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Hiniesto-Iñigo I, Sridhar A, Louradour J, De la Cruz A, Lundholm S, Jauregi-Miguel A, Giannetti F, Sala L, Odening KE, Larsson HP, Ottosson NE, Liin SI. Rescue of loss-of-function long QT syndrome-associated mutations in K V7.1/KCNE1 by the endocannabinoid N-arachidonoyl-L-serine (ARA-S). Br J Pharmacol 2025. [PMID: 40083204 DOI: 10.1111/bph.70008] [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: 07/17/2024] [Revised: 12/19/2024] [Accepted: 01/17/2025] [Indexed: 03/16/2025] Open
Abstract
BACKGROUND AND PURPOSE Congenital long QT syndrome (LQTS) involves genetic mutations affecting ion channels, leading to a prolonged QT interval and increased risk of potentially lethal ventricular arrhythmias. Mutations in the genes encoding KV7.1/KCNE1 are the most frequent, with channel loss-of-function contributing to LQTS. The endocannabinoid N-arachidonoyl-L-serine (ARA-S) has been shown to facilitate activation of wild type KV7.1/KCNE1 channels and to counteract a prolonged QT interval in isolated guinea pig hearts. In this study, we examine the ability of ARA-S to facilitate activation of LQTS-associated mutations, in various regions of the channel, and hence to counteract loss-of-function. EXPERIMENTAL APPROACH The two-electrode voltage clamp technique on Xenopus oocytes expressing human KV7.1/KCNE1 channels was used to investigate the effects of ARA-S in 20 LQTS type 1-associated mutations distributed across the channel. Thereafter, different electrophysiology was used to assess ARA-S effects in mammalian cells. KEY RESULTS ARA-S enhanced the function of all mutated channels by shifting V50 and increasing current amplitude. However, the magnitude of effect varied, related to whether mutations were in one of the two putative ARA-S binding sites on the channel as suggested by molecular dynamics simulations. ARA-S displayed translational potential by facilitating channel opening in mammalian cells and shortening the action potential duration in cardiomyocytes. CONCLUSIONS AND IMPLICATIONS This study demonstrates the rescuing capability of ARA-S on a diverse set of LQTS mutants. These insights may aid in developing drug compounds using ARA-S sites and mechanisms and guide interpretation of which LQTS mutants respond well to such compounds.
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Affiliation(s)
- Irene Hiniesto-Iñigo
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Akshay Sridhar
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Julien Louradour
- Translational Cardiology, Department of Physiology and Department of Cardiology, University of Bern, University Hospital Bern, Bern, Switzerland
| | - Alicia De la Cruz
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Siri Lundholm
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Amaia Jauregi-Miguel
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Chemical Biology Consortium Sweden (CBCS), SciLifeLab, Stockholm, Sweden
| | - Federica Giannetti
- Istituto Auxologico Italiano IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy
| | - Luca Sala
- Istituto Auxologico Italiano IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Katja E Odening
- Translational Cardiology, Department of Physiology and Department of Cardiology, University of Bern, University Hospital Bern, Bern, Switzerland
| | - H Peter Larsson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Nina E Ottosson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Chemical Biology Consortium Sweden (CBCS), SciLifeLab, Stockholm, Sweden
| | - Sara I Liin
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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Kekenes-Huskey PM, Burgess DE, Sun B, Bartos DC, Rozmus ER, Anderson CL, January CT, Eckhardt LL, Delisle BP. Mutation-Specific Differences in Kv7.1 ( KCNQ1) and Kv11.1 ( KCNH2) Channel Dysfunction and Long QT Syndrome Phenotypes. Int J Mol Sci 2022; 23:7389. [PMID: 35806392 PMCID: PMC9266926 DOI: 10.3390/ijms23137389] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
The electrocardiogram (ECG) empowered clinician scientists to measure the electrical activity of the heart noninvasively to identify arrhythmias and heart disease. Shortly after the standardization of the 12-lead ECG for the diagnosis of heart disease, several families with autosomal recessive (Jervell and Lange-Nielsen Syndrome) and dominant (Romano-Ward Syndrome) forms of long QT syndrome (LQTS) were identified. An abnormally long heart rate-corrected QT-interval was established as a biomarker for the risk of sudden cardiac death. Since then, the International LQTS Registry was established; a phenotypic scoring system to identify LQTS patients was developed; the major genes that associate with typical forms of LQTS were identified; and guidelines for the successful management of patients advanced. In this review, we discuss the molecular and cellular mechanisms for LQTS associated with missense variants in KCNQ1 (LQT1) and KCNH2 (LQT2). We move beyond the "benign" to a "pathogenic" binary classification scheme for different KCNQ1 and KCNH2 missense variants and discuss gene- and mutation-specific differences in K+ channel dysfunction, which can predispose people to distinct clinical phenotypes (e.g., concealed, pleiotropic, severe, etc.). We conclude by discussing the emerging computational structural modeling strategies that will distinguish between dysfunctional subtypes of KCNQ1 and KCNH2 variants, with the goal of realizing a layered precision medicine approach focused on individuals.
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Affiliation(s)
- Peter M. Kekenes-Huskey
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Don E. Burgess
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.E.B.); (E.R.R.)
| | - Bin Sun
- Department of Pharmacology, Harbin Medical University, Harbin 150081, China;
| | | | - Ezekiel R. Rozmus
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.E.B.); (E.R.R.)
| | - Corey L. Anderson
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (C.L.A.); (C.T.J.); (L.L.E.)
| | - Craig T. January
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (C.L.A.); (C.T.J.); (L.L.E.)
| | - Lee L. Eckhardt
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (C.L.A.); (C.T.J.); (L.L.E.)
| | - Brian P. Delisle
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.E.B.); (E.R.R.)
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3
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Bains S, Dotzler SM, Krijger C, Giudicessi JR, Ye D, Bikker H, Rohatgi RK, Tester DJ, Bos JM, Wilde AAM, Ackerman MJ. A phenotype-enhanced variant classification framework to decrease the burden of missense variants of uncertain significance in type 1 long QT syndrome. Heart Rhythm 2021; 19:435-442. [PMID: 34798354 DOI: 10.1016/j.hrthm.2021.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Pathogenic/likely pathogenic (P/LP) variants in the KCNQ1-encoded Kv7.1 potassium channel cause type 1 long QT syndrome (LQT1). Despite the revamped 2015 American College of Medical Genetics (ACMG) variant interpretation guidelines, the burden of KCNQ1 variants of uncertain significance (VUS) in patients with LQTS remains ∼30%. OBJECTIVE The purpose of this study was to determine whether a phenotype-enhanced (PE) variant classification approach could reduce the VUS burden in LQTS genetic testing. METHODS Retrospective analysis was performed on 79 KCNQ1 missense variants in 356 patients from Mayo Clinic and an independent cohort of 42 variants in 225 patients from Amsterdam University Medical Center (UMC). Each variant was classified initially using the ACMG guidelines and then readjudicated using a PE-ACMG framework that incorporated the LQTS clinical diagnostic Schwartz score plus 4 "LQT1-defining features": broad-based/slow upstroke T waves, syncope/seizure during exertion, swimming-associated events, and a maladaptive LQT1 treadmill stress test. RESULTS According to the ACMG guidelines, Mayo Clinic variants were classified as follows: 17 of 79 P variants (22%), 34 of 79 LP variants (43%), and 28 of 79 VUS (35%). Similarly, for Amsterdam UMC, the variant distribution was 9 of 42 P variants (22%), 14 of 42 LP variants (33%), and 19 of 42 variants VUS (45%). After PE-ACMG readjudication, the total VUS burden decreased significantly from 28 (35%) to 13 (16%) (P = .0007) for Mayo Clinic and from 19 (45%) to 12 (29%) (P = .02) for Amsterdam UMC. CONCLUSION Phenotype-guided variant adjudication decreased significantly the VUS burden of LQT1 case-derived KCNQ1 missense variants in 2 independent cohorts. This study demonstrates the value of incorporating LQT1-specific phenotype/clinical data to aid in the interpretation of KCNQ1 missense variants identified during genetic testing for LQTS.
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Affiliation(s)
- Sahej Bains
- Medical Scientist Training Program, Mayo Clinic, Rochester, Minnesota; Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Steven M Dotzler
- Medical Scientist Training Program, Mayo Clinic, Rochester, Minnesota; Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Christian Krijger
- Department of Experimental Cardiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - John R Giudicessi
- Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, Minnesota
| | - Dan Ye
- Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Hennie Bikker
- Department of Human Genetics, University of Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Ram K Rohatgi
- Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), Mayo Clinic, Rochester, Minnesota
| | - David J Tester
- Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, Minnesota; Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), Mayo Clinic, Rochester, Minnesota
| | - J Martijn Bos
- Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, Minnesota; Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), Mayo Clinic, Rochester, Minnesota
| | - Arthur A M Wilde
- Department of Experimental Cardiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Department of Cardiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael J Ackerman
- Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, Minnesota; Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), Mayo Clinic, Rochester, Minnesota.
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4
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Isogenic Sets of hiPSC-CMs Harboring Distinct KCNH2 Mutations Differ Functionally and in Susceptibility to Drug-Induced Arrhythmias. Stem Cell Reports 2021; 15:1127-1139. [PMID: 33176122 PMCID: PMC7664051 DOI: 10.1016/j.stemcr.2020.10.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/26/2022] Open
Abstract
Mutations in KCNH2 can lead to long QT syndrome type 2. Variable disease manifestation observed with this channelopathy is associated with the location and type of mutation within the protein, complicating efforts to predict patient risk. Here, we demonstrated phenotypic differences in cardiomyocytes derived from isogenic human induced pluripotent stem cells (hiPSC-CMs) genetically edited to harbor mutations either within the pore or tail region of the ion channel. Electrophysiological analysis confirmed that the mutations prolonged repolarization of the hiPSC-CMs, with differences between the mutations evident in monolayer cultures. Blocking the hERG channel revealed that the pore-loop mutation conferred greater susceptibility to arrhythmic events. These findings showed that subtle phenotypic differences related to KCNH2 mutations could be captured by hiPSC-CMs under genetically matched conditions. Moreover, the results support hiPSC-CMs as strong candidates for evaluating the underlying severity of individual KCNH2 mutations in humans, which could facilitate patient risk stratification. Mutation-specific differences detected in hiPSC-CMs with same genetic background APD and FPD in the hERG pore variant hiPSC-CMs more prolonged than the tail variant The pore variant was also more susceptible to drug-induced arrhythmic events Potential strategy to determine KCNH2 mutation-specific arrhythmic risk
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Leonard RJ, Preston CC, Gucwa ME, Afeworki Y, Selya AS, Faustino RS. Protein Subdomain Enrichment of NUP155 Variants Identify a Novel Predicted Pathogenic Hotspot. Front Cardiovasc Med 2020; 7:8. [PMID: 32118046 PMCID: PMC7019101 DOI: 10.3389/fcvm.2020.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/17/2020] [Indexed: 01/05/2023] Open
Abstract
Functional variants in nuclear envelope genes are implicated as underlying causes of cardiopathology. To examine the potential association of single nucleotide variants of nucleoporin genes with cardiac disease, we employed a prognostic scoring approach to investigate variants of NUP155, a nucleoporin gene clinically linked with atrial fibrillation. Here we implemented bioinformatic profiling and predictive scoring, based on the gnomAD, National Heart Lung and Blood Institute-Exome Sequencing Project (NHLBI-ESP) Exome Variant Server, and dbNSFP databases to identify rare single nucleotide variants (SNVs) of NUP155 potentially associated with cardiopathology. This predictive scoring revealed 24 SNVs of NUP155 as potentially cardiopathogenic variants located primarily in the N-terminal crescent-shaped domain of NUP155. In addition, a predicted NUP155 R672G variant prioritized in our study was mapped to a region within the alpha helical stack of the crescent domain of NUP155. Bioinformatic analysis of inferred protein-protein interactions of NUP155 revealed over representation of top functions related to molecular transport, RNA trafficking, and RNA post-transcriptional modification. Topology analysis revealed prioritized hubs critical for maintaining network integrity and informational flow that included FN1, SIRT7, and CUL7 with nodal enrichment of RNA helicases in the topmost enriched subnetwork. Furthermore, integration of the top 5 subnetworks to capture network topology of an expanded framework revealed that FN1 maintained its hub status, with elevation of EED, CUL3, and EFTUD2. This is the first study to report novel discovery of a NUP155 subdomain hotspot that enriches for allelic variants of NUP155 predicted to be clinically damaging, and supports a role for RNA metabolism in cardiac disease and development.
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Affiliation(s)
- Riley J. Leonard
- Genetics and Genomics Group, Sanford Research, Sioux Falls, SD, United States
- Department of Biology, College of St. Benedict/St. John's University, Collegeville, MN, United States
| | - Claudia C. Preston
- Genetics and Genomics Group, Sanford Research, Sioux Falls, SD, United States
| | - Melanie E. Gucwa
- Genetics and Genomics Group, Sanford Research, Sioux Falls, SD, United States
- Department of Biology, Carthage College, Kenosha, WI, United States
| | - Yohannes Afeworki
- Functional Genomics & Bioinformatics Core Facility, Sanford Research, Sioux Falls, SD, United States
| | - Arielle S. Selya
- Behavioral Sciences Group, Sanford Research, Sioux Falls, SD, United States
| | - Randolph S. Faustino
- Genetics and Genomics Group, Sanford Research, Sioux Falls, SD, United States
- Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, United States
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6
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Giudicessi JR. Machine Learning and Rare Variant Adjudication in Type 1 Long QT Syndrome. ACTA ACUST UNITED AC 2019; 10:CIRCGENETICS.117.001944. [PMID: 29021308 DOI: 10.1161/circgenetics.117.001944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- John R Giudicessi
- From the Departments of Cardiovascular Medicine and Internal Medicine (Clinician-Investigator Training Program), Mayo Clinic, Rochester, MN.
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7
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Jones EG, Mazaheri N, Maroofian R, Zamani M, Seifi T, Sedaghat A, Shariati G, Jamshidi Y, Allen HD, Wehrens XHT, Galehdari H, Landstrom AP. Analysis of enriched rare variants in JPH2-encoded junctophilin-2 among Greater Middle Eastern individuals reveals a novel homozygous variant associated with neonatal dilated cardiomyopathy. Sci Rep 2019; 9:9038. [PMID: 31227780 PMCID: PMC6588559 DOI: 10.1038/s41598-019-44987-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
Junctophilin-2 (JPH2) is a part of the junctional membrane complex that facilitates calcium-handling in the cardiomyocyte. Previously, missense variants in JPH2 have been linked to hypertrophic cardiomyopathy; however, pathogenic "loss of function" (LOF) variants have not been described. Family-based genetic analysis of GME individuals with cardiomyopathic disease identified an Iranian patient with dilated cardiomyopathy (DCM) as a carrier of a novel, homozygous single nucleotide insertion in JPH2 resulting in a stop codon (JPH2-p.E641*). A second Iranian family with consanguineous parents hosting an identical heterozygous variant had 2 children die in childhood from cardiac failure. To characterize ethnicity-dependent genetic variability in JPH2 and to identify homozygous JPH2 variants associated with cardiac disease, we identified variants in JPH2 in a worldwide control cohort (gnomAD) and 2 similar cohorts from the Greater Middle East (GME Variome, Iranome). These were compared against ethnicity-matched clinical whole exome sequencing (WES) referral tests and a case cohort of individuals with hypertrophic cardiomyopathy (HCM) based on comprehensive review of the literature. Worldwide, 1.45% of healthy individuals hosted a rare JPH2 variant with a significantly higher proportion among GME individuals (4.45%); LOF variants were rare overall (0.04%) yet were most prevalent in GME (0.21%). The increased prevalence of LOF variants in GME individuals was corroborated among region-specific, clinical WES cohorts. In conclusion, we report ethnic-specific differences in JPH2 rare variants, with GME individuals being at higher risk of hosting homozygous LOF variants. This conclusion is supported by the identification of a novel JPH2 LOF variant confirmed by segregation analysis resulting in autosomal recessive pediatric DCM due to presumptive JPH2 truncation.
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Affiliation(s)
- Edward G Jones
- Department of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine, Houston, Texas, United States
| | - Neda Mazaheri
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Reza Maroofian
- Molecular and Clinical Sciences Institute, St George's University of London, London, United Kingdom
| | - Mina Zamani
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Tahereh Seifi
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Alireza Sedaghat
- Diabetes Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Yalda Jamshidi
- Molecular and Clinical Sciences Institute, St George's University of London, London, United Kingdom
| | - Hugh D Allen
- Department of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine, Houston, Texas, United States
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, United States
| | - Xander H T Wehrens
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular Physiology and Biophysics, Department of Medicine, Section of Cardiology, Center for Space Medicine, Baylor College of Medicine, Houston, Texas, United States
| | - Hamid Galehdari
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Andrew P Landstrom
- Department of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine, Houston, Texas, United States.
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, United States.
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, United States.
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8
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Kapplinger JD, Pundi KN, Larson NB, Callis TE, Tester DJ, Bikker H, Wilde AAM, Ackerman MJ. Yield of the RYR2 Genetic Test in Suspected Catecholaminergic Polymorphic Ventricular Tachycardia and Implications for Test Interpretation. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e001424. [PMID: 29453246 DOI: 10.1161/circgen.116.001424] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 12/18/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Pathogenic RYR2 variants account for ≈60% of clinically definite cases of catecholaminergic polymorphic ventricular tachycardia. However, the rate of rare benign RYR2 variants identified in the general population remains a challenge for genetic test interpretation. Therefore, we examined the results of the RYR2 genetic test among patients referred for commercial genetic testing and examined factors impacting variant interpretability. METHODS Frequency and location comparisons were made for RYR2 variants identified among 1355 total patients of varying clinical certainty and 60 706 Exome Aggregation Consortium controls. The impact of the clinical phenotype on the yield of RYR2 variants was examined. Six in silico tools were assessed using patient- and control-derived variants. RESULTS A total of 18.2% (218/1200) of patients referred for commercial testing hosted rare RYR2 variants, statistically less than the 59% (46/78) yield among clinically definite cases, resulting in a much higher potential genetic false discovery rate among referrals considering the 3.2% background rate of rare, benign RYR2 variants. Exclusion of clearly putative pathogenic variants further complicates the interpretation of the next novel RYR2 variant. Exonic/topologic analyses revealed overrepresentation of patient variants in exons covering only one third of the protein. In silico tools largely failed to show evidence toward enhancement of variant interpretation. CONCLUSIONS Current expert recommendations have resulted in increased use of RYR2 genetic testing in patients with questionable clinical phenotypes. Using the largest to date catecholaminergic polymorphic ventricular tachycardia patient versus control comparison, this study highlights important variables in the interpretation of variants to overcome the 3.2% background rate that confounds RYR2 variant interpretation.
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Affiliation(s)
- Jamie D Kapplinger
- From the Mayo Clinic School of Medicine (J.D.K., M.J.A.), Medical Scientist Training Program (J.D.K., M.J.A.), Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory (J.D.K., D.J.T., M.J.A.), Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (N.B.L.), Division of Heart Rhythm Services, Department of Cardiovascular Diseases (D.J.T., M.J.A.), and Division of Pediatric Cardiology, Department of Pediatrics (M.J.A.), Mayo Clinic, Rochester, MN; Department of Medicine, Stanford University, Stanford, CA (K.N.P.); Transgenomic Inc, New Haven, CT (T.E.C.); and Department of Clinical Genetics (H.B.) and Heart Centre, Department of Clinical and Experimental Cardiology (A.A.M.W.), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Krishna N Pundi
- From the Mayo Clinic School of Medicine (J.D.K., M.J.A.), Medical Scientist Training Program (J.D.K., M.J.A.), Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory (J.D.K., D.J.T., M.J.A.), Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (N.B.L.), Division of Heart Rhythm Services, Department of Cardiovascular Diseases (D.J.T., M.J.A.), and Division of Pediatric Cardiology, Department of Pediatrics (M.J.A.), Mayo Clinic, Rochester, MN; Department of Medicine, Stanford University, Stanford, CA (K.N.P.); Transgenomic Inc, New Haven, CT (T.E.C.); and Department of Clinical Genetics (H.B.) and Heart Centre, Department of Clinical and Experimental Cardiology (A.A.M.W.), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Nicholas B Larson
- From the Mayo Clinic School of Medicine (J.D.K., M.J.A.), Medical Scientist Training Program (J.D.K., M.J.A.), Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory (J.D.K., D.J.T., M.J.A.), Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (N.B.L.), Division of Heart Rhythm Services, Department of Cardiovascular Diseases (D.J.T., M.J.A.), and Division of Pediatric Cardiology, Department of Pediatrics (M.J.A.), Mayo Clinic, Rochester, MN; Department of Medicine, Stanford University, Stanford, CA (K.N.P.); Transgenomic Inc, New Haven, CT (T.E.C.); and Department of Clinical Genetics (H.B.) and Heart Centre, Department of Clinical and Experimental Cardiology (A.A.M.W.), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Thomas E Callis
- From the Mayo Clinic School of Medicine (J.D.K., M.J.A.), Medical Scientist Training Program (J.D.K., M.J.A.), Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory (J.D.K., D.J.T., M.J.A.), Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (N.B.L.), Division of Heart Rhythm Services, Department of Cardiovascular Diseases (D.J.T., M.J.A.), and Division of Pediatric Cardiology, Department of Pediatrics (M.J.A.), Mayo Clinic, Rochester, MN; Department of Medicine, Stanford University, Stanford, CA (K.N.P.); Transgenomic Inc, New Haven, CT (T.E.C.); and Department of Clinical Genetics (H.B.) and Heart Centre, Department of Clinical and Experimental Cardiology (A.A.M.W.), Academic Medical Center, University of Amsterdam, The Netherlands
| | - David J Tester
- From the Mayo Clinic School of Medicine (J.D.K., M.J.A.), Medical Scientist Training Program (J.D.K., M.J.A.), Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory (J.D.K., D.J.T., M.J.A.), Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (N.B.L.), Division of Heart Rhythm Services, Department of Cardiovascular Diseases (D.J.T., M.J.A.), and Division of Pediatric Cardiology, Department of Pediatrics (M.J.A.), Mayo Clinic, Rochester, MN; Department of Medicine, Stanford University, Stanford, CA (K.N.P.); Transgenomic Inc, New Haven, CT (T.E.C.); and Department of Clinical Genetics (H.B.) and Heart Centre, Department of Clinical and Experimental Cardiology (A.A.M.W.), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Hennie Bikker
- From the Mayo Clinic School of Medicine (J.D.K., M.J.A.), Medical Scientist Training Program (J.D.K., M.J.A.), Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory (J.D.K., D.J.T., M.J.A.), Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (N.B.L.), Division of Heart Rhythm Services, Department of Cardiovascular Diseases (D.J.T., M.J.A.), and Division of Pediatric Cardiology, Department of Pediatrics (M.J.A.), Mayo Clinic, Rochester, MN; Department of Medicine, Stanford University, Stanford, CA (K.N.P.); Transgenomic Inc, New Haven, CT (T.E.C.); and Department of Clinical Genetics (H.B.) and Heart Centre, Department of Clinical and Experimental Cardiology (A.A.M.W.), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Arthur A M Wilde
- From the Mayo Clinic School of Medicine (J.D.K., M.J.A.), Medical Scientist Training Program (J.D.K., M.J.A.), Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory (J.D.K., D.J.T., M.J.A.), Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (N.B.L.), Division of Heart Rhythm Services, Department of Cardiovascular Diseases (D.J.T., M.J.A.), and Division of Pediatric Cardiology, Department of Pediatrics (M.J.A.), Mayo Clinic, Rochester, MN; Department of Medicine, Stanford University, Stanford, CA (K.N.P.); Transgenomic Inc, New Haven, CT (T.E.C.); and Department of Clinical Genetics (H.B.) and Heart Centre, Department of Clinical and Experimental Cardiology (A.A.M.W.), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Michael J Ackerman
- From the Mayo Clinic School of Medicine (J.D.K., M.J.A.), Medical Scientist Training Program (J.D.K., M.J.A.), Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory (J.D.K., D.J.T., M.J.A.), Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (N.B.L.), Division of Heart Rhythm Services, Department of Cardiovascular Diseases (D.J.T., M.J.A.), and Division of Pediatric Cardiology, Department of Pediatrics (M.J.A.), Mayo Clinic, Rochester, MN; Department of Medicine, Stanford University, Stanford, CA (K.N.P.); Transgenomic Inc, New Haven, CT (T.E.C.); and Department of Clinical Genetics (H.B.) and Heart Centre, Department of Clinical and Experimental Cardiology (A.A.M.W.), Academic Medical Center, University of Amsterdam, The Netherlands.
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9
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Giudicessi JR, Roden DM, Wilde AAM, Ackerman MJ. Classification and Reporting of Potentially Proarrhythmic Common Genetic Variation in Long QT Syndrome Genetic Testing. Circulation 2019; 137:619-630. [PMID: 29431662 DOI: 10.1161/circulationaha.117.030142] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The acquired and congenital forms of long QT syndrome represent 2 distinct but clinically and genetically intertwined disorders of cardiac repolarization characterized by the shared final common pathway of QT interval prolongation and risk of potentially life-threatening arrhythmias. Over the past 2 decades, our understanding of the spectrum of genetic variation that (1) perturbs the function of cardiac ion channel macromolecular complexes and intracellular calcium-handling proteins, (2) underlies acquired/congenital long QT syndrome susceptibility, and (3) serves as a determinant of QT interval duration in the general population has grown exponentially. In turn, these molecular insights led to the development and increased utilization of clinically impactful genetic testing for congenital long QT syndrome. However, the widespread adoption and potential misinterpretation of the 2015 American College of Medical Genetics and Genomics variant classification and reporting guidelines may have contributed unintentionally to the reduced reporting of common genetic variants, with compelling epidemiological and functional evidence to support a potentially proarrhythmic role in patients with congenital and acquired long QT syndrome. As a result, some genetic testing reports may fail to convey the full extent of a patient's genetic susceptibility for a potentially life-threatening arrhythmia to the ordering healthcare professional. In this white paper, we examine the current classification and reporting (or lack thereof) of potentially proarrhythmic common genetic variants and investigate potential mechanisms to facilitate the reporting of these genetic variants without increasing the risk of diagnostic miscues.
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Affiliation(s)
- John R Giudicessi
- Departments of Cardiovascular Medicine and Internal Medicine, Clinician-Investigator Training Program, Mayo Clinic, Rochester, MN (J.R.G)
| | - Dan M Roden
- Departments of Biomedical Informatics, Medicine, and Pharmacology, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN (D.M.R.)
| | - Arthur A M Wilde
- Department of Clinical and Experimental Cardiology, Academic Medical Center, University of Amsterdam, The Netherlands (A.A.M.W.)
| | - Michael J Ackerman
- Departments of Cardiovascular Diseases, Pediatrics, and Molecular Pharmacology and Experimental Therapeutics, Divisions of Heart Rhythm Services and Pediatric Cardiology, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (M.J.A.)
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10
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Abbasi Y, Jabbari J, Jabbari R, Glinge C, Izadyar S, Spiekerkoetter E, Zamanian RT, Carlsen J, Tfelt‐Hansen J. Exome data clouds the pathogenicity of genetic variants in Pulmonary Arterial Hypertension. Mol Genet Genomic Med 2018; 6:835-844. [PMID: 30084161 PMCID: PMC6160702 DOI: 10.1002/mgg3.452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 04/25/2018] [Accepted: 06/03/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND We aimed to provide a set of previously reported PAH-associated missense and nonsense variants, and evaluate the pathogenicity of those variants. METHODS The Human Gene Mutation Database, PubMed, and Google Scholar were searched for previously reported PAH-associated genes and variants. Thereafter, both exome sequencing project and exome aggregation consortium as background population searched for previously reported PAH-associated missense and nonsense variants. The pathogenicity of previously reported PAH-associated missense variants evaluated by using four in silico prediction tools. RESULTS In total, 14 PAH-associated genes and 180 missense and nonsense variants were gathered. The BMPR2, the most frequent reported gene, encompasses 135 of 180 missense and nonsense variants. The exome sequencing project comprised 9, and the exome aggregation consortium counted 25 of 180 PAH-associated missense and nonsense variants. The TOPBP1 and ENG genes are unlikely to be the monogenic cause of PAH pathogenesis based on allele frequency in background population and prediction analysis. CONCLUSION This is the first evaluation of previously reported PAH-associated missense and nonsense variants. The BMPR2 identified as the major gene out of 14 PAH-associated genes. Based on findings, the ENG and TOPBP1 gene are not likely to be the monogenic cause of PAH.
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Affiliation(s)
- Yeganeh Abbasi
- Heart CentreDepartment of CardiologyCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
- Department of CardiologySection for Pulmonary Hypertension and Right Heart FailureCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
| | | | - Reza Jabbari
- Heart CentreDepartment of CardiologyCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
- Department of CardiologySection for Pulmonary Hypertension and Right Heart FailureCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
| | - Charlotte Glinge
- Heart CentreDepartment of CardiologyCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
| | - Seyed Bahador Izadyar
- Heart CentreDepartment of CardiologyCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
| | - Edda Spiekerkoetter
- Division of Pulmonary and Critical CareStanford University School of MedicineCalifornia
| | - Roham T. Zamanian
- Division of Pulmonary and Critical CareStanford University School of MedicineCalifornia
| | - Jørn Carlsen
- Heart CentreDepartment of CardiologyCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
- Department of CardiologySection for Pulmonary Hypertension and Right Heart FailureCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
| | - Jacob Tfelt‐Hansen
- Heart CentreDepartment of CardiologyCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
- Department of CardiologySection for Pulmonary Hypertension and Right Heart FailureCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
- Department of Forensic MedicineFaculty of Medical SciencesUniversity of CopenhagenDenmark
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11
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Li B, Mendenhall JL, Kroncke BM, Taylor KC, Huang H, Smith DK, Vanoye CG, Blume JD, George AL, Sanders CR, Meiler J. Predicting the Functional Impact of KCNQ1 Variants of Unknown Significance. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.117.001754. [PMID: 29021305 DOI: 10.1161/circgenetics.117.001754] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/24/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND An emerging standard-of-care for long-QT syndrome uses clinical genetic testing to identify genetic variants of the KCNQ1 potassium channel. However, interpreting results from genetic testing is confounded by the presence of variants of unknown significance for which there is inadequate evidence of pathogenicity. METHODS AND RESULTS In this study, we curated from the literature a high-quality set of 107 functionally characterized KCNQ1 variants. Based on this data set, we completed a detailed quantitative analysis on the sequence conservation patterns of subdomains of KCNQ1 and the distribution of pathogenic variants therein. We found that conserved subdomains generally are critical for channel function and are enriched with dysfunctional variants. Using this experimentally validated data set, we trained a neural network, designated Q1VarPred, specifically for predicting the functional impact of KCNQ1 variants of unknown significance. The estimated predictive performance of Q1VarPred in terms of Matthew's correlation coefficient and area under the receiver operating characteristic curve were 0.581 and 0.884, respectively, superior to the performance of 8 previous methods tested in parallel. Q1VarPred is publicly available as a web server at http://meilerlab.org/q1varpred. CONCLUSIONS Although a plethora of tools are available for making pathogenicity predictions over a genome-wide scale, previous tools fail to perform in a robust manner when applied to KCNQ1. The contrasting and favorable results for Q1VarPred suggest a promising approach, where a machine-learning algorithm is tailored to a specific protein target and trained with a functionally validated data set to calibrate informatics tools.
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Affiliation(s)
- Bian Li
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Jeffrey L Mendenhall
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Brett M Kroncke
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Keenan C Taylor
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Hui Huang
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Derek K Smith
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Carlos G Vanoye
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Jeffrey D Blume
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Alfred L George
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Charles R Sanders
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.)
| | - Jens Meiler
- From the Department of Chemistry (B.L., J.L.M., J.M.), Center for Structural Biology (B.L., J.L.M., B.M.K., K.C.T., H.H., C.R.S., J.M.), Department of Biochemistry (B.M.K., H.H., C.R.S.), and Department of Biostatistics (D.K.S., J.D.B.), Vanderbilt University, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (B.M.K., C.R.S.); and Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., A.L.G.).
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12
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Huang H, Kuenze G, Smith JA, Taylor KC, Duran AM, Hadziselimovic A, Meiler J, Vanoye CG, George AL, Sanders CR. Mechanisms of KCNQ1 channel dysfunction in long QT syndrome involving voltage sensor domain mutations. SCIENCE ADVANCES 2018; 4:eaar2631. [PMID: 29532034 PMCID: PMC5842040 DOI: 10.1126/sciadv.aar2631] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/02/2018] [Indexed: 05/21/2023]
Abstract
Mutations that induce loss of function (LOF) or dysfunction of the human KCNQ1 channel are responsible for susceptibility to a life-threatening heart rhythm disorder, the congenital long QT syndrome (LQTS). Hundreds of KCNQ1 mutations have been identified, but the molecular mechanisms responsible for impaired function are poorly understood. We investigated the impact of 51 KCNQ1 variants with mutations located within the voltage sensor domain (VSD), with an emphasis on elucidating effects on cell surface expression, protein folding, and structure. For each variant, the efficiency of trafficking to the plasma membrane, the impact of proteasome inhibition, and protein stability were assayed. The results of these experiments combined with channel functional data provided the basis for classifying each mutation into one of six mechanistic categories, highlighting heterogeneity in the mechanisms resulting in channel dysfunction or LOF. More than half of the KCNQ1 LOF mutations examined were seen to destabilize the structure of the VSD, generally accompanied by mistrafficking and degradation by the proteasome, an observation that underscores the growing appreciation that mutation-induced destabilization of membrane proteins may be a common human disease mechanism. Finally, we observed that five of the folding-defective LQTS mutant sites are located in the VSD S0 helix, where they interact with a number of other LOF mutation sites in other segments of the VSD. These observations reveal a critical role for the S0 helix as a central scaffold to help organize and stabilize the KCNQ1 VSD and, most likely, the corresponding domain of many other ion channels.
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Affiliation(s)
- Hui Huang
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240, USA
| | - Jarrod A. Smith
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Keenan C. Taylor
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Amanda M. Duran
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240, USA
| | - Arina Hadziselimovic
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Bioinformatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Carlos G. Vanoye
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alfred L. George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Charles R. Sanders
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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13
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Natarajan P, Gold NB, Bick AG, McLaughlin H, Kraft P, Rehm HL, Peloso GM, Wilson JG, Correa A, Seidman JG, Seidman CE, Kathiresan S, Green RC. Aggregate penetrance of genomic variants for actionable disorders in European and African Americans. Sci Transl Med 2017; 8:364ra151. [PMID: 27831900 DOI: 10.1126/scitranslmed.aag2367] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/30/2016] [Indexed: 12/21/2022]
Abstract
In populations that have not been selected for family history of disease, it is unclear how commonly pathogenic variants (PVs) in disease-associated genes for rare Mendelian conditions are found and how often they are associated with clinical features of these conditions. We conducted independent, prospective analyses of participants in two community-based epidemiological studies to test the hypothesis that persons carrying PVs in any of 56 genes that lead to 24 dominantly inherited, actionable conditions are more likely to exhibit the clinical features of the corresponding diseases than those without PVs. Among 462 European American Framingham Heart Study (FHS) and 3223 African-American Jackson Heart Study (JHS) participants who were exome-sequenced, we identified and classified 642 and 4429 unique variants, respectively, in these 56 genes while blinded to clinical data. In the same participants, we ascertained related clinical features from the participants' clinical history of cancer and most recent echocardiograms, electrocardiograms, and lipid measurements, without knowledge of variant classification. PVs were found in 5 FHS (1.1%) and 31 JHS (1.0%) participants. Carriers of PVs were more likely than expected, on the basis of incidence in noncarriers, to have related clinical features in both FHS (80.0% versus 12.4%) and JHS (26.9% versus 5.4%), yielding standardized incidence ratios of 6.4 [95% confidence interval (CI), 1.7 to 16.5; P = 7 × 10-4) in FHS and 4.7 (95% CI, 1.9 to 9.7; P = 3 × 10-4) in JHS. Individuals unselected for family history who carry PVs in 56 genes for actionable conditions have an increased aggregated risk of developing clinical features associated with the corresponding diseases.
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Affiliation(s)
- Pradeep Natarajan
- Center for Human Genetic Research, Cardiovascular Research Center, and Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nina B Gold
- Harvard Medical School, Boston, MA 02115, USA.,Boston Children's Hospital, Boston, MA 02115, USA
| | - Alexander G Bick
- Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Heather McLaughlin
- Harvard Medical School, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.,Partners HealthCare Personalized Medicine, Boston, MA 02115, USA
| | - Peter Kraft
- Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Heidi L Rehm
- Harvard Medical School, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.,Partners HealthCare Personalized Medicine, Boston, MA 02115, USA
| | - Gina M Peloso
- Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Adolfo Correa
- Departments of Pediatrics and Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jonathan G Seidman
- Harvard Medical School, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christine E Seidman
- Harvard Medical School, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sekar Kathiresan
- Center for Human Genetic Research, Cardiovascular Research Center, and Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Robert C Green
- Harvard Medical School, Boston, MA 02115, USA. .,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Partners HealthCare Personalized Medicine, Boston, MA 02115, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
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14
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Repeat genetic testing with targeted capture sequencing in primary arrhythmia syndrome and cardiomyopathy. Eur J Hum Genet 2017; 25:1313-1323. [PMID: 29255176 DOI: 10.1038/s41431-017-0004-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 11/09/2022] Open
Abstract
In inherited primary arrhythmia syndromes (PAS) and cardiomyopathies (CMP), the yield of genetic testing varies between 20 and 75% in different diseases according to studies performed in the pre next-generation sequencing (NGS) era. It is unknown whether retesting historical negative samples with NGS techniques is worthwhile. Therefore, we assessed the value of NGS-based panel testing in previously genotype negative-phenotype positive probands. We selected 107 patients (47 PAS and 60 CMP) with a clear phenotype who remained genotype negative after genetic analysis of the main genes implicated in their specific phenotype. Targeted sequencing of the coding regions of 71 PAS- and CMP-related genes was performed. Variant interpretation and classification was done according to a cardiology-specific scoring algorithm ('Amsterdam criteria') and the ACMG-AMP criteria. Co-segregation analysis was performed when DNA and clinical data of family members were available. Finally, a genetic diagnosis could be established in 21 patients (20%), 5 PAS (11%) and 16 CMP (27%) patients, respectively. The increased detection rate was due to sequencing of novel genes in 52% of the cases and due to technical failures with the historical analysis in 48%. A total of 118 individuals were informed about their carrier state and either reassured or scheduled for proper follow-up. To conclude, genetic retesting in clinically overt PAS and CMP cases, who were genotype negative with older techniques, resulted in an additional genetic diagnosis in up to 20% of the cases. This clearly supports a policy for genetic retesting with NGS-based panels.
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15
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Paludan-Müller C, Ahlberg G, Ghouse J, Herfelt C, Svendsen JH, Haunsø S, Kanters JK, Olesen MS. Integration of 60,000 exomes and ACMG guidelines question the role of Catecholaminergic Polymorphic Ventricular Tachycardia-associated variants. Clin Genet 2016; 91:63-72. [PMID: 27538377 DOI: 10.1111/cge.12847] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/12/2016] [Accepted: 08/15/2016] [Indexed: 01/13/2023]
Abstract
Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT) is a highly lethal cardiac arrhythmia disease occurring during exercise or psychological stress. CPVT has an estimated prevalence of 1:10,000 and has mainly been associated with variants in calcium-regulating genes. Identification of potential false-positive pathogenic variants was conducted by searching the Exome Aggregation Consortium (ExAC) database (n = 60,706) for variants reported to be associated with CPVT. The pathogenicity of the interrogated variants was assessed using guidelines from the American College of Medical Genetics and Genomics (ACMG) and in silico prediction tools. Of 246 variants 38 (15%) variants previously associated with CPVT were identified in the ExAC database. We predicted the CPVT prevalence to be 1:132. The ACMG standards classified 29% of ExAC variants as pathogenic or likely pathogenic. The in silico predictions showed a reduced probability of disease-causing effect for the variants identified in the exome database (p < 0.001). We have observed a large overrepresentation of previously CPVT-associated variants in a large exome database. Based on the frequency of CPVT in the general population, it is less likely that the previously proposed variants are associated with a highly penetrant monogenic form of the disease.
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Affiliation(s)
- C Paludan-Müller
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Department of Biomedical Sciences, University of Copenhagen, Denmark.,Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - G Ahlberg
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Department of Biomedical Sciences, University of Copenhagen, Denmark.,Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - J Ghouse
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Department of Biomedical Sciences, University of Copenhagen, Denmark.,Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - C Herfelt
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Department of Biomedical Sciences, University of Copenhagen, Denmark.,Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - J H Svendsen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Department of Biomedical Sciences, University of Copenhagen, Denmark.,Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health Sciences, Copenhagen, Denmark
| | - S Haunsø
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Department of Biomedical Sciences, University of Copenhagen, Denmark.,Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health Sciences, Copenhagen, Denmark
| | - J K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedicine, University of Copenhagen, Copenhagen, Denmark.,Department of Cardiology, Herlev and Gentofte University Hospitals, Copenhagen, Denmark
| | - M S Olesen
- Danish National Research Foundation Centre for Cardiac Arrhythmia, Department of Biomedical Sciences, University of Copenhagen, Denmark.,Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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16
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Lahrouchi N, Behr ER, Bezzina CR. Next-Generation Sequencing in Post-mortem Genetic Testing of Young Sudden Cardiac Death Cases. Front Cardiovasc Med 2016; 3:13. [PMID: 27303672 PMCID: PMC4885007 DOI: 10.3389/fcvm.2016.00013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/02/2016] [Indexed: 12/19/2022] Open
Abstract
Sudden cardiac death (SCD) in the young (<40 years) occurs in the setting of a variety of rare inherited cardiac disorders and is a disastrous event for family members. Establishing the cause of SCD is important as it permits the pre-symptomatic identification of relatives at risk of SCD. Sudden arrhythmic death syndrome (SADS) is defined as SCD in the setting of negative autopsy findings and toxicological analysis. In such cases, reaching a diagnosis is even more challenging and post-mortem genetic testing can crucially contribute to the identification of the underlying cause of death. In this review, we will discuss the current achievements of “the molecular autopsy” in young SADS cases and provide an overview of key challenges in assessing pathogenicity (i.e., causality) of genetic variants identified through next-generation sequencing.
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Affiliation(s)
- Najim Lahrouchi
- Department of Clinical and Experimental Cardiology, Heart Center, AMC , Amsterdam , Netherlands
| | - Elijah R Behr
- Cardiology Clinical Academic Group, St George's University of London , London , UK
| | - Connie R Bezzina
- Department of Clinical and Experimental Cardiology, Heart Center, AMC , Amsterdam , Netherlands
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17
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Vyas B, Puri RD, Namboodiri N, Nair M, Sharma D, Movva S, Saxena R, Bohora S, Aggarwal N, Vora A, Kumar J, Singh T, Verma IC. KCNQ1 mutations associated with Jervell and Lange-Nielsen syndrome and autosomal recessive Romano-Ward syndrome in India-expanding the spectrum of long QT syndrome type 1. Am J Med Genet A 2016; 170:1510-9. [PMID: 27041150 DOI: 10.1002/ajmg.a.37636] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 03/07/2016] [Indexed: 01/07/2023]
Abstract
Long QT syndrome type 1 (LQT1) is the most common type of all Long QT syndromes (LQTS) and occurs due to mutations in KCNQ1. Biallelic mutations with deafness is called Jervell and Lange-Nielsen syndrome (JLNS) and without deafness is autosomal recessive Romano-Ward syndrome (AR RWS). In this prospective study, we report biallelic mutations in KCNQ1 in Indian patients with LQT1 syndrome. Forty patients with a clinical diagnosis of LQT1 syndrome were referred for molecular testing. Of these, 18 were excluded from the analysis as they did not fulfill the inclusion criteria of broad T wave ECG pattern of the study. Direct sequencing of KCNQ1 was performed in 22 unrelated probands, parents and at-risk family members. Mutations were identified in 17 patients, of which seven had heterozygous mutations and were excluded in this analysis. Biallelic mutations were identified in 10 patients. Five of 10 patients did not have deafness and were categorized as AR RWS, the rest being JLNS. Eight mutations identified in this study have not been reported in the literature and predicted to be pathogenic by in silico analysis. We hypothesize that the homozygous biallelic mutations identified in 67% of families was due to endogamous marriages in the absence of consanguinity. This study presents biallelic gene mutations in KCNQ1 in Asian Indian patients with AR JLNS and RWS. It adds to the scant worldwide literature of mutation studies in AR RWS. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bijal Vyas
- Centre of Medical Genetics, Sir Ganga Ram Hospital, Delhi, India
| | - Ratna D Puri
- Centre of Medical Genetics, Sir Ganga Ram Hospital, Delhi, India
| | - Narayanan Namboodiri
- Department of Cardiology, Sree Chitra Institute for Medical Sciences & Technology, Kerala, India
| | - Mohan Nair
- Department of Cardiology, Holy Family Hospital, Delhi, India
| | - Deepak Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Sireesha Movva
- Centre of Medical Genetics, Sir Ganga Ram Hospital, Delhi, India
| | - Renu Saxena
- Centre of Medical Genetics, Sir Ganga Ram Hospital, Delhi, India
| | - Shomu Bohora
- Department of Cardiology, Baroda Heart Institute & Research Centre, Gujarat, India
| | - Neeraj Aggarwal
- Department of Paediatric Cardiology, Sir Ganga Ram Hospital, Delhi, India
| | - Amit Vora
- Department of Cardiology, Glenmark Cardiac Centre, Mumbai, Maharashtra, India
| | - Jatinder Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Tarandeep Singh
- Department of Cardiology, U N Mehta Institute of Cardiology & Research Centre, Gujarat, India
| | - Ishwar C Verma
- Centre of Medical Genetics, Sir Ganga Ram Hospital, Delhi, India
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18
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The role of genetic testing in unexplained sudden death. Transl Res 2016; 168:59-73. [PMID: 26143861 DOI: 10.1016/j.trsl.2015.06.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 06/08/2015] [Accepted: 06/11/2015] [Indexed: 12/19/2022]
Abstract
Most sudden deaths are because of a cardiac etiology and are termed sudden cardiac death (SCD). In younger individuals coronary artery disease is less prevalent and cardiac genetic disorders are more common. If sudden death is unexplained despite an appropriate autopsy and toxicologic assessment the term sudden arrhythmic death syndrome (SADS) may be used. This is an umbrella term and common underlying etiologies are primary arrhythmia syndromes with a familial basis such as Brugada syndrome, long QT syndrome, and subtle forms of cardiomyopathy. The first clinical presentation of these conditions is often SCD, which makes identification, screening, and risk stratification crucial to avert further deaths. This review will focus on genetic testing in the context of family screening. It will address the role of the "molecular autopsy" alongside current postmortem practices in the evaluation of SADS deaths. We describe the current data underlying genetic testing in these conditions, explore the potential for next-generation sequencing, and discuss the inherent diagnostic problems in determination of pathogenicity.
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19
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Itoh H, Crotti L, Aiba T, Spazzolini C, Denjoy I, Fressart V, Hayashi K, Nakajima T, Ohno S, Makiyama T, Wu J, Hasegawa K, Mastantuono E, Dagradi F, Pedrazzini M, Yamagishi M, Berthet M, Murakami Y, Shimizu W, Guicheney P, Schwartz PJ, Horie M. The genetics underlying acquired long QT syndrome: impact for genetic screening. Eur Heart J 2015; 37:1456-64. [PMID: 26715165 DOI: 10.1093/eurheartj/ehv695] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 12/01/2015] [Indexed: 12/19/2022] Open
Abstract
AIMS Acquired long QT syndrome (aLQTS) exhibits QT prolongation and Torsades de Pointes ventricular tachycardia triggered by drugs, hypokalaemia, or bradycardia. Sometimes, QTc remains prolonged despite elimination of triggers, suggesting the presence of an underlying genetic substrate. In aLQTS subjects, we assessed the prevalence of mutations in major LQTS genes and their probability of being carriers of a disease-causing genetic variant based on clinical factors. METHODS AND RESULTS We screened for the five major LQTS genes among 188 aLQTS probands (55 ± 20 years, 140 females) from Japan, France, and Italy. Based on control QTc (without triggers), subjects were designated 'true aLQTS' (QTc within normal limits) or 'unmasked cLQTS' (all others) and compared for QTc and genetics with 2379 members of 1010 genotyped congenital long QT syndrome (cLQTS) families. Cardiac symptoms were present in 86% of aLQTS subjects. Control QTc of aLQTS was 453 ± 39 ms, shorter than in cLQTS (478 ± 46 ms, P < 0.001) and longer than in non-carriers (406 ± 26 ms, P < 0.001). In 53 (28%) aLQTS subjects, 47 disease-causing mutations were identified. Compared with cLQTS, in 'true aLQTS', KCNQ1 mutations were much less frequent than KCNH2 (20% [95% CI 7-41%] vs. 64% [95% CI 43-82%], P < 0.01). A clinical score based on control QTc, age, and symptoms allowed identification of patients more likely to carry LQTS mutations. CONCLUSION A third of aLQTS patients carry cLQTS mutations, those on KCNH2 being more common. The probability of being a carrier of cLQTS disease-causing mutations can be predicted by simple clinical parameters, thus allowing possibly cost-effective genetic testing leading to cascade screening for identification of additional at-risk family members.
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Affiliation(s)
- Hideki Itoh
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan Inserm, UMR_S1166, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S1166, Institut de recherche sur les maladies cardiovasculaires, du métabolisme et de la nutrition, Paris, France Institute of Cardiometabolism and Nutrition (ICAN), Paris, France
| | - Lia Crotti
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Takeshi Aiba
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Carla Spazzolini
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy
| | - Isabelle Denjoy
- AP-HP, Hôpital Bichat, Service de Cardiologie, Centre de Référence des Maladies Cardiaques Héréditaires, Université Denis Diderot, Paris 7, Paris, France
| | - Véronique Fressart
- Inserm, UMR_S1166, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S1166, Institut de recherche sur les maladies cardiovasculaires, du métabolisme et de la nutrition, Paris, France Institute of Cardiometabolism and Nutrition (ICAN), Paris, France AP-HP, Groupe Hospitalier Pitié-Salpétrière, Service de Biochimie Métabolique, UF Cardiogénétique et Myogénétique Moléculaire et Cellulaire, Paris, France
| | - Kenshi Hayashi
- Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Tadashi Nakajima
- Department of Medicine and Biological Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Seiko Ohno
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Takeru Makiyama
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jie Wu
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan Department of Pharmacology, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Kanae Hasegawa
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Elisa Mastantuono
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Federica Dagradi
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy
| | - Matteo Pedrazzini
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy
| | - Masakazu Yamagishi
- Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Myriam Berthet
- Inserm, UMR_S1166, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S1166, Institut de recherche sur les maladies cardiovasculaires, du métabolisme et de la nutrition, Paris, France Institute of Cardiometabolism and Nutrition (ICAN), Paris, France
| | - Yoshitaka Murakami
- Medical Statistics, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, Osaka, Japan Department of Cardiovascular Medicine, Nippon Medical School, Tokyo, Japan
| | - Pascale Guicheney
- Inserm, UMR_S1166, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S1166, Institut de recherche sur les maladies cardiovasculaires, du métabolisme et de la nutrition, Paris, France Institute of Cardiometabolism and Nutrition (ICAN), Paris, France
| | - Peter J Schwartz
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy
| | - Minoru Horie
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
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20
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Abbasi Y, Jabbari J, Jabbari R, Yang RQ, Risgaard B, Køber L, Haunsø S, Tfelt-Hansen J. The pathogenicity of genetic variants previously associated with left ventricular non-compaction. Mol Genet Genomic Med 2015; 4:135-42. [PMID: 27066506 PMCID: PMC4799875 DOI: 10.1002/mgg3.182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 09/29/2015] [Accepted: 09/29/2015] [Indexed: 12/05/2022] Open
Abstract
Background Left ventricular non‐compaction (LVNC) is a rare cardiomyopathy. Many genetic variants have been associated with LVNC. However, the number of the previous LVNC‐associated variants that are common in the background population remains unknown. The aim of this study was to provide an updated list of previously reported LVNC‐associated variants with biologic description and investigate the prevalence of LVNC variants in healthy general population to find false‐positive LVNC‐associated variants. Methods and Results The Human Gene Mutation Database and PubMed were systematically searched to identify all previously reported LVNC‐associated variants. Thereafter, the Exome Sequencing Project (ESP) and the Exome Aggregation Consortium (ExAC), that both represent the background population, was searched for all variants. Four in silico prediction tools were assessed to determine the functional effects of these variants. The prediction results of those identified in the ESP and ExAC and those not identified in the ESP and ExAC were compared. In 12 genes, 60 LVNC‐associated missense/nonsense variants were identified. MYH7 was the predominant gene, encompassing 24 of the 60 LVNC‐associated variants. The ESP only harbored nine and ExAC harbored 18 of the 60 LVNC‐associated variants. In total, eight out of nine ESP‐positive variants overlapped with the 18 variants identified in ExAC database. Conclusions In this article, we identified 9 ESP‐positive and 18 ExAC‐positive variants of 60 previously reported LVNC‐associated variants, suggesting that these variants are not necessarily the monogenic cause of LVNC.
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Affiliation(s)
- Yeganeh Abbasi
- The Danish National Research Foundation Center for Cardiac Arrhythmia (DARC)CopenhagenDenmark; Laboratory of Molecular CardiologyDepartment of CardiologyThe Heart CentreCopenhagen University Hospital RigshospitaletCopenhagenDenmark; Department of CardiologyThe Heart CenterRigshospitaletCopenhagenDenmark
| | - Javad Jabbari
- The Danish National Research Foundation Center for Cardiac Arrhythmia (DARC)CopenhagenDenmark; Laboratory of Molecular CardiologyDepartment of CardiologyThe Heart CentreCopenhagen University Hospital RigshospitaletCopenhagenDenmark; Department of CardiologyThe Heart CenterRigshospitaletCopenhagenDenmark
| | - Reza Jabbari
- The Danish National Research Foundation Center for Cardiac Arrhythmia (DARC)CopenhagenDenmark; Laboratory of Molecular CardiologyDepartment of CardiologyThe Heart CentreCopenhagen University Hospital RigshospitaletCopenhagenDenmark; Department of CardiologyThe Heart CenterRigshospitaletCopenhagenDenmark
| | - Ren-Qiang Yang
- The Danish National Research Foundation Center for Cardiac Arrhythmia (DARC)CopenhagenDenmark; Laboratory of Molecular CardiologyDepartment of CardiologyThe Heart CentreCopenhagen University Hospital RigshospitaletCopenhagenDenmark; Department of CardiologyInstitute of Cardiovascular DiseaseThe Heart CenterThe Second Affiliated HospitalNanchang UniversityNanchangChina
| | - Bjarke Risgaard
- The Danish National Research Foundation Center for Cardiac Arrhythmia (DARC)CopenhagenDenmark; Laboratory of Molecular CardiologyDepartment of CardiologyThe Heart CentreCopenhagen University Hospital RigshospitaletCopenhagenDenmark; Department of CardiologyThe Heart CenterRigshospitaletCopenhagenDenmark
| | - Lars Køber
- Department of CardiologyThe Heart CenterRigshospitaletCopenhagenDenmark; Department of Clinical MedicineFaculty of Health and Medical ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Stig Haunsø
- The Danish National Research Foundation Center for Cardiac Arrhythmia (DARC)CopenhagenDenmark; Laboratory of Molecular CardiologyDepartment of CardiologyThe Heart CentreCopenhagen University Hospital RigshospitaletCopenhagenDenmark; Department of CardiologyThe Heart CenterRigshospitaletCopenhagenDenmark; Department of Clinical MedicineFaculty of Health and Medical ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Jacob Tfelt-Hansen
- The Danish National Research Foundation Center for Cardiac Arrhythmia (DARC)CopenhagenDenmark; Laboratory of Molecular CardiologyDepartment of CardiologyThe Heart CentreCopenhagen University Hospital RigshospitaletCopenhagenDenmark; Department of CardiologyThe Heart CenterRigshospitaletCopenhagenDenmark; Department of Clinical MedicineFaculty of Health and Medical ScienceUniversity of CopenhagenCopenhagenDenmark
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21
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Jabbari J, Olesen MS, Yuan L, Nielsen JB, Liang B, Macri V, Christophersen IE, Nielsen N, Sajadieh A, Ellinor PT, Grunnet M, Haunsø S, Holst AG, Svendsen JH, Jespersen T. Common and rare variants in SCN10A modulate the risk of atrial fibrillation. ACTA ACUST UNITED AC 2015; 8:64-73. [PMID: 25691686 DOI: 10.1161/hcg.0000000000000022] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Genome-wide association studies have shown that the common single nucleotide polymorphism rs6800541 located in SCN10A, encoding the voltage-gated Nav1.8 sodium channel, is associated with PR-interval prolongation and atrial fibrillation (AF). Single nucleotide polymorphism rs6800541 is in high linkage disequilibrium with the nonsynonymous variant in SCN10A, rs6795970 (V1073A, r(2)=0.933). We therefore sought to determine whether common and rare SCN10A variants are associated with early onset AF. METHODS AND RESULTS SCN10A was sequenced in 225 AF patients in whom there was no evidence of other cardiovascular disease or dysfunction (lone AF). In an association study of the rs6795970 single nucleotide polymorphism variant, we included 515 AF patients and 2 control cohorts of 730 individuals free of AF and 6161 randomly sampled individuals. Functional characterization of SCN10A variants was performed by whole-cell patch-clamping. In the lone AF cohort, 9 rare missense variants and 1 splice site donor variant were detected. Interestingly, AF patients were found to have higher G allele frequency of rs6795970, which encodes the alanine variant at position 1073 (described from here on as A1073, odds ratio =1.35 [1.16-1.54]; P=2.3×10(-5)). Both of the common variants, A1073 and P1092, induced a gain-of-channel function, whereas the rare missense variants, V94G and R1588Q, resulted in a loss-of-channel function. CONCLUSIONS The common variant A1073 is associated with increased susceptibility to AF. Both rare and common variants have effect on the function of the channel, indicating that these variants influence susceptibility to AF. Hence, our study suggests that SCN10A variations are involved in the genesis of AF.
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Affiliation(s)
- Javad Jabbari
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Morten S Olesen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Lei Yuan
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Jonas B Nielsen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Bo Liang
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Vincenzo Macri
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Ingrid E Christophersen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Nikolaj Nielsen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Ahmad Sajadieh
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Patrick T Ellinor
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Morten Grunnet
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Stig Haunsø
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Anders G Holst
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Jesper H Svendsen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.)
| | - Thomas Jespersen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA (M.V., P.T.E) and Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E); Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Rud, Norway (I.E.C.); Department of Cardiology, Copenhagen University Hospital of Bispebjerg, Bispebjerg, Denmark (A.S.); and LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark (S.H.).
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22
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Campuzano O, Sanchez-Molero O, Mademont-Soler I, Riuró H, Allegue C, Coll M, Pérez-Serra A, Mates J, Picó F, Iglesias A, Brugada R. Rare Titin (TTN) Variants in Diseases Associated with Sudden Cardiac Death. Int J Mol Sci 2015; 16:25773-25787. [PMID: 26516846 PMCID: PMC4632826 DOI: 10.3390/ijms161025773] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/12/2015] [Accepted: 10/19/2015] [Indexed: 01/24/2023] Open
Abstract
A leading cause of death in western countries is sudden cardiac death, and can be associated with genetic disease. Next-generation sequencing has allowed thorough analysis of genes associated with this entity, including, most recently, titin. We aimed to identify potentially pathogenic genetic variants in titin. A total of 1126 samples were analyzed using a custom sequencing panel including major genes related to sudden cardiac death. Our cohort was divided into three groups: 432 cases from patients with cardiomyopathies, 130 cases from patients with channelopathies, and 564 post-mortem samples from individuals showing anatomical healthy hearts and non-conclusive causes of death after comprehensive autopsy. None of the patients included had definite pathogenic variants in the genes analyzed by our custom cardio-panel. Retrospective analysis comparing the in-house database and available public databases also was performed. We identified 554 rare variants in titin, 282 of which were novel. Seven were previously reported as pathogenic. Of these 554 variants, 493 were missense variants, 233 of which were novel. Of all variants identified, 399 were unique and 155 were identified at least twice. No definite pathogenic variants were identified in any of genes analyzed. We identified rare, mostly novel, titin variants that seem to play a potentially pathogenic role in sudden cardiac death. Additional studies should be performed to clarify the role of these variants in sudden cardiac death.
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Affiliation(s)
- Oscar Campuzano
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona 17190, Spain.
- Medical Science Department, School of Medicine, University of Girona, Girona 17071, Spain.
| | | | - Irene Mademont-Soler
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona 17190, Spain.
| | - Helena Riuró
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona 17190, Spain.
| | - Catarina Allegue
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona 17190, Spain.
| | - Monica Coll
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona 17190, Spain.
| | | | - Jesus Mates
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona 17190, Spain.
| | - Ferran Picó
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona 17190, Spain.
| | - Anna Iglesias
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona 17190, Spain.
| | - Ramon Brugada
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona 17190, Spain.
- Medical Science Department, School of Medicine, University of Girona, Girona 17071, Spain.
- Cardiovascular Genetics Clinic, Hospital Josep Trueta, Girona 17007, Spain.
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23
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Ackerman MJ. Genetic purgatory and the cardiac channelopathies: Exposing the variants of uncertain/unknown significance issue. Heart Rhythm 2015; 12:2325-31. [PMID: 26144349 DOI: 10.1016/j.hrthm.2015.07.002] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 10/23/2022]
Abstract
Merriam-Webster's online dictionary defines purgatory as "an intermediate state after death for expiatory purification" or more specifically as "a place or state of punishment wherein according to Roman Catholic doctrine the souls of those who die in God׳s grace may make satisfaction for past sins and so become fit for heaven." Alternatively, it is defined as "a place or state of temporary suffering or misery." Either way, purgatory is a place where you are stuck, and you don't want to be stuck there. It is in this context that the term genetic purgatory is introduced. Genetic purgatory is a place where the genetic test-ordering physician and patients and their families are stuck when a variant of uncertain/unknown significance (VUS) has been elucidated. It is in this dark place where suffering and misery are occurring because of unenlightened handling of a VUS, which includes using the VUS for predictive genetic testing and making radical treatment recommendations based on the presence or absence of a so-called maybe mutation. Before one can escape from this miserable place, one must first recognize that one is stuck there. Hence, the purpose of this review article is to fully expose the VUS issue as it relates to the cardiac channelopathies and make the cardiologists/geneticists/genetic counselors who order such genetic tests believers in genetic purgatory. Only then can one meaningfully attempt to get out of that place and seek to promote a VUS to disease-causative mutation status or demote it to an utterly innocuous and irrelevant variant.
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Affiliation(s)
- Michael J Ackerman
- Departments of Medicine, Pediatrics, and Molecular Pharmacology & Experimental Therapeutics, Divisions of Cardiovascular Medicine, Pediatric Cardiology, and the Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota.
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24
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Hoshi M, Liu H, Kaufman ES, Deschênes I. Polygenic Case of Long QT Syndrome Confirmed through Functional Characterization Informs the Interpretation of Genetic Screening Results. HeartRhythm Case Rep 2015. [PMID: 26213684 PMCID: PMC4509597 DOI: 10.1016/j.hrcr.2015.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Malcolm Hoshi
- The Heart and Vascular Research Center, Department of Medicine, MetroHealth Campus, Case Western Reserve University, Cleveland, Ohio ; Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio
| | - Haiyan Liu
- The Heart and Vascular Research Center, Department of Medicine, MetroHealth Campus, Case Western Reserve University, Cleveland, Ohio
| | - Elizabeth S Kaufman
- The Heart and Vascular Research Center, Department of Medicine, MetroHealth Campus, Case Western Reserve University, Cleveland, Ohio
| | - Isabelle Deschênes
- The Heart and Vascular Research Center, Department of Medicine, MetroHealth Campus, Case Western Reserve University, Cleveland, Ohio ; Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio
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25
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Hayashi K, Konno T, Tada H, Tani S, Liu L, Fujino N, Nohara A, Hodatsu A, Tsuda T, Tanaka Y, Kawashiri MA, Ino H, Makita N, Yamagishi M. Functional Characterization of Rare Variants Implicated in Susceptibility to Lone Atrial Fibrillation. Circ Arrhythm Electrophysiol 2015; 8:1095-104. [PMID: 26129877 DOI: 10.1161/circep.114.002519] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 06/19/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND Few rare variants in atrial fibrillation (AF)-associated genes have been functionally characterized to identify a causal relationship between these variants and development of AF. We here sought to determine the clinical effect of rare variants in AF-associated genes in patients with lone AF and characterized these variants electrophysiologically and bioinformatically. METHODS AND RESULTS We screened all coding regions in 12 AF-associated genes in 90 patients with lone AF, with an onset of 47±11 years (66 men; mean age, 56±13 years) by high-resolution melting curve analysis and DNA sequencing. The potassium and sodium currents were analyzed using whole-cell patch clamping. In addition to using 4 individual in silico prediction tools, we extended those predictions to an integrated tool (Combined Annotation Dependent Depletion). We identified 7 rare variants in KCNA5, KCNQ1, KCNH2, SCN5A, and SCN1B genes in 8 patients: 2 of 8 probands had a family history of AF. Electrophysiological studies revealed that 2 variants showed a loss-of-function, and 4 variants showed a gain-of-function. Five of 6 variants with electrophysiological abnormalities were predicted as pathogenic by Combined Annotation Dependent Depletion scores. CONCLUSIONS In our cohort of patients with lone AF, 7 rare variants in cardiac ion channels were identified in 8 probands. A combination of electrophysiological studies and in silico predictions showed that these variants could contribute to the development of lone AF, although further in vivo study is necessary to confirm these results. More than half of AF-associated rare variants showed gain-of-function behavior, which may be targeted using genotype-specific pharmacological therapy.
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Affiliation(s)
- Kenshi Hayashi
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.).
| | - Tetsuo Konno
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Hayato Tada
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Satoyuki Tani
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Li Liu
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Noboru Fujino
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Atsushi Nohara
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Akihiko Hodatsu
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Toyonobu Tsuda
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Yoshihiro Tanaka
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Masa-aki Kawashiri
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Hidekazu Ino
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Naomasa Makita
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
| | - Masakazu Yamagishi
- From the Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan (K.H., T.K., H.T., S.T., L.L., N.F., A.N., A.H., T.T., Y.T., M.K., M.Y.); Department of Cardiology, Komatsu Municipal Hospital, Komatsu, Japan (H.I.); and Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan (N.M.)
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26
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Behr ER, Savio-Galimberti E, Barc J, Holst AG, Petropoulou E, Prins BP, Jabbari J, Torchio M, Berthet M, Mizusawa Y, Yang T, Nannenberg EA, Dagradi F, Weeke P, Bastiaenan R, Ackerman MJ, Haunso S, Leenhardt A, Kääb S, Probst V, Redon R, Sharma S, Wilde A, Tfelt-Hansen J, Schwartz P, Roden DM, Bezzina CR, Olesen M, Darbar D, Guicheney P, Crotti L, Jamshidi Y. Role of common and rare variants in SCN10A: results from the Brugada syndrome QRS locus gene discovery collaborative study. Cardiovasc Res 2015; 106:520-9. [PMID: 25691538 PMCID: PMC4447806 DOI: 10.1093/cvr/cvv042] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 01/27/2015] [Indexed: 12/19/2022] Open
Abstract
AIMS Brugada syndrome (BrS) remains genetically heterogeneous and is associated with slowed cardiac conduction. We aimed to identify genetic variation in BrS cases at loci associated with QRS duration. METHODS AND RESULTS A multi-centre study sequenced seven candidate genes (SCN10A, HAND1, PLN, CASQ2, TKT, TBX3, and TBX5) in 156 Caucasian SCN5A mutation-negative BrS patients (80% male; mean age 48) with symptoms (64%) and/or a family history of sudden death (47%) or BrS (18%). Forty-nine variants were identified: 18 were rare (MAF <1%) and non-synonymous; and 11/18 (61.1%), mostly in SCN10A, were predicted as pathogenic using multiple bioinformatics tools. Allele frequencies were compared with the Exome Sequencing and UK10K Projects. SKAT methods tested rare variation in SCN10A finding no statistically significant difference between cases and controls. Co-segregation analysis was possible for four of seven probands carrying a novel pathogenic variant. Only one pedigree (I671V/G1299A in SCN10A) showed co-segregation. The SCN10A SNP V1073 was, however, associated strongly with BrS [66.9 vs. 40.1% (UK10K) OR (95% CI) = 3.02 (2.35-3.87), P = 8.07 × 10-19]. Voltage-clamp experiments for NaV1.8 were performed for SCN10A common variants V1073, A1073, and rare variants of interest: A200V and I671V. V1073, A200V and I671V, demonstrated significant reductions in peak INa compared with ancestral allele A1073 (rs6795970). CONCLUSION Rare variants in the screened QRS-associated genes (including SCN10A) are not responsible for a significant proportion of SCN5A mutation negative BrS. The common SNP SCN10A V1073 was strongly associated with BrS and demonstrated loss of NaV1.8 function, as did rare variants in isolated patients.
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Affiliation(s)
- Elijah R Behr
- Human Genetics Research Centre, ICCS, St George's University of London, London SW17 0RE, UK
| | - Eleonora Savio-Galimberti
- Divisions of Cardiovascular Medicine and Clinical Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Julien Barc
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, Netherlands
| | - Anders G Holst
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Novo Nordisk A/S, Denmark
| | - Evmorfia Petropoulou
- Human Genetics Research Centre, ICCS, St George's University of London, London SW17 0RE, UK
| | - Bram P Prins
- Human Genetics Research Centre, ICCS, St George's University of London, London SW17 0RE, UK
| | - Javad Jabbari
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark LEO Pharma A/S, Denmark
| | - Margherita Torchio
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin, Milan, Italy
| | - Myriam Berthet
- Inserm, UMR S1166, Faculté de Médecine Pierre et Marie Curie, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR S1166, Paris, France Institute of Cardiometabolism & Nutrition, ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Yuka Mizusawa
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, Netherlands
| | - Tao Yang
- Divisions of Cardiovascular Medicine and Clinical Pharmacology, Vanderbilt University, Nashville, TN, USA
| | | | - Federica Dagradi
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin, Milan, Italy
| | - Peter Weeke
- Divisions of Cardiovascular Medicine and Clinical Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Rachel Bastiaenan
- Human Genetics Research Centre, ICCS, St George's University of London, London SW17 0RE, UK
| | - Michael J Ackerman
- Division of Cardiovascular Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA Division of Pediatric Cardiology, Department of Pediatrics & Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Stig Haunso
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Department of Medicine and Surgery, University of Copenhagen, Copenhagen, Denmark
| | - Antoine Leenhardt
- AP-HP, Hôpital Bichat, Service de Cardiologie et Centre de Référence des Maladies Cardiaques Héréditaires, Paris, France
| | - Stefan Kääb
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Vincent Probst
- Inserm, UMR 1087, l'institut du Thorax, Nantes, France CHU Nantes, l'institut du Thorax, Service de Cardiologie, Nantes, France
| | - Richard Redon
- Inserm, UMR 1087, l'institut du Thorax, Nantes, France CHU Nantes, l'institut du Thorax, Service de Cardiologie, Nantes, France
| | - Sanjay Sharma
- Human Genetics Research Centre, ICCS, St George's University of London, London SW17 0RE, UK
| | - Arthur Wilde
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, Netherlands Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia
| | - Jacob Tfelt-Hansen
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Department of Medicine and Surgery, University of Copenhagen, Copenhagen, Denmark
| | - Peter Schwartz
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin, Milan, Italy
| | - Dan M Roden
- Divisions of Cardiovascular Medicine and Clinical Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Connie R Bezzina
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, Netherlands
| | - Morten Olesen
- Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark
| | - Dawood Darbar
- Divisions of Cardiovascular Medicine and Clinical Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Pascale Guicheney
- Inserm, UMR S1166, Faculté de Médecine Pierre et Marie Curie, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR S1166, Paris, France Institute of Cardiometabolism & Nutrition, ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Lia Crotti
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin, Milan, Italy Inserm, UMR 1087, l'institut du Thorax, Nantes, France Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Yalda Jamshidi
- Human Genetics Research Centre, ICCS, St George's University of London, London SW17 0RE, UK
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27
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Assessment of the predictive accuracy of five in silico prediction tools, alone or in combination, and two metaservers to classify long QT syndrome gene mutations. BMC MEDICAL GENETICS 2015; 16:34. [PMID: 25967940 PMCID: PMC4630850 DOI: 10.1186/s12881-015-0176-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/22/2015] [Indexed: 11/27/2022]
Abstract
Background Long QT syndrome (LQTS) is an autosomal dominant condition predisposing to sudden death from malignant arrhythmia. Genetic testing identifies many missense single nucleotide variants of uncertain pathogenicity. Establishing genetic pathogenicity is an essential prerequisite to family cascade screening. Many laboratories use in silico prediction tools, either alone or in combination, or metaservers, in order to predict pathogenicity; however, their accuracy in the context of LQTS is unknown. We evaluated the accuracy of five in silico programs and two metaservers in the analysis of LQTS 1–3 gene variants. Methods The in silico tools SIFT, PolyPhen-2, PROVEAN, SNPs&GO and SNAP, either alone or in all possible combinations, and the metaservers Meta-SNP and PredictSNP, were tested on 312 KCNQ1, KCNH2 and SCN5A gene variants that have previously been characterised by either in vitro or co-segregation studies as either “pathogenic” (283) or “benign” (29). The accuracy, sensitivity, specificity and Matthews Correlation Coefficient (MCC) were calculated to determine the best combination of in silico tools for each LQTS gene, and when all genes are combined. Results The best combination of in silico tools for KCNQ1 is PROVEAN, SNPs&GO and SIFT (accuracy 92.7%, sensitivity 93.1%, specificity 100% and MCC 0.70). The best combination of in silico tools for KCNH2 is SIFT and PROVEAN or PROVEAN, SNPs&GO and SIFT. Both combinations have the same scores for accuracy (91.1%), sensitivity (91.5%), specificity (87.5%) and MCC (0.62). In the case of SCN5A, SNAP and PROVEAN provided the best combination (accuracy 81.4%, sensitivity 86.9%, specificity 50.0%, and MCC 0.32). When all three LQT genes are combined, SIFT, PROVEAN and SNAP is the combination with the best performance (accuracy 82.7%, sensitivity 83.0%, specificity 80.0%, and MCC 0.44). Both metaservers performed better than the single in silico tools; however, they did not perform better than the best performing combination of in silico tools. Conclusions The combination of in silico tools with the best performance is gene-dependent. The in silico tools reported here may have some value in assessing variants in the KCNQ1 and KCNH2 genes, but caution should be taken when the analysis is applied to SCN5A gene variants. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0176-z) contains supplementary material, which is available to authorized users.
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28
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Leong IUS, Stuckey A, Lai D, Skinner JR, Love DR. Assessment of the predictive accuracy of five in silico prediction tools, alone or in combination, and two metaservers to classify long QT syndrome gene mutations. BMC MEDICAL GENETICS 2015. [PMID: 25967940 DOI: 10.1186/s12881‐015‐0176‐z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Long QT syndrome (LQTS) is an autosomal dominant condition predisposing to sudden death from malignant arrhythmia. Genetic testing identifies many missense single nucleotide variants of uncertain pathogenicity. Establishing genetic pathogenicity is an essential prerequisite to family cascade screening. Many laboratories use in silico prediction tools, either alone or in combination, or metaservers, in order to predict pathogenicity; however, their accuracy in the context of LQTS is unknown. We evaluated the accuracy of five in silico programs and two metaservers in the analysis of LQTS 1-3 gene variants. METHODS The in silico tools SIFT, PolyPhen-2, PROVEAN, SNPs&GO and SNAP, either alone or in all possible combinations, and the metaservers Meta-SNP and PredictSNP, were tested on 312 KCNQ1, KCNH2 and SCN5A gene variants that have previously been characterised by either in vitro or co-segregation studies as either "pathogenic" (283) or "benign" (29). The accuracy, sensitivity, specificity and Matthews Correlation Coefficient (MCC) were calculated to determine the best combination of in silico tools for each LQTS gene, and when all genes are combined. RESULTS The best combination of in silico tools for KCNQ1 is PROVEAN, SNPs&GO and SIFT (accuracy 92.7%, sensitivity 93.1%, specificity 100% and MCC 0.70). The best combination of in silico tools for KCNH2 is SIFT and PROVEAN or PROVEAN, SNPs&GO and SIFT. Both combinations have the same scores for accuracy (91.1%), sensitivity (91.5%), specificity (87.5%) and MCC (0.62). In the case of SCN5A, SNAP and PROVEAN provided the best combination (accuracy 81.4%, sensitivity 86.9%, specificity 50.0%, and MCC 0.32). When all three LQT genes are combined, SIFT, PROVEAN and SNAP is the combination with the best performance (accuracy 82.7%, sensitivity 83.0%, specificity 80.0%, and MCC 0.44). Both metaservers performed better than the single in silico tools; however, they did not perform better than the best performing combination of in silico tools. CONCLUSIONS The combination of in silico tools with the best performance is gene-dependent. The in silico tools reported here may have some value in assessing variants in the KCNQ1 and KCNH2 genes, but caution should be taken when the analysis is applied to SCN5A gene variants.
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Affiliation(s)
- Ivone U S Leong
- Diagnostic Genetics, LabPlus, Auckland City Hospital, Auckland, New Zealand.
| | - Alexander Stuckey
- Bioinformatics Institute, University of Auckland, Auckland, New Zealand.
| | - Daniel Lai
- Green Lane Paediatric and Congenital Cardiac Services, Starship Children's Hospital, Private Bag 92024, Auckland, 1142, New Zealand.
| | - Jonathan R Skinner
- Green Lane Paediatric and Congenital Cardiac Services, Starship Children's Hospital, Private Bag 92024, Auckland, 1142, New Zealand. .,Cardiac Inherited Disease Group, Auckland City Hospital, Auckland, New Zealand. .,Department of Child Health, University of Auckland, Auckland, New Zealand.
| | - Donald R Love
- Department of Child Health, University of Auckland, Auckland, New Zealand.
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29
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Partemi S, Vidal MC, Striano P, Campuzano O, Allegue C, Pezzella M, Elia M, Parisi P, Belcastro V, Casellato S, Giordano L, Mastrangelo M, Pietrafusa N, Striano S, Zara F, Bianchi A, Buti D, La Neve A, Tassinari CA, Oliva A, Brugada R. Genetic and forensic implications in epilepsy and cardiac arrhythmias: a case series. Int J Legal Med 2015; 129:495-504. [PMID: 25119684 DOI: 10.1007/s00414-014-1063-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/05/2014] [Indexed: 12/27/2022]
Abstract
Epilepsy affects approximately 3% of the world's population, and sudden death is a significant cause of death in this population. Sudden unexpected death in epilepsy (SUDEP) accounts for up to 17% of all these cases, which increases the rate of sudden death by 24-fold as compared to the general population. The underlying mechanisms are still not elucidated, but recent studies suggest the possibility that a common genetic channelopathy might contribute to both epilepsy and cardiac disease to increase the incidence of death via a lethal cardiac arrhythmia. We performed genetic testing in a large cohort of individuals with epilepsy and cardiac conduction disorders in order to identify genetic mutations that could play a role in the mechanism of sudden death. Putative pathogenic disease-causing mutations in genes encoding cardiac ion channel were detected in 24% of unrelated individuals with epilepsy. Segregation analysis through genetic screening of the available family members and functional studies are crucial tasks to understand and to prove the possible pathogenicity of the variant, but in our cohort, only two families were available. Despite further research should be performed to clarify the mechanism of coexistence of both clinical conditions, genetic analysis, applied also in post-mortem setting, could be very useful to identify genetic factors that predispose epileptic patients to sudden death, helping to prevent sudden death in patients with epilepsy.
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Affiliation(s)
- Sara Partemi
- Institute of Legal Medicine, School of Medicine, Catholic University, Rome, Italy
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30
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Kapplinger JD, Giudicessi JR, Ye D, Tester DJ, Callis TE, Valdivia CR, Makielski JC, Wilde AA, Ackerman MJ. Enhanced Classification of Brugada Syndrome-Associated and Long-QT Syndrome-Associated Genetic Variants in the SCN5A-Encoded Na(v)1.5 Cardiac Sodium Channel. ACTA ACUST UNITED AC 2015; 8:582-95. [PMID: 25904541 DOI: 10.1161/circgenetics.114.000831] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 04/09/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND A 2% to 5% background rate of rare SCN5A nonsynonymous single nucleotide variants (nsSNVs) among healthy individuals confounds clinical genetic testing. Therefore, the purpose of this study was to enhance interpretation of SCN5A nsSNVs for clinical genetic testing using estimated predictive values derived from protein-topology and 7 in silico tools. METHODS AND RESULTS Seven in silico tools were used to assign pathogenic/benign status to nsSNVs from 2888 long-QT syndrome cases, 2111 Brugada syndrome cases, and 8975 controls. Estimated predictive values were determined for each tool across the entire SCN5A-encoded Na(v)1.5 channel as well as for specific topographical regions. In addition, the in silico tools were assessed for their ability to correlate with cellular electrophysiology studies. In long-QT syndrome, transmembrane segments S3-S5+S6 and the DIII/DIV linker region were associated with high probability of pathogenicity. For Brugada syndrome, only the transmembrane spanning domains had a high probability of pathogenicity. Although individual tools distinguished case- and control-derived SCN5A nsSNVs, the composite use of multiple tools resulted in the greatest enhancement of interpretation. The use of the composite score allowed for enhanced interpretation for nsSNVs outside of the topological regions that intrinsically had a high probability of pathogenicity, as well as within the transmembrane spanning domains for Brugada syndrome nsSNVs. CONCLUSIONS We have used a large case/control study to identify regions of Na(v)1.5 associated with a high probability of pathogenicity. Although topology alone would leave the variants outside these identified regions in genetic purgatory, the synergistic use of multiple in silico tools may help promote or demote a variant's pathogenic status.
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Affiliation(s)
- Jamie D Kapplinger
- From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.)
| | - John R Giudicessi
- From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.)
| | - Dan Ye
- From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.)
| | - David J Tester
- From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.)
| | - Thomas E Callis
- From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.)
| | - Carmen R Valdivia
- From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.)
| | - Jonathan C Makielski
- From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.)
| | - Arthur A Wilde
- From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.)
| | - Michael J Ackerman
- From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.).
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31
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Enhancing the Predictive Power of Mutations in the C-Terminus of the KCNQ1-Encoded Kv7.1 Voltage-Gated Potassium Channel. J Cardiovasc Transl Res 2015; 8:187-97. [PMID: 25854863 DOI: 10.1007/s12265-015-9622-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/22/2015] [Indexed: 01/17/2023]
Abstract
Despite the overrepresentation of Kv7.1 mutations among patients with a robust diagnosis of long QT syndrome (LQTS), a background rate of innocuous Kv7.1 missense variants observed in healthy controls creates ambiguity in the interpretation of LQTS genetic test results. A recent study showed that the probability of pathogenicity for rare missense mutations depends in part on the topological location of the variant in Kv7.1's various structure-function domains. Since the Kv7.1's C-terminus accounts for nearly 50 % of the overall protein and nearly 50 % of the overall background rate of rare variants falls within the C-terminus, further enhancement in mutation calling may provide guidance in distinguishing pathogenic long QT syndrome type 1 (LQT1)-causing mutations from rare non-disease-causing variants in the Kv7.1's C-terminus. Therefore, we have used conservation analysis and a large case-control study to generate topology-based estimative predictive values to aid in interpretation, identifying three regions of high conservation within the Kv7.1's C-terminus which have a high probability of LQT1 pathogenicity.
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32
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Jabbari J, Olesen MS, Yuan L, Nielsen JB, Liang B, Macri V, Christophersen IE, Nielsen N, Sajadieh A, Ellinor PT, Grunnet M, Haunsø S, Holst AG, Svendsen JH, Jespersen T. Common and Rare Variants in
SCN10A
Modulate the Risk of Atrial Fibrillation. ACTA ACUST UNITED AC 2015. [DOI: 10.1161/circgenetics.113.000442] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background—
Genome-wide association studies have shown that the common single nucleotide polymorphism rs6800541 located in
SCN10A
, encoding the voltage-gated Na
v
1.8 sodium channel, is associated with PR-interval prolongation and atrial fibrillation (AF). Single nucleotide polymorphism rs6800541 is in high linkage disequilibrium with the nonsynonymous variant in
SCN10A
, rs6795970 (V1073A,
r
2
=0.933). We therefore sought to determine whether common and rare
SCN10A
variants are associated with early onset AF.
Methods and Results—
SCN10A
was sequenced in 225 AF patients in whom there was no evidence of other cardiovascular disease or dysfunction (lone AF). In an association study of the rs6795970 single nucleotide polymorphism variant, we included 515 AF patients and 2 control cohorts of 730 individuals free of AF and 6161 randomly sampled individuals. Functional characterization of
SCN10A
variants was performed by whole-cell patch-clamping. In the lone AF cohort, 9 rare missense variants and 1 splice site donor variant were detected. Interestingly, AF patients were found to have higher G allele frequency of rs6795970, which encodes the alanine variant at position 1073 (described from here on as A1073, odds ratio =1.35 [1.16−1.54];
P
=2.3×10
−5
). Both of the common variants, A1073 and P1092, induced a gain-of-channel function, whereas the rare missense variants, V94G and R1588Q, resulted in a loss-of-channel function.
Conclusions—
The common variant A1073 is associated with increased susceptibility to AF. Both rare and common variants have effect on the function of the channel, indicating that these variants influence susceptibility to AF. Hence, our study suggests that
SCN10A
variations are involved in the genesis of AF.
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Affiliation(s)
- Javad Jabbari
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Morten S. Olesen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Lei Yuan
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Jonas B. Nielsen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Bo Liang
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Vincenzo Macri
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Ingrid E. Christophersen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Nikolaj Nielsen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Ahmad Sajadieh
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Patrick T. Ellinor
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Morten Grunnet
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Stig Haunsø
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Anders G. Holst
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Jesper H. Svendsen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
| | - Thomas Jespersen
- From the The Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Department of Biomedical Sciences (J.J., M.S.O., L.Y., J.B.N., B.L., N.N., M.G., S.H., A.G.H., J.H.S., T.J.), Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet (J.J., M.S.O., J.B.N., S.H., A.G.H., J.H.S.), and Department of Clinical Medicine (S.H., J.H.S.), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular Research Center,
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Ruklisa D, Ware JS, Walsh R, Balding DJ, Cook SA. Bayesian models for syndrome- and gene-specific probabilities of novel variant pathogenicity. Genome Med 2015; 7:5. [PMID: 25649125 PMCID: PMC4308924 DOI: 10.1186/s13073-014-0120-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 12/05/2014] [Indexed: 12/04/2022] Open
Abstract
Background With the advent of affordable and comprehensive sequencing technologies, access to molecular genetics for clinical diagnostics and research applications is increasing. However, variant interpretation remains challenging, and tools that close the gap between data generation and data interpretation are urgently required. Here we present a transferable approach to help address the limitations in variant annotation. Methods We develop a network of Bayesian logistic regression models that integrate multiple lines of evidence to evaluate the probability that a rare variant is the cause of an individual’s disease. We present models for genes causing inherited cardiac conditions, though the framework is transferable to other genes and syndromes. Results Our models report a probability of pathogenicity, rather than a categorisation into pathogenic or benign, which captures the inherent uncertainty of the prediction. We find that gene- and syndrome-specific models outperform genome-wide approaches, and that the integration of multiple lines of evidence performs better than individual predictors. The models are adaptable to incorporate new lines of evidence, and results can be combined with familial segregation data in a transparent and quantitative manner to further enhance predictions. Though the probability scale is continuous, and innately interpretable, performance summaries based on thresholds are useful for comparisons. Using a threshold probability of pathogenicity of 0.9, we obtain a positive predictive value of 0.999 and sensitivity of 0.76 for the classification of variants known to cause long QT syndrome over the three most important genes, which represents sufficient accuracy to inform clinical decision-making. A web tool APPRAISE [http://www.cardiodb.org/APPRAISE] provides access to these models and predictions. Conclusions Our Bayesian framework provides a transparent, flexible and robust framework for the analysis and interpretation of rare genetic variants. Models tailored to specific genes outperform genome-wide approaches, and can be sufficiently accurate to inform clinical decision-making. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0120-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - James S Ware
- NIHR Biomedical Research Unit in Cardiovascular Disease at Royal Brompton and Harefield NHS Foundation Trust and Imperial College, London, UK ; National Heart and Lung Institute, Imperial College, London, UK
| | - Roddy Walsh
- NIHR Biomedical Research Unit in Cardiovascular Disease at Royal Brompton and Harefield NHS Foundation Trust and Imperial College, London, UK
| | - David J Balding
- UCL Genetics Institute, London, UK ; Current address: Department of Genetics and Department of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Stuart A Cook
- NIHR Biomedical Research Unit in Cardiovascular Disease at Royal Brompton and Harefield NHS Foundation Trust and Imperial College, London, UK ; National Heart and Lung Institute, Imperial College, London, UK ; National Heart Centre, Singapore, Singapore ; Duke-National University, Singapore, Singapore
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34
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Riuró H, Campuzano O, Berne P, Arbelo E, Iglesias A, Pérez-Serra A, Coll-Vidal M, Partemi S, Mademont-Soler I, Picó F, Allegue C, Oliva A, Gerstenfeld E, Sarquella-Brugada G, Castro-Urda V, Fernández-Lozano I, Mont L, Brugada J, Scornik FS, Brugada R. Genetic analysis, in silico prediction, and family segregation in long QT syndrome. Eur J Hum Genet 2015; 23:79-85. [PMID: 24667783 PMCID: PMC4266740 DOI: 10.1038/ejhg.2014.54] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/23/2014] [Accepted: 02/19/2014] [Indexed: 01/24/2023] Open
Abstract
The heritable cardiovascular disorder long QT syndrome (LQTS), characterized by prolongation of the QT interval on electrocardiogram, carries a high risk of sudden cardiac death. We sought to add new data to the existing knowledge of genetic mutations contributing to LQTS to both expand our understanding of its genetic basis and assess the value of genetic testing in clinical decision-making. Direct sequencing of the five major contributing genes, KCNQ1, KCNH2, SCN5A, KCNE1, and KCNE2, was performed in a cohort of 115 non-related LQTS patients. Pathogenicity of the variants was analyzed using family segregation, allele frequency from public databases, conservation analysis, and Condel and Provean in silico predictors. Phenotype-genotype correlations were analyzed statistically. Sequencing identified 36 previously described and 18 novel mutations. In 51.3% of the index cases, mutations were found, mostly in KCNQ1, KCNH2, and SCN5A; 5.2% of cases had multiple mutations. Pathogenicity analysis revealed 39 mutations as likely pathogenic, 12 as VUS, and 3 as non-pathogenic. Clinical analysis revealed that 75.6% of patients with QTc≥500 ms were genetically confirmed. Our results support the use of genetic testing of KCNQ1, KCNH2, and SCN5A as part of the diagnosis of LQTS and to help identify relatives at risk of SCD. Further, the genetic tools appear more valuable as disease severity increases. However, the identification of genetic variations in the clinical investigation of single patients using bioinformatic tools can produce erroneous conclusions regarding pathogenicity. Therefore segregation studies are key to determining causality.
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Affiliation(s)
- Helena Riuró
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
- Department of Medical Sciences, Medical School, Universitat de Girona, Girona, Spain
| | - Oscar Campuzano
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
- Department of Medical Sciences, Medical School, Universitat de Girona, Girona, Spain
| | - Paola Berne
- Hospital Clínic de Barcelona, Barcelona, Spain
| | | | - Anna Iglesias
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
- Department of Medical Sciences, Medical School, Universitat de Girona, Girona, Spain
| | - Alexandra Pérez-Serra
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
| | - Mònica Coll-Vidal
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
- Institute of Forensic Medicine, Catholic University, Rome, Italy
| | - Sara Partemi
- Institute of Forensic Medicine, Catholic University, Rome, Italy
| | - Irene Mademont-Soler
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
| | - Ferran Picó
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
| | - Catarina Allegue
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
- Department of Medical Sciences, Medical School, Universitat de Girona, Girona, Spain
| | - Antonio Oliva
- Institute of Forensic Medicine, Catholic University, Rome, Italy
| | | | | | | | | | - Lluís Mont
- Hospital Clínic de Barcelona, Barcelona, Spain
| | | | - Fabiana S Scornik
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
- Department of Medical Sciences, Medical School, Universitat de Girona, Girona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
- Department of Medical Sciences, Medical School, Universitat de Girona, Girona, Spain
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35
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Large-scale mutational analysis of Kv11.1 reveals molecular insights into type 2 long QT syndrome. Nat Commun 2014; 5:5535. [PMID: 25417810 PMCID: PMC4243539 DOI: 10.1038/ncomms6535] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 10/09/2014] [Indexed: 12/23/2022] Open
Abstract
It has been suggested that deficient protein trafficking to the cell membrane is the dominant mechanism associated with type 2 Long QT syndrome (LQT2) caused by Kv11.1 potassium channel missense mutations, and that for many mutations the trafficking defect can be corrected pharmacologically. However, this inference was based on expression of a small number of Kv11.1 mutations. We performed a comprehensive analysis of 167 LQT2-linked missense mutations in four Kv11.1 structural domains and found that deficient protein trafficking is the dominant mechanism for all domains except for the distal carboxy-terminus. Also, most pore mutations--in contrast to intracellular domain mutations--were found to have severe dominant-negative effects when co-expressed with wild-type subunits. Finally, pharmacological correction of the trafficking defect in homomeric mutant channels was possible for mutations within all structural domains. However, pharmacological correction is dramatically improved for pore mutants when co-expressed with wild-type subunits to form heteromeric channels.
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36
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Akilzhanova A, Guelly C, Nuralinov O, Nurkina Z, Nazhat D, Smagulov S, Tursunbekov A, Alzhanova A, Rashbayeva G, Abdrakhmanov A, Dosmagambet S, Trajanoski S, Zhumadilov Z, Sharman A, Bekbosynova M. RYR2 sequencing reveals novel missense mutations in a Kazakh idiopathic ventricular tachycardia study cohort. PLoS One 2014; 9:e101059. [PMID: 24978818 PMCID: PMC4076244 DOI: 10.1371/journal.pone.0101059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 05/07/2014] [Indexed: 12/15/2022] Open
Abstract
Channelopathies, caused by disturbed potassium or calcium ion management in cardiac myocytes are a major cause of heart failure and sudden cardiac death worldwide. The human ryanodine receptor 2 (RYR2) is one of the key players tightly regulating calcium efflux from the sarcoplasmic reticulum to the cytosol and found frequently mutated (<60%) in context of catecholaminergic polymorphic ventricular tachycardia (CPVT1). We tested 35 Kazakhstani patients with episodes of ventricular arrhythmia, two of those with classical CPVT characteristics and 33 patients with monomorphic idiopathic ventricular arrhythmia, for variants in the hot-spot regions of the RYR2 gene. This approach revealed two novel variants; one de-novo RYR2 mutation (c13892A>T; p.D4631V) in a CPVT patient and a novel rare variant (c5428G>C; p.V1810L) of uncertain significance in a patient with VT of idiopathic origin which we suggest represents a low-penetrance or susceptibility variant. In addition we identified a known variant previously associated with arrhythmogenic right ventricular dysplasia type2 (ARVD2). Combining sets of prediction scores and reference databases appeared fundamental to predict the pathogenic potential of novel and rare missense variants in populations where genotype data are rare.
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Affiliation(s)
- Ainur Akilzhanova
- Department of Genomic and Personalized Medicine, Center for Life Sciences, Nazarbayev University, Astana, Republic of Kazakhstan
- * E-mail:
| | - Christian Guelly
- Center of Medical Research, Medical University of Graz, Graz, Austria, Graz, Austria
| | - Omirbek Nuralinov
- National Scientific Cardiac Surgery Center, Astana, Republic of Kazakhstan
| | - Zhannur Nurkina
- Department of Genomic and Personalized Medicine, Center for Life Sciences, Nazarbayev University, Astana, Republic of Kazakhstan
| | - Dinara Nazhat
- National Scientific Cardiac Surgery Center, Astana, Republic of Kazakhstan
| | - Shalkhar Smagulov
- National Scientific Cardiac Surgery Center, Astana, Republic of Kazakhstan
| | - Azat Tursunbekov
- National Scientific Cardiac Surgery Center, Astana, Republic of Kazakhstan
| | - Anar Alzhanova
- National Scientific Cardiac Surgery Center, Astana, Republic of Kazakhstan
| | | | - Ayan Abdrakhmanov
- National Scientific Cardiac Surgery Center, Astana, Republic of Kazakhstan
| | | | - Slave Trajanoski
- Center of Medical Research, Medical University of Graz, Graz, Austria, Graz, Austria
| | - Zhaxybay Zhumadilov
- Department of Genomic and Personalized Medicine, Center for Life Sciences, Nazarbayev University, Astana, Republic of Kazakhstan
| | - Almaz Sharman
- Department of Genomic and Personalized Medicine, Center for Life Sciences, Nazarbayev University, Astana, Republic of Kazakhstan
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Yang RQ, Jabbari J, Cheng XS, Jabbari R, Nielsen JB, Risgaard B, Chen X, Sajadieh A, Haunsø S, Svendsen JH, Olesen MS, Tfelt-Hansen J. New population-based exome data question the pathogenicity of some genetic variants previously associated with Marfan syndrome. BMC Genet 2014; 15:74. [PMID: 24941995 PMCID: PMC4070351 DOI: 10.1186/1471-2156-15-74] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 06/02/2014] [Indexed: 12/14/2022] Open
Abstract
Background Marfan syndrome (MFS) is a rare autosomal dominantly inherited connective tissue disorder with an estimated prevalence of 1:5,000. More than 1000 variants have been previously reported to be associated with MFS. However, the disease-causing effect of these variants may be questionable as many of the original studies used low number of controls. To study whether there are possible false-positive variants associated with MFS, four in silico prediction tools (SIFT, Polyphen-2, Grantham score, and conservation across species) were used to predict the pathogenicity of these variant. Results Twenty-three out of 891 previously MFS-associated variants were identified in the ESP. These variants were distributed on 100 heterozygote carriers in 6494 screened individuals. This corresponds to a genotype prevalence of 1:65 for MFS. Using a more conservative approach (cutoff value of >2 carriers in the EPS), 10 variants affected a total of 82 individuals. This gives a genotype prevalence of 1:79 (82:6494) in the ESP. A significantly higher frequency of MFS-associated variants not present in the ESP were predicted to be pathogenic with the agreement of ≥3 prediction tools, compared to the variants present in the ESP (p = 3.5 × 10−15). Conclusions This study showed a higher genotype prevalence of MFS than expected from the phenotype prevalence in the general population. The high genotype prevalence suggests that these variants are not the monogenic cause of MFS. Therefore, caution should be taken with regard to disease stratification based on these previously reported MFS-associated variants.
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Affiliation(s)
- Ren-Qiang Yang
- Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
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Olesen MS, Andreasen L, Jabbari J, Refsgaard L, Haunsø S, Olesen SP, Nielsen JB, Schmitt N, Svendsen JH. Very early-onset lone atrial fibrillation patients have a high prevalence of rare variants in genes previously associated with atrial fibrillation. Heart Rhythm 2014; 11:246-51. [DOI: 10.1016/j.hrthm.2013.10.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Indexed: 01/18/2023]
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Yoshinaga M, Kucho Y, Sarantuya J, Ninomiya Y, Horigome H, Ushinohama H, Shimizu W, Horie M. Genetic Characteristics of Children and Adolescents With Long-QT Syndrome Diagnosed by School-Based Electrocardiographic Screening Programs. Circ Arrhythm Electrophysiol 2014; 7:107-12. [DOI: 10.1161/circep.113.000426] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
A school-based electrocardiographic screening program has been developed in Japan. However, few data are available on the genetic characteristics of pediatric patients with long-QT syndrome who were diagnosed by this program.
Methods and Results—
A total of 117 unrelated probands aged ≤18 years were the subjects who were referred to our centers for genetic testing. Of these, 69 subjects diagnosed by the program formed the screened group. A total of 48 subjects were included in the clinical group and were diagnosed with long-QT syndrome–related symptoms, familial study, or by chance. Mutations were classified as radical, of high probability of pathogenicity, or of uncertain significance. Two subjects in the clinical group died. Genotypes were identified in 50 (72%) and 23 (48%) of subjects in the screened and clinical groups, respectively. Of the
KCNQ1
or
KCNH2
mutations, 31 of 33 (94%) in the screened group and 14 of 15 (93%) in the clinical group were radical and of high probability of pathogenicity. Prevalence of symptoms before (9/69 versus 31/48;
P
<0.0001) and after (12/69 versus 17/48;
P
=0.03) diagnosis was significantly lower in the screened group when compared with that in the clinical group although the QTc values, family history of long-QT syndrome, sudden death, and follow-up periods were not different between the groups.
Conclusions—
These data suggest that the screening program may be effective for early diagnosis of long-QT syndrome that may allow intervention before symptoms. In addition, screened patients should have follow-up equivalent to clinically identified patients.
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Affiliation(s)
- Masao Yoshinaga
- From the Department of Pediatrics, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan (M.Y., Y.K., Y.N.); Department of Molecular Biology and Genetics, School of Bio-medicine, Health Sciences University of Mongolia, Ulaanbaatar, Mongolia (J.S.); Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan (H.H.); Department of Cardiology, Fukuoka Children’s Hospital and Medical Center for Infectious Diseases, Fukuoka, Japan (H.U.); Department of
| | - Yu Kucho
- From the Department of Pediatrics, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan (M.Y., Y.K., Y.N.); Department of Molecular Biology and Genetics, School of Bio-medicine, Health Sciences University of Mongolia, Ulaanbaatar, Mongolia (J.S.); Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan (H.H.); Department of Cardiology, Fukuoka Children’s Hospital and Medical Center for Infectious Diseases, Fukuoka, Japan (H.U.); Department of
| | - Jav Sarantuya
- From the Department of Pediatrics, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan (M.Y., Y.K., Y.N.); Department of Molecular Biology and Genetics, School of Bio-medicine, Health Sciences University of Mongolia, Ulaanbaatar, Mongolia (J.S.); Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan (H.H.); Department of Cardiology, Fukuoka Children’s Hospital and Medical Center for Infectious Diseases, Fukuoka, Japan (H.U.); Department of
| | - Yumiko Ninomiya
- From the Department of Pediatrics, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan (M.Y., Y.K., Y.N.); Department of Molecular Biology and Genetics, School of Bio-medicine, Health Sciences University of Mongolia, Ulaanbaatar, Mongolia (J.S.); Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan (H.H.); Department of Cardiology, Fukuoka Children’s Hospital and Medical Center for Infectious Diseases, Fukuoka, Japan (H.U.); Department of
| | - Hitoshi Horigome
- From the Department of Pediatrics, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan (M.Y., Y.K., Y.N.); Department of Molecular Biology and Genetics, School of Bio-medicine, Health Sciences University of Mongolia, Ulaanbaatar, Mongolia (J.S.); Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan (H.H.); Department of Cardiology, Fukuoka Children’s Hospital and Medical Center for Infectious Diseases, Fukuoka, Japan (H.U.); Department of
| | - Hiroya Ushinohama
- From the Department of Pediatrics, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan (M.Y., Y.K., Y.N.); Department of Molecular Biology and Genetics, School of Bio-medicine, Health Sciences University of Mongolia, Ulaanbaatar, Mongolia (J.S.); Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan (H.H.); Department of Cardiology, Fukuoka Children’s Hospital and Medical Center for Infectious Diseases, Fukuoka, Japan (H.U.); Department of
| | - Wataru Shimizu
- From the Department of Pediatrics, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan (M.Y., Y.K., Y.N.); Department of Molecular Biology and Genetics, School of Bio-medicine, Health Sciences University of Mongolia, Ulaanbaatar, Mongolia (J.S.); Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan (H.H.); Department of Cardiology, Fukuoka Children’s Hospital and Medical Center for Infectious Diseases, Fukuoka, Japan (H.U.); Department of
| | - Minoru Horie
- From the Department of Pediatrics, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan (M.Y., Y.K., Y.N.); Department of Molecular Biology and Genetics, School of Bio-medicine, Health Sciences University of Mongolia, Ulaanbaatar, Mongolia (J.S.); Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan (H.H.); Department of Cardiology, Fukuoka Children’s Hospital and Medical Center for Infectious Diseases, Fukuoka, Japan (H.U.); Department of
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Bartos DC, Giudicessi JR, Tester DJ, Ackerman MJ, Ohno S, Horie M, Gollob MH, Burgess DE, Delisle BP. A KCNQ1 mutation contributes to the concealed type 1 long QT phenotype by limiting the Kv7.1 channel conformational changes associated with protein kinase A phosphorylation. Heart Rhythm 2013; 11:459-68. [PMID: 24269949 DOI: 10.1016/j.hrthm.2013.11.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Indexed: 11/17/2022]
Abstract
BACKGROUND Type 1 long QT syndrome (LQT1) is caused by loss-of-function mutations in the KCNQ1-encoded Kv7.1 channel that conducts the slowly activating component of the delayed rectifier K(+) current (IKs). Clinically, the diagnosis of LQT1 is complicated by variable phenotypic expressivity, whereby approximately 25% of genotype-positive individuals present with concealed LQT1 (resting corrected QT [QTc] interval ≤460 ms). OBJECTIVE To determine whether a specific molecular mechanism contributes to concealed LQT1. METHODS We identified a multigenerational LQT1 family whereby 79% of the patients genotype-positive for p.Ile235Asn-KCNQ1 (I235N-Kv7.1) have concealed LQT1. We assessed the effect I235N-Kv7.1 has on IKs and the ventricular action potential (AP) by using in vitro analysis and computational simulations. RESULTS Clinical data showed that all 10 patients with I235N-Kv7.1 have normal resting QTc intervals but abnormal QTc interval prolongation during the recovery phase of an electrocardiographic treadmill stress test. Voltage-clamping HEK293 cells coexpressing wild-type Kv7.1 and I235N-Kv7.1 (to mimic the patients' genotypes) showed that I235N-Kv7.1 generated relatively normal functioning Kv7.1 channels but were insensitive to protein kinase A (PKA) activation. Phosphomimetic and quinidine sensitivity studies suggest that I235N-Kv7.1 limits the conformational changes in Kv7.1 channels, which are necessary to upregulate IKs after PKA phosphorylation. Computational ventricular AP simulations predicted that the PKA insensitivity of I235N-Kv7.1 is primarily responsible for prolonging the AP with β-adrenergic stimulation, especially at slower cycle lengths. CONCLUSIONS KCNQ1 mutations that generate relatively normal Kv7.1 channels, but limit the upregulation of IKs by PKA activation, likely contribute to concealed LQT1.
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Affiliation(s)
- Daniel C Bartos
- Department of Physiology, Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - John R Giudicessi
- Departments of Medicine, Pediatrics, and Molecular Pharmacology and Experimental Therapeutics, Divisions of Cardiovascular Diseases and Pediatric Cardiology, Mayo Clinic, Rochester, Minnesota
| | - David J Tester
- Departments of Medicine, Pediatrics, and Molecular Pharmacology and Experimental Therapeutics, Divisions of Cardiovascular Diseases and Pediatric Cardiology, Mayo Clinic, Rochester, Minnesota
| | - Michael J Ackerman
- Departments of Medicine, Pediatrics, and Molecular Pharmacology and Experimental Therapeutics, Divisions of Cardiovascular Diseases and Pediatric Cardiology, Mayo Clinic, Rochester, Minnesota
| | - Seiko Ohno
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Sciences, Seta-tsukinowa, Otsu, Japan
| | - Minoru Horie
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Sciences, Seta-tsukinowa, Otsu, Japan
| | - Michael H Gollob
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Don E Burgess
- Department of Physiology, Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Brian P Delisle
- Department of Physiology, Center for Muscle Biology, University of Kentucky, Lexington, Kentucky.
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Berge KE, Leren TP. Genetics of hypertrophic cardiomyopathy in Norway. Clin Genet 2013; 86:355-60. [PMID: 24111713 DOI: 10.1111/cge.12286] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/20/2013] [Accepted: 09/20/2013] [Indexed: 11/27/2022]
Abstract
Genetic testing for hypertrophic cardiomyopathy (HCM) became available in Norway in 2003. Here, we describe the results of this testing in probands with HCM referred until the end of 2012. The translated exons of MYBPC3, MYH7, TNNI3, TNNT2, MYL2 and MYL3 were analyzed in two groups of probands. In Group 1, comprising 696 probands above 1 year of age, a mutation was found in 203 patients (29.2%). Of those, 5.9% were carriers of two mutations. Mean age in double mutation carriers, single mutation carriers and mutation negative probands was 44 years (± 19 years), 50 years (± 5 years) and 55 years (± 6 years), respectively. In Group 2, comprising 26 infants below the age of 1, a mutation was found in 15.4%. A total of 120 different mutations were found of which 51 (42.5%) were novel.
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Affiliation(s)
- K E Berge
- Department of Medical Genetics, Oslo University Hospital Ullevaal, Oslo, Norway
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Jabbari J, Jabbari R, Nielsen MW, Holst AG, Nielsen JB, Haunsø S, Tfelt-Hansen J, Svendsen JH, Olesen MS. New Exome Data Question the Pathogenicity of Genetic Variants Previously Associated With Catecholaminergic Polymorphic Ventricular Tachycardia. ACTA ACUST UNITED AC 2013; 6:481-9. [DOI: 10.1161/circgenetics.113.000118] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Background—
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a lethal, rare hereditary disease with an estimated prevalence of 1:10 000. The genetic variants that cause CPVT are usually highly penetrant. To date, about 189 variants in 5 genes (
RYR2, CASQ2, CALM1, TRND
, and
KCNJ2
) have been associated with CPVT pathogenesis.
Methods and Results—
The Exome Sequencing Project database (ESP; n= 6503) was systematically searched for previously published missense and nonsense CPVT–associated variants reported in several comprehensive reviews and in 2 databases: The Human Gene Mutation Database and The Inherited Arrhythmias Database. We used 4 different prediction tools to assess all missense variants previously associated with CPVT and compared the prediction of protein damage between CPVT-associated variants identified in the ESP and those variants not identified in the ESP. We identified 11% of the variants previously associated with CPVT in the ESP population. In the literature, 57% of these variants were reported as novel disease-causing variants absent in the healthy control subjects. These putative CPVT variants were identified in 41 out of 6131 subjects in the ESP population, corresponding to a prevalence of CPVT of up to 1:150. Using an agreement of ≥3, in silico prediction tools showed a significantly higher frequency of damaging variants among the CPVT-associated variants not identified in the ESP database (83%) compared with those variants identified in the ESP (50%;
P
=0.021).
Conclusions—
We identified a substantial overrepresentation of CPVT-associated variants in a large exome database, suggesting that these variants are not necessarily the monogenic cause of CPVT.
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Affiliation(s)
- Javad Jabbari
- From the Danish National Research Foundation Centre for Cardiac Arrhythmia (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); and Department of Clinical Medicine, Faculty of Health Sciences (S.H., J.T.-H., J.H.S.), University of Copenhagen, Copenhagen, Denmark
| | - Reza Jabbari
- From the Danish National Research Foundation Centre for Cardiac Arrhythmia (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); and Department of Clinical Medicine, Faculty of Health Sciences (S.H., J.T.-H., J.H.S.), University of Copenhagen, Copenhagen, Denmark
| | - Morten W. Nielsen
- From the Danish National Research Foundation Centre for Cardiac Arrhythmia (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); and Department of Clinical Medicine, Faculty of Health Sciences (S.H., J.T.-H., J.H.S.), University of Copenhagen, Copenhagen, Denmark
| | - Anders G. Holst
- From the Danish National Research Foundation Centre for Cardiac Arrhythmia (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); and Department of Clinical Medicine, Faculty of Health Sciences (S.H., J.T.-H., J.H.S.), University of Copenhagen, Copenhagen, Denmark
| | - Jonas B. Nielsen
- From the Danish National Research Foundation Centre for Cardiac Arrhythmia (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); and Department of Clinical Medicine, Faculty of Health Sciences (S.H., J.T.-H., J.H.S.), University of Copenhagen, Copenhagen, Denmark
| | - Stig Haunsø
- From the Danish National Research Foundation Centre for Cardiac Arrhythmia (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); and Department of Clinical Medicine, Faculty of Health Sciences (S.H., J.T.-H., J.H.S.), University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- From the Danish National Research Foundation Centre for Cardiac Arrhythmia (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); and Department of Clinical Medicine, Faculty of Health Sciences (S.H., J.T.-H., J.H.S.), University of Copenhagen, Copenhagen, Denmark
| | - Jesper H. Svendsen
- From the Danish National Research Foundation Centre for Cardiac Arrhythmia (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); and Department of Clinical Medicine, Faculty of Health Sciences (S.H., J.T.-H., J.H.S.), University of Copenhagen, Copenhagen, Denmark
| | - Morten S. Olesen
- From the Danish National Research Foundation Centre for Cardiac Arrhythmia (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); Laboratory for Molecular Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital (J.J., R.J., M.W.N., A.G.H., J.B.N., S.H., J.T.-H., J.H.S., M.S.O.); and Department of Clinical Medicine, Faculty of Health Sciences (S.H., J.T.-H., J.H.S.), University of Copenhagen, Copenhagen, Denmark
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Abstract
Congenital long QT syndrome (LQTS) is a genetically heterogeneous group of heritable disorders of myocardial repolarization linked by the shared clinical phenotype of QT prolongation on electrocardiogram and an increased risk of potentially life-threatening cardiac arrhythmias. At the molecular level, mutations in 15 distinct LQTS-susceptibility genes that encode ion channel pore-forming α-subunits and accessory β-subunits central to the electromechanical function of the heart have been implicated in its pathogenesis. Over the past 2 decades, our evolving understanding of the electrophysiological mechanisms by which specific genetic substrates perturb the cardiac action potential has translated into vastly improved approaches to the diagnosis, risk stratification, and treatment of patients with LQTS. In this review, we describe how our understanding of the molecular underpinnings of LQTS has yielded numerous clinically meaningful genotype-phenotype correlations and how these insights have translated into genotype- and phenotype-guided approaches to the clinical management of LQTS.
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Affiliation(s)
| | - Michael J. Ackerman
- Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN
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Genetic testing in heritable cardiac arrhythmia syndromes: differentiating pathogenic mutations from background genetic noise. Curr Opin Cardiol 2013; 28:63-71. [PMID: 23128497 DOI: 10.1097/hco.0b013e32835b0a41] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW In this review, we summarize the basic principles governing rare variant interpretation in the heritable cardiac arrhythmia syndromes, focusing on recent advances that have led to disease-specific approaches to the interpretation of positive genetic testing results. RECENT FINDINGS Elucidation of the genetic substrates underlying heritable cardiac arrhythmia syndromes has unearthed new arrhythmogenic mechanisms and given rise to a number of clinically meaningful genotype-phenotype correlations. As such, genetic testing for these disorders now carries important diagnostic, prognostic, and therapeutic implications. Recent large-scale systematic studies designed to explore the background genetic 'noise' rate associated with these genetic tests have provided important insights and enhanced how positive genetic testing results are interpreted for these potentially lethal, yet highly treatable, cardiovascular disorders. SUMMARY Clinically available genetic tests for heritable cardiac arrhythmia syndromes allow the identification of potentially at-risk family members and contribute to the risk-stratification and selection of therapeutic interventions in affected individuals. The systematic evaluation of the 'signal-to-noise' ratio associated with these genetic tests has proven critical and essential to assessing the probability that a given variant represents a rare pathogenic mutation or an equally rare, yet innocuous, genetic bystander.
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Reassessing the pathogenicity of rare variants in inherited heart disease. Heart Rhythm 2013; 10:560-1. [DOI: 10.1016/j.hrthm.2013.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Indexed: 11/24/2022]
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Abriel H, Zaklyazminskaya EV. A modern approach to classify missense mutations in cardiac channelopathy genes. ACTA ACUST UNITED AC 2013; 5:487-9. [PMID: 23074335 DOI: 10.1161/circgenetics.112.964809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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Risgaard B, Jabbari R, Refsgaard L, Holst AG, Haunsø S, Sadjadieh A, Winkel BG, Olesen MS, Tfelt-Hansen J. High prevalence of genetic variants previously associated with Brugada syndrome in new exome data. Clin Genet 2013; 84:489-95. [PMID: 23414114 DOI: 10.1111/cge.12126] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/13/2013] [Indexed: 01/08/2023]
Abstract
More than 300 variants in 12 genes have been associated with Brugada syndrome (BrS) which has a prevalence ranging between 1:2000 and 1:100,000. Until recently, there has been little knowledge regarding the distribution of genetic variations in the general population. This problem was partly solved, when exome data from the NHLI GO Exome Sequencing Project (ESP) was published. In this study, we aimed to report the prevalence of previously BrS-associated variants in the ESP population. We performed a search in ESP for variants previously associated with BrS. In addition, four variants in ESP were genotyped in a second Danish control population (n = 536) with available electrocardiograms. In ESP, we identified 38 of 355 (10%) variants, distributed on 272 heterozygote carriers and two homozygote carriers. The genes investigated were on average screened in 6258 individuals. This corresponds to a surprisingly high genotype prevalence of 1:23 (274:6258). Genotyping the four common ESP-derived variants CACNA2D1 S709N, SCN5A F2004L, CACNB2 S143F, and CACNB2 T450I in the Danish controls, we found a genotype prevalence comparable with that found in ESP. We suggest that exome data are used in research, as an additive tool to predict the pathogenicity of variants in patients suspected for BrS.
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Affiliation(s)
- B Risgaard
- Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), University of Copenhagen, Copenhagen, Denmark; Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre; Department of Cardiology, The Heart Centre, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
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Mutations in genes encoding cardiac ion channels previously associated with sudden infant death syndrome (SIDS) are present with high frequency in new exome data. Can J Cardiol 2013; 29:1104-9. [PMID: 23465283 DOI: 10.1016/j.cjca.2012.12.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/23/2012] [Accepted: 12/03/2012] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Sudden infant death syndrome (SIDS) is the leading cause of death in the first 6 months after birth in the industrialized world. The genetic contribution to SIDS has been investigated intensively and to date, 14 cardiac channelopathy genes have been associated with SIDS. Newly published data from National Heart, Lung, and Blood Institute Grand Opportunity (NHLBI GO) Exome Sequencing Project (ESP) provided important knowledge on genetic variation in the background population. Our aim was to identify all variants previously associated with SIDS in ESP to improve the discrimination between plausible disease-causing mutations and variants most likely to be false-positive. METHODS The PubMed database was searched to identify SIDS-associated channelopathy variants and the prevalence of these in the ESP population (6500 individuals) were obtained. In silico prediction tools were applied to variants present in ESP and 6 SIDS-associated variants (CAV3 p.C72W, p.T78M; KCNH2 p.R148W, and SCN5A p.S216L, p.V1951L, p.F2004L) were genotyped in our own control population. RESULTS Nineteen different missense variants previously associated with SIDS were identified in ESP affecting 225 of 6424 alleles. This corresponds to 1:29 individuals in the ESP population being carriers of a SIDS-associated variant. Genotyping of 6 SIDS-associated variants in our own controls revealed frequencies comparable with those found in ESP. CONCLUSIONS A very high prevalence of previously SIDS-associated variants was identified in exome data from population studies. Our findings indicate that the suggested disease-causing role of some of these variants is questionable. A cautious interpretation of these variants must be made when found in SIDS victims.
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