Division of Cardiology, New York University School of Medicine, New York, NY.
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17
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Ghouse J, Skov MW, Bigseth RS, Ahlberg G, Kanters JK, Olesen MS. Distinguishing pathogenic mutations from background genetic noise in cardiology: The use of large genome databases for genetic interpretation. Clin Genet 2017; 93:459-466. [PMID: 28589536 DOI: 10.1111/cge.13066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
Advances in clinical genetic testing have led to increased insight into the human genome, including how challenging it is to interpret rare genetic variation. In some cases, the ability to detect genetic mutations exceeds the ability to understand their clinical impact, limiting the advantage of these technologies. Obstacles in genomic medicine are many and include: understanding the level of certainty/uncertainty behind pathogenicity determination, the numerous different variant interpretation-guidelines used by clinical laboratories, delivering the certain or uncertain result to the patient, helping patients evaluate medical decisions in light of uncertainty regarding the consequence of the findings. Through publication of large publicly available exome/genome databases, researchers and physicians are now able to highlight dubious variants previously associated with different cardiac traits. Also, continuous efforts through data sharing, international collaborative efforts to develop disease-gene-specific guidelines, and computational analyses using large data, will indubitably assist in better variant interpretation and classification. This article discusses the current, and quickly changing, state of variant interpretation resources within cardiovascular genetic research, e.g., publicly available databases and ways of how cardiovascular genetic counselors and geneticists can aid in improving variant interpretation in cardiology.
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Affiliation(s)
- J Ghouse
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - M W Skov
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - R S Bigseth
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - G Ahlberg
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - J K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - M S Olesen
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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18
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Dewar LJ, Alcaide M, Fornika D, D’Amato L, Shafaatalab S, Stevens CM, Balachandra T, Phillips SM, Sanatani S, Morin RD, Tibbits GF. Investigating the Genetic Causes of Sudden Unexpected Death in Children Through Targeted Next-Generation Sequencing Analysis. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.116.001738. [DOI: 10.1161/circgenetics.116.001738] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 04/25/2017] [Indexed: 12/27/2022]
Abstract
Background—
Inherited arrhythmia syndromes are responsible for a significant portion of autopsy-negative sudden unexpected death (SUD) cases, but molecular autopsy used to identify potentially causal variants is not routinely included in SUD investigations. We collaborated with a medical examiner's office to assist in finding a diagnosis for their autopsy-negative child SUD cases.
Methods and Results—
191 child SUD cases (<5 years of age) were selected for analyses. Our next generation sequencing panel incorporated 38 inherited arrhythmia syndrome candidate genes and another 33 genes not previously investigated for variants that may underlie SUDY pathophysiology. Overall, we identified 11 potentially causal disease-associated variants in 12 cases, for an overall yield of 6.3%. We also identified 31 variants of uncertain significance in 36 cases and 16 novel variants predicted to be pathogenic in silico in 15 cases. The disease-associated variants were reported to the medical examiner to notify surviving relatives and recommend clinical assessment.
Conclusions—
We have identified variants that may assist in the diagnosis of at least 6.3% of autopsy-negative child SUD cases and reduce risk of future SUD in surviving relatives. We recommend a cautious approach to variant interpretation. We also suggest inclusion of cardiomyopathy genes as well as other candidate SUD genes in molecular autopsy analyses.
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Affiliation(s)
- Laura J. Dewar
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Miguel Alcaide
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Daniel Fornika
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Luisa D’Amato
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Sanam Shafaatalab
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Charles M. Stevens
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Thambirajah Balachandra
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Susan M. Phillips
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Shubhayan Sanatani
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Ryan D. Morin
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Glen F. Tibbits
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
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19
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Haggerty CM, James CA, Calkins H, Tichnell C, Leader JB, Hartzel DN, Nevius CD, Pendergrass SA, Person TN, Schwartz M, Ritchie MD, Carey DJ, Ledbetter DH, Williams MS, Dewey FE, Lopez A, Penn J, Overton JD, Reid JG, Lebo M, Mason-Suares H, Austin-Tse C, Rehm HL, Delisle BP, Makowski DJ, Mehra VC, Murray MF, Fornwalt BK. Electronic health record phenotype in subjects with genetic variants associated with arrhythmogenic right ventricular cardiomyopathy: a study of 30,716 subjects with exome sequencing. Genet Med 2017; 19:1245-1252. [PMID: 28471438 PMCID: PMC5671380 DOI: 10.1038/gim.2017.40] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/03/2017] [Indexed: 01/24/2023] Open
Abstract
Purpose Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart disease. Clinical follow-up of incidental findings in ARVC-associated genes is recommended. We aimed to determine the prevalence of disease thus ascertained. Methods 30,716 individuals underwent exome sequencing. Variants in PKP2, DSG2, DSC2, DSP, JUP, TMEM43, or TGFβ3 that were database-listed as pathogenic or likely pathogenic were identified and evidence-reviewed. For subjects with putative loss-of-function (pLOF) variants or variants of uncertain significance (VUS), electronic health records (EHR) were reviewed for ARVC diagnosis, diagnostic criteria, and International Classification of Diseases (ICD-9) codes. Results 18 subjects had pLOF variants; none had an EHR diagnosis of ARVC. Of 14 patients with an electrocardiogram (ECG), one had a minor diagnostic criterion, 13 were normal. 184 subjects had VUSs; none had an ARVC diagnosis. In subjects with VUSs, there was no difference in the proportion with major (4%) or minor (13%) ECG diagnostic criteria compared to variant-negative controls. ICD-9 codes showed no difference in defibrillator utilization, electrophysiologic abnormalities or non-ischemic cardiomyopathies in patients with pLOF or VUSs compared to controls. Conclusion pLOF variants in an unselected cohort were not associated with ARVC phenotypes based on EHR review. The negative predictive value of EHR review remains uncertain.
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Affiliation(s)
- Christopher M Haggerty
- Department of Imaging Science and Innovation, Geisinger Health System, Danville, Pennsylvania, USA
| | - Cynthia A James
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hugh Calkins
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Crystal Tichnell
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joseph B Leader
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Dustin N Hartzel
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Christopher D Nevius
- Department of Imaging Science and Innovation, Geisinger Health System, Danville, Pennsylvania, USA
| | - Sarah A Pendergrass
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Thomas N Person
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Marci Schwartz
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Marylyn D Ritchie
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - David J Carey
- Weis Center for Health Research, Geisinger Health System, Danville, Pennsylvania, USA
| | - David H Ledbetter
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Frederick E Dewey
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Alexander Lopez
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - John Penn
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - John D Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Jeffrey G Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Matthew Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Christina Austin-Tse
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian P Delisle
- Department of Physiology, University of Kentucky, Lexington, Kentucky, USA
| | - Daniel J Makowski
- Division of Cardiology, Geisinger Health System, Danville, Pennsylvania, USA
| | - Vishal C Mehra
- Division of Cardiology, Geisinger Health System, Danville, Pennsylvania, USA
| | - Michael F Murray
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Brandon K Fornwalt
- Department of Imaging Science and Innovation, Geisinger Health System, Danville, Pennsylvania, USA
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20
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Kobayashi Y, Yang S, Nykamp K, Garcia J, Lincoln SE, Topper SE. Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Genome Med 2017; 9:13. [PMID: 28166811 PMCID: PMC5295186 DOI: 10.1186/s13073-017-0403-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/13/2017] [Indexed: 12/25/2022] Open
Abstract
Background The frequency of a variant in the general population is a key criterion used in the clinical interpretation of sequence variants. With certain exceptions, such as founder mutations, the rarity of a variant is a prerequisite for pathogenicity. However, defining the threshold at which a variant should be considered “too common” is challenging and therefore diagnostic laboratories have typically set conservative allele frequency thresholds. Methods Recent publications of large population sequencing data, such as the Exome Aggregation Consortium (ExAC) database, provide an opportunity to characterize with accuracy and precision the frequency distributions of very rare disease-causing alleles. Allele frequencies of pathogenic variants in ClinVar, as well as variants expected to be pathogenic through the nonsense-mediated decay (NMD) pathway, were analyzed to study the burden of pathogenic variants in 79 genes of clinical importance. Results Of 1364 BRCA1 and BRCA2 variants that are well characterized as pathogenic or that are expected to lead to NMD, 1350 variants had an allele frequency of less than 0.0025%. The remaining 14 variants were previously published founder mutations. Importantly, we observed no difference in the distributions of pathogenic variants expected to be lead to NMD compared to those that are not. Therefore, we expanded the analysis to examine the distributions of NMD expected variants in 77 additional genes. These 77 genes were selected to represent a broad set of clinical areas, modes of inheritance, and penetrance. Among these variants, most (97.3%) had an allele frequency of less than 0.01%. Furthermore, pathogenic variants with allele frequencies greater than 0.01% were well characterized in publications and included many founder mutations. Conclusions The observations made in this study suggest that, with certain caveats, a very low allele frequency threshold can be adopted to more accurately interpret sequence variants. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0403-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuya Kobayashi
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA.
| | - Shan Yang
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| | - Keith Nykamp
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| | - John Garcia
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| | | | - Scott E Topper
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
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