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Wei M, Li Y, Liu X, Zhou K, Qiu Y, Liu L, Huang L, Liu Z. Case report: Additional variants induced sudden cardiac death among pediatric ACM with DSG2 homozygous mutant genotype: a report of three cases. Front Genet 2024; 15:1428796. [PMID: 39253717 PMCID: PMC11381389 DOI: 10.3389/fgene.2024.1428796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/05/2024] [Indexed: 09/11/2024] Open
Abstract
Background Mutations in genes encoding desmosomal proteins are the leading cause of arrhythmogenic cardiomyopathy (ACM). The majority of the inherited ACM cases demonstrate autosomal dominant genotype. Several cases with the homozygous DSG2 c.1592T>G (p.F531C) variant genotype demonstrate adverse clinical outcomes, but the roles of associated genetic mutations are not clear. In this report, we describe three ACM cases with the homozygous DSG2 c.1592T>G (p.F531C) variant genotype combined with additional heterozygous cardiomyopathy-related genetic mutations that cause aggravated clinical manifestations and worse clinical outcomes. Case presentation The three reported probands demonstrated similar clinical presentations such as heart failure, cardiac enlargement, and lethal arrhythmias. All of them experienced sudden cardiac death (SCD) before undergoing implantable cardioverter defibrillator (ICD) or heart transplantations. Whole-exome sequencing analysis demonstrated that the three patients inherited the homozygous DSG2 c.1592T>G (p.F531C) variant. Furthermore, probands I, II, and III also inherited additional heterozygous cardiomyopathy-associated mutations, including DSP c.7883T>C, SCN5a c.3577C>T, or MYH7 c.427C>T, respectively. These variants were confirmed as pathogenetic variants. A systematic review of all the reported ACM cases with the homozygous DSG2 variants suggested that the additional genetic mutations contributed to the early age onset of ACM and lethal cardiac events. Conclusion In conclusion, we report three rare cases of ACM with the same homozygous DSG2 variant in combination with additional heterozygous mutations in cardiomyopathy-associated genes. A systematic review of all the ACM cases with homozygous DSG2 variants demonstrated that the additional genetic variants contributed to the aggravated clinical manifestations and worse clinical symptoms of the ACM patients because of homozygous DSG2 mutations, including early disease onset and lethal cardiac events. Our data suggested that comprehensive genetic evaluation should be performed to identify any potential additional pathogenic variants that may significantly influence the clinical prognosis and outcomes of patients with ACM. The knowledge of underlying molecular mutations would be useful in designing better therapeutic strategies for ACM patients with multiple genetic mutations.
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Affiliation(s)
- Meng Wei
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoliang Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Qiu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lei Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lili Huang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhongqiang Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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Hammer-Hansen S, Stoltze U, Bartels E, Hansen TVO, Byrjalsen A, Tybjærg-Hansen A, Juul K, Schmiegelow K, Tfelt J, Bundgaard H, Wadt K, Diness BR. Actionability and familial uptake following opportunistic genomic screening in a pediatric cancer cohort. Eur J Hum Genet 2024; 32:846-857. [PMID: 38740897 PMCID: PMC11220050 DOI: 10.1038/s41431-024-01618-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Abstract
The care for patients with serious conditions is increasingly guided by genomic medicine, and genomic medicine may equally transform care for healthy individual if genomic population screening is implemented. This study examines the medical impact of opportunistic genomic screening (OGS) in a cohort of patients undergoing comprehensive genomic germline DNA testing for childhood cancer, including the impact on their relatives. Medical actionability and uptake after cascade testing in the period following disclosure of OGS results was quantified. A secondary finding was reported to 19/595 (3.2%) probands primarily in genes related to cardiovascular and lipid disorders. After a mean follow up time of 1.6 years (Interquartile range (IQR): 0.57-1.92 yrs.) only 12 (63%) of these variants were found to be medically actionable. Clinical follow up or treatment was planned in 16 relatives, and as in the probands, the prescribed treatment was primarily betablockers or cholesterol lowering therapy. No invasive procedures or implantation of medical devices were performed in probands or relatives, and no reproductive counseling was requested. After an average of 1.6 years of follow-up 2.25 relatives per family with an actionable finding had been tested. This real-world experience of OGS grants new insight into the practical implementation effects and derived health care demands of genotype-first screening. The resulting health care effect and impact on demand for genetic counseling and workup in relatives extends beyond the effect in the probands.
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Affiliation(s)
- Sophia Hammer-Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Stoltze
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Emil Bartels
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anna Byrjalsen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anne Tybjærg-Hansen
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Klaus Juul
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Jacob Tfelt
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Forensic Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Henning Bundgaard
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Birgitte Rode Diness
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
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3
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Azimi A, Soveizi M, Salmanipour A, Mozafarybazargany M, Ghaffari Jolfayi A, Maleki M, Kalayinia S. Identification of a novel likely pathogenic TPM1 variant linked to hypertrophic cardiomyopathy in a family with sudden cardiac death. ESC Heart Fail 2024. [PMID: 38874371 DOI: 10.1002/ehf2.14906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/19/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024] Open
Abstract
AIMS Hypertrophic cardiomyopathy (HCM) is an autosomal dominant genetic cardiac disorder characterized by unexplained left ventricular hypertrophy. It can cause a wide spectrum of clinical manifestations, ranging from asymptomatic to heart failure and sudden cardiac death (SCD). Approximately half of HCM cases are caused by variants in sarcomeric proteins, including α-tropomyosin (TPM1). In this study, we aimed to characterize the clinical and molecular phenotype of HCM in an Iranian pedigree with SCD. METHODS AND RESULTS The proband and available family members underwent comprehensive clinical evaluations, including echocardiography, cardiac magnetic resonance (CMR) imaging and electrocardiography (ECG). Whole-exome sequencing (WES) was performed in all available family members to identify the causal variant, which was validated, and segregation analysis was conducted via Sanger sequencing. WES identified a novel missense variant, c.761A>G:p.D254G (NM_001018005.2), in the TPM1 gene, in the proband, his father and one of his sisters. Bioinformatic analysis predicted it to be likely pathogenic. Clinical features in affected individuals were consistent with HCM. CONCLUSIONS The identification of a novel TPM1 variant in a family with HCM and SCD underscores the critical role of genetic screening in at-risk families. Early detection of pathogenic variants can facilitate timely intervention and management, potentially reducing the risk of SCD in individuals with HCM.
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Affiliation(s)
- Amir Azimi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mahdieh Soveizi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Salmanipour
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Amir Ghaffari Jolfayi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
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4
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Vokač D, Stangler Herodež Š, Krgović D, Kokalj Vokač N. The Role of Next-Generation Sequencing in the Management of Patients with Suspected Non-Ischemic Cardiomyopathy after Syncope or Termination of Sudden Arrhythmic Death. Genes (Basel) 2024; 15:72. [PMID: 38254962 PMCID: PMC10815304 DOI: 10.3390/genes15010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Cardiac arrhythmias and sudden death are frequent in patients with non-ischemic cardiomyopathy and can precede heart failure or additional symptoms where malignant cardiac arrhythmias are mostly the consequence of advanced cardiomyopathy and heart failure. Finding these subgroups and making an early diagnosis could be lifesaving. In our retrospective study, we are presenting arrhythmic types of frequent cardiomyopathies where an arrhythmogenic substrate is less well defined, as in ischemic or structural heart disease. In the period of 2 years, next-generation sequencing (NGS) tests along with standard clinical tests were performed in 208 patients (67 women and 141 men; mean age, 51.2 ± 19.4 years) without ischemic or an overt structural heart disease after syncope or aborted sudden cardiac death. Genetic variants were detected in 34.4% of the study population, with a significant proportion of pathogenic variants (P) (14.4%) and variants of unknown significance (VUS) (20%). Regardless of genotype, all patients were stratified according to clinical guidelines for aggressive treatment of sudden cardiac death with an implantable cardioverter defibrillator (ICD). The P variant identified by NGS serves for an accurate diagnosis and, thus, better prevention and specific treatment of patients and their relatives. Results in our study suggest that targeted sequencing of genes associated with cardiovascular disease is an important addendum for final diagnosis, allowing the identification of a molecular genetic cause in a vast proportion of patients for a definitive diagnosis and a more specific way of treatment. VUS in this target population poses a high risk and should be considered possibly pathogenic in reanalysis.
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Affiliation(s)
- Damijan Vokač
- Department of Cardiology and Angiology, Division of Internal Medicine, University Medical Centre Maribor, 2000 Maribor, Slovenia;
| | - Špela Stangler Herodež
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
| | - Danijela Krgović
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
| | - Nadja Kokalj Vokač
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
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5
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Aghamir SMK, Roudgari H, Heidari H, Salimi Asl M, Jafari Abarghan Y, Soleimani V, Mashhadi R, Khatami F. Whole Exome Sequencing to Find Candidate Variants for the Prediction of Kidney Transplantation Efficacy. Genes (Basel) 2023; 14:1251. [PMID: 37372431 PMCID: PMC10298443 DOI: 10.3390/genes14061251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 06/29/2023] Open
Abstract
INTRODUCTION Kidney transplantation is the optimal treatment strategy for some end-stage renal disease (ESRD); however, graft survival and the success of the transplantation depend on several elements, including the genetics of recipients. In this study, we evaluated exon loci variants based on a high-resolution Next Generation Sequencing (NGS) method. METHODS We evaluated whole-exome sequencing (WES) of transplanted kidney recipients in a prospective study. The study involved a total of 10 patients (5 without a history of rejection and 5 with). About five milliliters of blood were collected for DNA extraction, followed by whole-exome sequencing based on molecular inversion probes (MIPs). RESULTS Sequencing and variant filtering identified nine pathogenic variants in rejecting patients (low survival). Interestingly, in five patients with successful kidney transplantation, we found 86 SNPs in 63 genes 61 were variants of uncertain significance (VUS), 5 were likely pathogenic, and five were likely benign/benign. The only overlap between rejecting and non-rejecting patients was SNPs rs529922492 in rejecting and rs773542127 in non-rejecting patients' MUC4 gene. CONCLUSIONS Nine variants of rs779232502, rs3831942, rs564955632, rs529922492, rs762675930, rs569593251, rs192347509, rs548514380, and rs72648913 have roles in short graft survival.
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Affiliation(s)
| | - Hassan Roudgari
- Genomic Research Centre (GRC), Shahid Beheshti University of Medical Sciences (SBMU), Tehran 1416634793, Iran
- Department of Applied Medicine, Medical School, Aberdeen University, Aberdeen AB24 3FX, UK
| | - Hassan Heidari
- Urology Research Center, Tehran University of Medical Sciences, Tehran P94V+8MF, Iran
| | - Mohammad Salimi Asl
- Urology Research Center, Tehran University of Medical Sciences, Tehran P94V+8MF, Iran
| | - Yousef Jafari Abarghan
- Deparment of Molecular Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 1696700, Iran
| | - Venous Soleimani
- Urology Research Center, Tehran University of Medical Sciences, Tehran P94V+8MF, Iran
| | - Rahil Mashhadi
- Urology Research Center, Tehran University of Medical Sciences, Tehran P94V+8MF, Iran
| | - Fatemeh Khatami
- Urology Research Center, Tehran University of Medical Sciences, Tehran P94V+8MF, Iran
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6
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Wilczewski CM, Obasohan J, Paschall JE, Zhang S, Singh S, Maxwell GL, Similuk M, Wolfsberg TG, Turner C, Biesecker LG, Katz AE. Genotype first: Clinical genomics research through a reverse phenotyping approach. Am J Hum Genet 2023; 110:3-12. [PMID: 36608682 PMCID: PMC9892776 DOI: 10.1016/j.ajhg.2022.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Although genomic research has predominantly relied on phenotypic ascertainment of individuals affected with heritable disease, the falling costs of sequencing allow consideration of genomic ascertainment and reverse phenotyping (the ascertainment of individuals with specific genomic variants and subsequent evaluation of physical characteristics). In this research modality, the scientific question is inverted: investigators gather individuals with a genomic variant and test the hypothesis that there is an associated phenotype via targeted phenotypic evaluations. Genomic ascertainment research is thus a model of predictive genomic medicine and genomic screening. Here, we provide our experience implementing this research method. We describe the infrastructure we developed to perform reverse phenotyping studies, including aggregating a super-cohort of sequenced individuals who consented to recontact for genomic ascertainment research. We assessed 13 studies completed at the National Institutes of Health (NIH) that piloted our reverse phenotyping approach. The studies can be broadly categorized as (1) facilitating novel genotype-disease associations, (2) expanding the phenotypic spectra, or (3) demonstrating ex vivo functional mechanisms of disease. We highlight three examples of reverse phenotyping studies in detail and describe how using a targeted reverse phenotyping approach (as opposed to phenotypic ascertainment or clinical informatics approaches) was crucial to the conclusions reached. Finally, we propose a framework and address challenges to building collaborative genomic ascertainment research programs at other institutions. Our goal is for more researchers to take advantage of this approach, which will expand our understanding of the predictive capability of genomic medicine and increase the opportunity to mitigate genomic disease.
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Affiliation(s)
- Caralynn M. Wilczewski
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Justice Obasohan
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Justin E. Paschall
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Suiyuan Zhang
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Sumeeta Singh
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - George L. Maxwell
- Women’s Health Integrated Research Center, Inova Health System, Falls Church, VA 22042, USA
| | - Morgan Similuk
- National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Tyra G. Wolfsberg
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Clesson Turner
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Leslie G. Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA,Corresponding author
| | - Alexander E. Katz
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
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7
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Tedesco B, Vendredy L, Timmerman V, Poletti A. The chaperone-assisted selective autophagy complex dynamics and dysfunctions. Autophagy 2023:1-23. [PMID: 36594740 DOI: 10.1080/15548627.2022.2160564] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Each protein must be synthesized with the correct amino acid sequence, folded into its native structure, and transported to a relevant subcellular location and protein complex. If any of these steps fail, the cell has the capacity to break down aberrant proteins to maintain protein homeostasis (also called proteostasis). All cells possess a set of well-characterized protein quality control systems to minimize protein misfolding and the damage it might cause. Autophagy, a conserved pathway for the degradation of long-lived proteins, aggregates, and damaged organelles, was initially characterized as a bulk degradation pathway. However, it is now clear that autophagy also contributes to intracellular homeostasis by selectively degrading cargo material. One of the pathways involved in the selective removal of damaged and misfolded proteins is chaperone-assisted selective autophagy (CASA). The CASA complex is composed of three main proteins (HSPA, HSPB8 and BAG3), essential to maintain protein homeostasis in muscle and neuronal cells. A failure in the CASA complex, caused by mutations in the respective coding genes, can lead to (cardio)myopathies and neurodegenerative diseases. Here, we summarize our current understanding of the CASA complex and its dynamics. We also briefly discuss how CASA complex proteins are involved in disease and may represent an interesting therapeutic target.Abbreviation ALP: autophagy lysosomal pathway; ALS: amyotrophic lateral sclerosis; AMOTL1: angiomotin like 1; ARP2/3: actin related protein 2/3; BAG: BAG cochaperone; BAG3: BAG cochaperone 3; CASA: chaperone-assisted selective autophagy; CMA: chaperone-mediated autophagy; DNAJ/HSP40: DnaJ heat shock protein family (Hsp40); DRiPs: defective ribosomal products; EIF2A/eIF2α: eukaryotic translation initiation factor 2A; EIF2AK1/HRI: eukaryotic translation initiation factor 2 alpha kinase 1; GABARAP: GABA type A receptor-associated protein; HDAC6: histone deacetylase 6; HSP: heat shock protein; HSPA/HSP70: heat shock protein family A (Hsp70); HSP90: heat shock protein 90; HSPB8: heat shock protein family B (small) member 8; IPV: isoleucine-proline-valine; ISR: integrated stress response; KEAP1: kelch like ECH associated protein 1; LAMP2A: lysosomal associated membrane protein 2A; LATS1: large tumor suppressor kinase 1; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOC: microtubule organizing center; MTOR: mechanistic target of rapamycin kinase; NFKB/NF-κB: nuclear factor kappa B; NFE2L2: NFE2 like bZIP transcription factor 2; PLCG/PLCγ: phospholipase C gamma; polyQ: polyglutamine; PQC: protein quality control; PxxP: proline-rich; RAN translation: repeat-associated non-AUG translation; SG: stress granule; SOD1: superoxide dismutase 1; SQSTM1/p62: sequestosome 1; STUB1/CHIP: STIP1 homology and U-box containing protein 1; STK: serine/threonine kinase; SYNPO: synaptopodin; TBP: TATA-box binding protein; TARDBP/TDP-43: TAR DNA binding protein; TFEB: transcription factor EB; TPR: tetratricopeptide repeats; TSC1: TSC complex subunit 1; UBA: ubiquitin associated; UPS: ubiquitin-proteasome system; WW: tryptophan-tryptophan; WWTR1: WW domain containing transcription regulator 1; YAP1: Yes1 associated transcriptional regulator.
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Affiliation(s)
- Barbara Tedesco
- Laboratory of Experimental Biology, Dipartimento di Scienze Farmacologiche e Biomolecolari, Dipartimento di Eccellenza 2018-2027, Università degli studi di Milano, Milan, Italy.,Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Leen Vendredy
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Angelo Poletti
- Laboratory of Experimental Biology, Dipartimento di Scienze Farmacologiche e Biomolecolari, Dipartimento di Eccellenza 2018-2027, Università degli studi di Milano, Milan, Italy
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8
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Ittiwut C, Mahasirimongkol S, Srisont S, Ittiwut R, Chockjamsai M, Durongkadech P, Sawaengdee W, Khunphon A, Larpadisorn K, Wattanapokayakit S, Wetchaphanphesat S, Arunotong S, Srimahachota S, Pittayawonganon C, Thammawijaya P, Sutdan D, Doungngern P, Khongphatthanayothin A, Kerr SJ, Shotelersuk V. Genetic basis of sudden death after COVID-19 vaccination in Thailand. Heart Rhythm 2022; 19:1874-1879. [PMID: 35934244 PMCID: PMC9352648 DOI: 10.1016/j.hrthm.2022.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 vaccination reduces morbidity and mortality associated with coronavirus disease 2019 (COVID-19); unfortunately, it is associated with serious adverse events, including sudden unexplained death (SUD). OBJECTIVE We aimed to study the genetic basis of SUD after COVID-19 vaccination in Thailand. METHODS From April to December 2021, cases with natural but unexplained death within 7 days of COVID-19 vaccination were enrolled for whole exome sequencing. RESULTS Thirteen were recruited, aged between 23 and 72 years; 10 (77%) were men, 12 were Thai; and 1 was Australian. Eight (61%) died after receiving the first dose of vaccine, and 7 (54%) died after receiving ChAdOx1 nCoV-19; however, there were no significant correlations between SUD and either the number or the type of vaccine. Fever was self-reported in 3 cases. Ten (77%) and 11 (85%) died within 24 hours and 3 days of vaccination, respectively. Whole exome sequencing analysis revealed that 5 cases harbored SCN5A variants that had previously been identified in patients with Brugada syndrome, giving an SCN5A variant frequency of 38% (5 of 13). This is a significantly higher rate than that observed in Thai SUD cases occurring 8-30 days after COVID-19 vaccination during the same period (10% [1 of 10]), in a Thai SUD cohort studied before the COVID-19 pandemic (12% [3 of 25]), and in our in-house exome database (12% [386 of 3231]). CONCLUSION These findings suggest that SCN5A variants may be associated with SUD within 7 days of COVID-19 vaccination, regardless of vaccine type, number of vaccine dose, and presence of underlying diseases or postvaccine fever.
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Affiliation(s)
- Chupong Ittiwut
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Surakameth Mahasirimongkol
- Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Smith Srisont
- Forensic Division, Pathology Department, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rungnapa Ittiwut
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Manoch Chockjamsai
- Forensic Department, Faculty of Medicine, Chiangmai University, Chiangmai, Thailand
| | | | - Waritta Sawaengdee
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Athiwat Khunphon
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Kanidsorn Larpadisorn
- Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Sukanya Wattanapokayakit
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Suppachok Wetchaphanphesat
- Strategy and Planning Division, Office of the Permanent Secretary, Ministry of Public Health, Nonthaburi, Thailand
| | - Surachet Arunotong
- Office of Disease Prevention and Control Region 1 Chiang Mai, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Chakrarat Pittayawonganon
- Division of Epidemiology, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Panithee Thammawijaya
- Division of Epidemiology, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Derek Sutdan
- Strategy and Planning Division, Office of the Permanent Secretary, Ministry of Public Health, Nonthaburi, Thailand
| | - Pawinee Doungngern
- Division of Epidemiology, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Apichai Khongphatthanayothin
- Center of Excellence in Arrhythmia Research, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Stephen J Kerr
- Center of Excellence for Biostatistics, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.
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9
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Tu P, Sun H, Zhang X, Ran Q, He Y, Ran S. Diverse cardiac phenotypes among different carriers of the same MYH7 splicing variant allele (c.732+1G>A) from a family. BMC Med Genomics 2022; 15:36. [PMID: 35209905 PMCID: PMC8876400 DOI: 10.1186/s12920-022-01186-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 02/17/2022] [Indexed: 11/17/2022] Open
Abstract
Background Left ventricular non-compaction cardiomyopathy (LVNC) is a rare congenital heart defect. Gene defections have been found in patients with LVNC and their family members; and MYH7 is the most frequent gene associated with LVNC. Methods We performed a complete prenatal ultrasound and echocardiographic examination on a fetus with cardiac abnormality and a parent–child trio whole-exome sequencing to identify the potential genetic causes. When the genetic abnormality in MYH7 was identified in the fetus, we performed echocardiography and genetic screening on its high-risk relatives. Results Second trimester ultrasound and echocardiography showed several malformations in the fetus: Ebstein’s anomaly (EA), heart dilatation, perimembranous ventricle septal defects, mild seroperitoneum, and single umbilical artery. Heterozygous genotyping of a splicing variant allele (NM_00025.3: c.732+G>A) was identified in this fetus and her mother, not her father, indicating a maternal inheritance. Subsequently, direct sequencing confirmed the presence of this splicing variant among her grandmother (mother of mother), mother, older sister, and herself in a heterozygous manner. No PCR products were amplified by qRT-PCR for the RNA samples extracted from peripheral blood cells. In addition to this proband who was diagnosed with EA, her older sister and grandmother (mother of mother) were diagnosed with isolated asymptomatic LVCN, but her mother was just a carrier with no marked clinical manifestations after family screening. Conclusion The presence of MYH7 splicing variant c.732+G>A can be inherited maternally, and its cardiac phenotypes are different from one carrier to another.
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Affiliation(s)
- Peng Tu
- Department of Ultrasound, Chongqing Health Center for Women and Children, 120 Longshan Road, Yubei District, Chongqing, 401147, China
| | - Hairui Sun
- Maternal-Fetal Consultation Center of Congenital Heart Disease, Department of Echocardiography, Beijing Anzhen Hospital, Capital Medical University, 2 Anzhen Road, Chaoyang District, Beijing, 100029, China
| | - Xiaohang Zhang
- Department of Ultrasound, Chongqing Health Center for Women and Children, 120 Longshan Road, Yubei District, Chongqing, 401147, China
| | - Qian Ran
- Department of Ultrasound, Chongqing Health Center for Women and Children, 120 Longshan Road, Yubei District, Chongqing, 401147, China
| | - Yihua He
- Maternal-Fetal Consultation Center of Congenital Heart Disease, Department of Echocardiography, Beijing Anzhen Hospital, Capital Medical University, 2 Anzhen Road, Chaoyang District, Beijing, 100029, China.
| | - Suzhen Ran
- Department of Ultrasound, Chongqing Health Center for Women and Children, 120 Longshan Road, Yubei District, Chongqing, 401147, China.
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10
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Lin H, Koren SA, Cvetojevic G, Girardi P, Johnson GV. The role of BAG3 in health and disease: A "Magic BAG of Tricks". J Cell Biochem 2022; 123:4-21. [PMID: 33987872 PMCID: PMC8590707 DOI: 10.1002/jcb.29952] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/25/2021] [Indexed: 01/03/2023]
Abstract
The multi-domain structure of Bcl-2-associated athanogene 3 (BAG3) facilitates its interaction with many different proteins that participate in regulating a variety of biological pathways. After revisiting the BAG3 literature published over the past ten years with Citespace software, we classified the BAG3 research into several clusters, including cancer, cardiomyopathy, neurodegeneration, and viral propagation. We then highlighted recent key findings in each cluster. To gain greater insight into the roles of BAG3, we analyzed five different published mass spectrometry data sets of proteins that co-immunoprecipitate with BAG3. These data gave us insight into universal, as well as cell-type-specific BAG3 interactors in cancer cells, cardiomyocytes, and neurons. Finally, we mapped variable BAG3 SNPs and also mutation data from previous publications to further explore the link between the domains and function of BAG3. We believe this review will provide a better understanding of BAG3 and direct future studies towards understanding BAG3 function in physiological and pathological conditions.
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Affiliation(s)
- Heng Lin
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Shon A. Koren
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Gregor Cvetojevic
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Peter Girardi
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Gail V.W. Johnson
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
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11
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Filatova EV, Krylova NS, Vlasov IN, Maslova MS, Poteshkina NG, Slominsky PA, Shadrina MI. Targeted exome analysis of Russian patients with hypertrophic cardiomyopathy. Mol Genet Genomic Med 2021; 9:e1808. [PMID: 34598319 PMCID: PMC8606207 DOI: 10.1002/mgg3.1808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/20/2022] Open
Abstract
Background Hypertrophic cardiomyopathy (HCM), described as the presence of hypertrophy of left ventricular, is the most prevalent heritable cardiovascular disease with predominantly an autosomal dominant type of inheritance. However, pathogenic alleles are not identified in at least 25% of patients with HCM, and the spectrum of pathogenic variants that contribute to the development of HCM in Russia has not been fully described. Therefore, the goal of our study was to identify genetic variants associated with the etiopathogenesis of HCM in Russian patients. Methods The study cohort included 98 unrelated adult patients with HCM. We performed targeted exome sequencing, an analysis using various algorithms for prediction of the impact of variants on protein structure and the prediction of pathogenicity using ACMG Guidelines. Results The frequency of pathogenic and likely pathogenic variants in all HCM‐related genes was 8% in our patients. We also identified 20 variants of uncertain significance in all HCM‐related genes. Conclusions The prevalence of individual pathogenic variants in HCM‐related genes in Russian population appears to be lower than in general European population, which could be explained by ethnic features of Russian population, age characteristics of our sample, or unidentified pathogenic variants in genes previously not linked with HCM.
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Affiliation(s)
- Elena V Filatova
- Institute of Molecular Genetics of National Research Centre, Moscow, Russia
| | - Natalia S Krylova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan N Vlasov
- Institute of Molecular Genetics of National Research Centre, Moscow, Russia
| | - Maria S Maslova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Petr A Slominsky
- Institute of Molecular Genetics of National Research Centre, Moscow, Russia
| | - Maria I Shadrina
- Institute of Molecular Genetics of National Research Centre, Moscow, Russia
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12
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Petrykey K, Rezgui AM, Guern ML, Beaulieu P, St-Onge P, Drouin S, Bertout L, Wang F, Baedke JL, Yasui Y, Hudson MM, Raboisson MJ, Laverdière C, Sinnett D, Andelfinger GU, Krajinovic M. Genetic factors in treatment-related cardiovascular complications in survivors of childhood acute lymphoblastic leukemia. Pharmacogenomics 2021; 22:885-901. [PMID: 34505544 PMCID: PMC9043873 DOI: 10.2217/pgs-2021-0067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/12/2021] [Indexed: 11/21/2022] Open
Abstract
Aim: Cardiovascular disease represents one of the main causes of secondary morbidity and mortality in patients with childhood cancer. Patients & methods: To further address this issue, we analyzed cardiovascular complications in relation to common and rare genetic variants derived through whole-exome sequencing from childhood acute lymphoblastic leukemia survivors (PETALE cohort). Results: Significant associations were detected among common variants in the TTN gene, left ventricular ejection fraction (p ≤ 0.0005), and fractional shortening (p ≤ 0.001). Rare variants enrichment in the NOS1, ABCG2 and NOD2 was observed in relation to left ventricular ejection fraction, and in NOD2 and ZNF267 genes in relation to fractional shortening. Following stratification according to risk groups, the modulatory effect of rare variants was additionally found in the CBR1, ABCC5 and AKR1C3 genes. None of the associations was replicated in St-Jude Lifetime Cohort Study. Conclusion: Further studies are needed to confirm whether the described genetic markers may be useful in identifying patients at increased risk of these complications.
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Affiliation(s)
- Kateryna Petrykey
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
- Department of Pharmacology & Physiology, Université de Montréal, QC, H3T 1J4, Canada
| | - Aziz M Rezgui
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
| | - Mathilde Le Guern
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
| | - Patrick Beaulieu
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
| | - Pascal St-Onge
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
| | - Simon Drouin
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
| | - Laurence Bertout
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
| | - Fan Wang
- Department of Epidemiology & Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jessica L Baedke
- Department of Epidemiology & Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yutaka Yasui
- Department of Epidemiology & Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Melissa M Hudson
- Department of Epidemiology & Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Marie-Josée Raboisson
- Department of Pediatrics, Université de Montréal, QC, H3T 1C5, Canada
- Cardiology Unit, Sainte-Justine University Health Center (SJUHC), Montreal, QC, H3T 1C5, Canada
| | - Caroline Laverdière
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
- Department of Pediatrics, Université de Montréal, QC, H3T 1C5, Canada
| | - Daniel Sinnett
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
- Department of Pediatrics, Université de Montréal, QC, H3T 1C5, Canada
| | - Gregor U Andelfinger
- Department of Pediatrics, Université de Montréal, QC, H3T 1C5, Canada
- Fetomaternal and Neonatal Pathologies Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC, H3T 1C5, Canada
| | - Maja Krajinovic
- Immune Diseases and Cancer Research Axis, Sainte-Justine University Health Center (SJUHC), Montreal, QC H3T 1C5, Canada
- Department of Pharmacology & Physiology, Université de Montréal, QC, H3T 1J4, Canada
- Department of Pediatrics, Université de Montréal, QC, H3T 1C5, Canada
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13
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Genetic investigations of 100 inherited cardiac disease-related genes in deceased individuals with schizophrenia. Int J Legal Med 2021; 135:1395-1405. [PMID: 33973092 DOI: 10.1007/s00414-021-02595-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022]
Abstract
Cardiac diseases and sudden cardiac death (SCD) are more prevalent in individuals diagnosed with schizophrenia compared to the general population, with especially coronary artery disease (CAD) as the major cardiovascular cause of death. Antipsychotic medications, genetics, and lifestyle factors may contribute to the increased SCD in individuals with schizophrenia. The role of antipsychotic medications and lifestyle factors have been widely investigated, while the genetic predisposition to inherited cardiac diseases in schizophrenia is poorly understood. In this study, we examined 100 genes associated with inherited cardiomyopathies and cardiac channelopathies in 97 deceased individuals diagnosed with schizophrenia for the prevalence of genetic variants associated with SCD. The deceased individuals had various causes of death and were included in the SURVIVE project, a prospective, autopsy-based study of mentally ill individuals in Denmark. This is the first study of multiple inherited cardiac disease-related genes in deceased individuals with diagnosed schizophrenia to shed light on the genetic predisposition to SCD in individuals with schizophrenia. We found no evidence for an overrepresentation of rare variants with high penetrance in inherited cardiac diseases, following the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG) consensus guidelines. However, we found that the deceased individuals had a statistically significantly increased polygenic burden caused by variants in the investigated heart genes compared to the general population. This indicates that common variants with smaller effects in heart genes may play a role in schizophrenia.
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14
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Delaney A, Burkholder AB, Lavender CA, Plummer L, Mericq V, Merino PM, Quinton R, Lewis KL, Meader BN, Albano A, Shaw ND, Welt CK, Martin KA, Seminara SB, Biesecker LG, Bailey-Wilson JE, Hall JE. Increased Burden of Rare Sequence Variants in GnRH-Associated Genes in Women With Hypothalamic Amenorrhea. J Clin Endocrinol Metab 2021; 106:e1441-e1452. [PMID: 32870266 PMCID: PMC7947783 DOI: 10.1210/clinem/dgaa609] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/28/2020] [Indexed: 12/17/2022]
Abstract
CONTEXT Functional hypothalamic amenorrhea (HA) is a common, acquired form of hypogonadotropic hypogonadism that occurs in the setting of energy deficits and/or stress. Variability in individual susceptibility to these stressors, HA heritability, and previous identification of several rare sequence variants (RSVs) in genes associated with the rare disorder, isolated hypogonadotropic hypogonadism (IHH), in individuals with HA suggest a possible genetic contribution to HA susceptibility. OBJECTIVE We sought to determine whether the burden of RSVs in IHH-related genes is greater in women with HA than controls. DESIGN We compared patients with HA to control women. SETTING The study was conducted at secondary referral centers. PATIENTS AND OTHER PARTICIPANTS Women with HA (n = 106) and control women (ClinSeq study; n = 468). INTERVENTIONS We performed exome sequencing in all patients and controls. MAIN OUTCOME MEASURE(S) The frequency of RSVs in 53 IHH-associated genes was determined using rare variant burden and association tests. RESULTS RSVs were overrepresented in women with HA compared with controls (P = .007). Seventy-eight heterozygous RSVs in 33 genes were identified in 58 women with HA (36.8% of alleles) compared to 255 RSVs in 41 genes among 200 control women (27.2%). CONCLUSIONS Women with HA are enriched for RSVs in genes that cause IHH, suggesting that variation in genes associated with gonadotropin-releasing hormone neuronal ontogeny and function may be a major determinant of individual susceptibility to developing HA in the face of diet, exercise, and/or stress.
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Affiliation(s)
- Angela Delaney
- National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Research Triangle Park, North Carolina
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Adam B Burkholder
- National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Research Triangle Park, North Carolina
| | - Christopher A Lavender
- National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Research Triangle Park, North Carolina
| | - Lacey Plummer
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Veronica Mericq
- Institute of Maternal and Child Research, University of Chile, Santiago, Chile
- Department of Pediatrics, Clínica Las Condes, Santiago, Chile
| | - Paulina M Merino
- Institute of Maternal and Child Research, University of Chile, Santiago, Chile
| | - Richard Quinton
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Katie L Lewis
- Medical Genomics & Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Brooke N Meader
- National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Research Triangle Park, North Carolina
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Alessandro Albano
- National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Research Triangle Park, North Carolina
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Natalie D Shaw
- National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Research Triangle Park, North Carolina
| | - Corrine K Welt
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, Utah
| | - Kathryn A Martin
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Stephanie B Seminara
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Leslie G Biesecker
- Medical Genomics & Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Baltimore, Maryland
| | - Janet E Hall
- National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Research Triangle Park, North Carolina
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15
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Yogasundaram H, Alhumaid W, Dzwiniel T, Christian S, Oudit GY. Cardiomyopathies and Genetic Testing in Heart Failure: Role in Defining Phenotype-Targeted Approaches and Management. Can J Cardiol 2021; 37:547-559. [PMID: 33493662 DOI: 10.1016/j.cjca.2021.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/29/2022] Open
Abstract
Cardiomyopathies represent an important cause of heart failure, often affecting young individuals, and have important implications for relatives. Genetic testing for cardiomyopathies is an established care pathway in contemporary cardiology practice. The primary cardiomyopathies where genetic testing is indicated are hypertrophic, dilated, arrhythmogenic, and restrictive cardiomyopathies, with left ventricular noncompaction as a variant phenotype. Early identification and initiation of therapies in patients with inherited cardiomyopathies allow for targeting asymptomatic and presymptomatic patients in stages A and B of the American College of Cardiology/American Heart Association classification of heart failure. The current approach for genetic testing uses gene panel-based testing with the ability to extend to whole-exome and whole-genome sequencing in rare instances. The central components of genetic testing include defining the genetic basis of the diagnosis, providing prognostic information, and the ability to screen and risk-stratify relatives. Genetic testing for cardiomyopathies should be coordinated by a multidisciplinary team including adult and pediatric cardiologists, genetic counsellors, and geneticists, with access to expertise in cardiac imaging and electrophysiology. A pragmatic approach for addressing genetic variants of uncertain significance is important. In this review, we highlight the indications for genetic testing in the various cardiomyopathies, the value of early diagnosis and treatment, family screening, and the care process involved in genetic counselling and testing.
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Affiliation(s)
- Haran Yogasundaram
- Department of Medicine, Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Waleed Alhumaid
- Department of Medicine, Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Tara Dzwiniel
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Susan Christian
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Gavin Y Oudit
- Department of Medicine, Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada.
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16
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Shahbazi S. Prediction and in silico validation of MYH7 gene missense variants in the Iranian population: a bioinformatics analysis based on Iranome database. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00058-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Identifying disease-causing genetic variants in a particular population improves the molecular diagnosis of genetic disorders. National genome databases provide valuable information on this matter. This study aimed to investigate the genomic variants of the MYH7 gene, related to the common heart disease, i.e., hereditary cardiomyopathy.
Results
MYH7 gene variants were extracted from the Iranome database and loaded into SPSS software. The filtration steps were performed based on the variant specification and with emphasis on identifying missense changes. Using predictive algorithms, different aspects of the changes such as allele frequency and functional defects were investigated. Our results showed that 41 (17.4%) coding variants were synonymous compared with 18 (7.7%) missense alterations. The missense variants were mostly observed in exons 20–40 that encode MyHC α-helical rod tail. The p.Pro211Leu, p.Arg787His, p.Val964Leu, p.Arg1277Gln, and p.Ala1603Thr were already known to be associated with inherited cardiomyopathy. Four of the missense variants, p.Asn1623Ser, p.Arg1588His, p.Phe1498Tyr, and p.Arg1129Ser, were located on MyHC α-helical rod tail and none of them was annotated on dbSNP or genomAD databases.
Conclusion
Our study showed several MYH7 variants associated with the disease in the Iranian population. The results emphasize the importance of analyzing the exons encoding MyHC α-helical rod tail. The investigation of genomic databases can be considered as a cost-effective strategy using targeted mutation detection analyses. The efficacy of this prediction method should be elucidated in further studies on patients’ cohorts.
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Secondary findings in inherited heart conditions: a genotype-first feasibility study to assess phenotype, behavioural and psychosocial outcomes. Eur J Hum Genet 2020; 28:1486-1496. [PMID: 32686758 PMCID: PMC7576165 DOI: 10.1038/s41431-020-0694-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/12/2020] [Accepted: 06/30/2020] [Indexed: 12/28/2022] Open
Abstract
Disclosing secondary findings (SF) from genome sequencing (GS) can alert carriers to disease risk. However, evidence around variant-disease association and consequences of disclosure for individuals and healthcare services is limited. We report on the feasibility of an approach to identification of SF in inherited cardiac conditions (ICC) genes in participants in a rare disease GS study, followed by targeted clinical evaluation. Qualitative methods were used to explore behavioural and psychosocial consequences of disclosure. ICC genes were analysed in genome sequence data from 7203 research participants; a two-stage approach was used to recruit genotype-blind variant carriers and matched controls. Cardiac-focused medical and family history collection and genetic counselling were followed by standard clinical tests, blinded to genotype. Pathogenic ICC variants were identified in 0.61% of individuals; 20 were eligible for the present study. Four variant carriers and seven non-carrier controls participated. One variant carrier had a family history of ICC and was clinically affected; a second was clinically unaffected and had no relevant family history. One variant, in two unrelated participants, was subsequently reclassified as being of uncertain significance. Analysis of qualitative data highlights participant satisfaction with approach, willingness to follow clinical recommendations, but variable outcomes of relatives’ engagement with healthcare services. In conclusion, when offered access to SF, many people choose not to pursue them. For others, disclosure of ICC SF in a specialist setting is valued and of likely clinical utility, and can be expected to identify individuals with, and without a phenotype.
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18
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Hamada Y, Yamamoto T, Nakamura Y, Sufu-Shimizu Y, Nanno T, Fukuda M, Ono M, Oda T, Okuda S, Ueyama T, Kobayashi S, Yano M. G790del mutation in DSC2 alone is insufficient to develop the pathogenesis of ARVC in a mouse model. Biochem Biophys Rep 2020; 21:100711. [PMID: 31872082 PMCID: PMC6909225 DOI: 10.1016/j.bbrep.2019.100711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart disease that causes heart failure and/or sudden cardiac death. Several desmosomal genes (DSC2, PKG, PKP2, DSP, and RyR2) are thought to be the causative gene involved in ARVC. Out of them, DSC2 mutations account for 2% of ARVC genetic abnormalities. This study aimed to clarify the effect of G790del mutation in DSC2 on the arrhythmogenic mechanism and cardiac function in a mouse model. RESULT Neither the heterozygous +/G790del nor homozygous G790del/G790del mice showed structural and functional defects in the right ventricle (RV) or lethal arrhythmia. The homozygous G790del/G790del 6-month-old mice slightly showed left ventricular (LV) dysfunction. Cell shortening decreased with prolongation of intracellular Ca2+ transient in cardiomyocytes isolated from the homozygous G790del/G790del mice, and spontaneous Ca2+ transients were frequently observed in response to isoproterenol. CONCLUSIONS G790del mutation in DSC2 was not relevant to the pathogenesis of ARVC, but showed a slight contractile dysfunction and Ca2+ dysregulation in the LV.
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Affiliation(s)
- Yoriomi Hamada
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Takeshi Yamamoto
- Faculty of Health Sciences, Yamaguchi University Graduate School of Medicine, Japan
| | - Yoshihide Nakamura
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Yoko Sufu-Shimizu
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Takuma Nanno
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Masakazu Fukuda
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Makoto Ono
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Tesuro Oda
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Shinichi Okuda
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Takeshi Ueyama
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Shigeki Kobayashi
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
| | - Masafumi Yano
- Department of Medicine and Clinical Science, Division of Cardiology, Yamaguchi University Graduate School of Medicine, Japan
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Liebrechts-Akkerman G, Liu F, van Marion R, Dinjens WNM, Kayser M. Explaining sudden infant death with cardiac arrhythmias: Complete exon sequencing of nine cardiac arrhythmia genes in Dutch SIDS cases highlights new and known DNA variants. Forensic Sci Int Genet 2020; 46:102266. [PMID: 32145446 DOI: 10.1016/j.fsigen.2020.102266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 01/23/2020] [Accepted: 02/26/2020] [Indexed: 01/11/2023]
Abstract
Previous studies suggested that Sudden Infant Death Syndrome (SIDS) can partially be genetically explained by cardiac arrhythmias; however, the number of individuals and populations investigated remain limited. We report the first SIDS study on cardiac arrhythmias genes from the Netherlands, a country with the lowest SIDS incidence likely due to parent education on awareness of environmental risk factors. By using targeted massively parallel sequencing (MPS) in 142 Dutch SIDS cases, we performed a complete exon screening of all 173 exons from 9 cardiac arrhythmias genes SCN5A, KCNQ1, KCNH2, KCNE1, KCNE2, CACNA1C, CAV3, ANK2 and KCNJ2 (∼34,000 base pairs), that were selected to harbour previously established SIDS-associated DNA variants. Motivated by the poor DNA quality from the paraffin embedded material used, the application of a conservative sequencing quality control protocol resulted in 102 SIDS cases surviving quality control. Amongst the 102 SIDS cases, we identified a total of 40 DNA variants in 8 cardiac arrhythmia genes found in 60 (58.8 %) cases. Statistical analyses using ancestry-adjusted reference population data and multiple test correction revealed that 13 (32.5 %) of the identified DNA variants in 6 cardiac arrhythmia genes were significantly associated with SIDS, which were observed in 15 (14.7 %) SIDS cases. These 13, and another three, DNA variants were classified as likely pathogenic for cardiac arrhythmias using the American College of Medical Genetics guidelines for interpretation of sequence variants. The 16 likely pathogenic DNA variants were found in 16 (15.7 %) SIDS cases, including i) 3 novel DNA variants not recorded in public databases ii) 7 known DNA variants for which significant SIDS association established here was previously unknown, and iii) 6 known DNA variants for which LQTS association was reported previously. By having replicated previously reported SIDS-associated DNA variants located in cardiac arrhythmia genes and by having highlighting novel SIDS-associated DNA variants in such genes, our findings provide additional empirical evidence for the partial genetic explanation of SIDS by cardiac arrhythmias. On a wider note, our study outcome stresses the need for routine post-mortem genetic screening of assumed SIDS cases, particularly for cardiac arrhythmia genes. When put in practise, it will allow preventing further sudden deaths (not only in infants) in the affected families, thereby allowing forensic molecular autopsy not only to provide answers on the cause of death, but moreover to save lives.
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Affiliation(s)
- Germaine Liebrechts-Akkerman
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ronald van Marion
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
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20
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Diebold I, Schön U, Scharf F, Benet-Pagès A, Laner A, Holinski-Feder E, Abicht A. Critical assessment of secondary findings in genes linked to primary arrhythmia syndromes. Hum Mutat 2020; 41:1025-1032. [PMID: 32048431 PMCID: PMC7187207 DOI: 10.1002/humu.23996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/16/2020] [Accepted: 02/09/2020] [Indexed: 12/15/2022]
Abstract
As comprehensive sequencing technologies gain widespread use, questions about so-called secondary findings (SF) require urgent consideration. The American College of Medical Genetics and Genomics has recommended to report SF in 59 genes (ACMG SF v2.0) including four actionable genes associated with inherited primary arrhythmia syndromes (IPAS) such as catecholaminergic polymorphic ventricular tachycardia, long QT syndrome, and Brugada syndrome. Databases provide conflicting results for the purpose of identifying pathogenic variants in SF associated with IPAS at a level of sufficient evidence for clinical return. As IPAS account for a significant proportion of sudden cardiac deaths (SCD) in young and apparently healthy individuals, variant interpretation has a great impact on diagnosis and prevention of disease. Of 6381 individuals, 0.4% carry pathogenic variants in one of the four actionable genes related to IPAS: RYR2, KCNQ1, KCNH2, and SCN5A. Comparison of the databases ClinVar, Leiden Open-source Variant Database, and Human Gene Mutation Database showed impactful differences (0.2% to 1.3%) in variant interpretation improvable by expert-curation depending on database and classification system used. These data further highlight the need for international consensus regarding the variant interpretation, and subsequently management of SF in particular with regard to treatable arrhythmic disorders with increased risk of SCD.
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Affiliation(s)
- Isabel Diebold
- Department of Genomics, Medical Genetics Center Munich, Munich, Germany.,Department of Pediatrics, Technical University of Munich School of Medicine, Munich, Germany
| | - Ulrike Schön
- Department of Genomics, Medical Genetics Center Munich, Munich, Germany
| | - Florentine Scharf
- Department of Genomics, Medical Genetics Center Munich, Munich, Germany
| | - Anna Benet-Pagès
- Department of Genomics, Medical Genetics Center Munich, Munich, Germany
| | - Andreas Laner
- Department of Genomics, Medical Genetics Center Munich, Munich, Germany
| | | | - Angela Abicht
- Department of Genomics, Medical Genetics Center Munich, Munich, Germany.,Department of Neurology, Friedrich-Baur-Institute, Klinikum der Ludwig-Maximilians-University, Munich, Germany
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21
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Larsen MK, Christiansen SL, Hertz CL, Frank-Hansen R, Jensen HK, Banner J, Morling N. Targeted molecular genetic testing in young sudden cardiac death victims from Western Denmark. Int J Legal Med 2019; 134:111-121. [DOI: 10.1007/s00414-019-02179-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/15/2019] [Indexed: 02/08/2023]
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22
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Faridi R, Tona R, Brofferio A, Hoa M, Olszewski R, Schrauwen I, Assir MZ, Bandesha AA, Khan AA, Rehman AU, Brewer C, Ahmed W, Leal SM, Riazuddin S, Boyden SE, Friedman TB. Mutational and phenotypic spectra of KCNE1 deficiency in Jervell and Lange-Nielsen Syndrome and Romano-Ward Syndrome. Hum Mutat 2019; 40:162-176. [PMID: 30461122 PMCID: PMC6328321 DOI: 10.1002/humu.23689] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/01/2018] [Accepted: 11/15/2018] [Indexed: 11/11/2022]
Abstract
KCNE1 encodes a regulatory subunit of the KCNQ1 potassium channel-complex. Both KCNE1 and KCNQ1 are necessary for normal hearing and cardiac ventricular repolarization. Recessive variants in these genes are associated with Jervell and Lange-Nielson syndrome (JLNS1 and JLNS2), a cardio-auditory syndrome characterized by congenital profound sensorineural deafness and a prolonged QT interval that can cause ventricular arrhythmias and sudden cardiac death. Some normal-hearing carriers of heterozygous missense variants of KCNE1 and KCNQ1 have prolonged QT intervals, a dominantly inherited phenotype designated Romano-Ward syndrome (RWS), which is also associated with arrhythmias and elevated risk of sudden death. Coassembly of certain mutant KCNE1 monomers with wild-type KCNQ1 subunits results in RWS by a dominant negative mechanism. This paper reviews variants of KCNE1 and their associated phenotypes, including biallelic truncating null variants of KCNE1 that have not been previously reported. We describe three homozygous nonsense mutations of KCNE1 segregating in families ascertained ostensibly for nonsyndromic deafness: c.50G>A (p.Trp17*), c.51G>A (p.Trp17*), and c.138C>A (p.Tyr46*). Some individuals carrying missense variants of KCNE1 have RWS. However, heterozygotes for loss-of-function variants of KCNE1 may have normal QT intervals while biallelic null alleles are associated with JLNS2, indicating a complex genotype-phenotype spectrum for KCNE1 variants.
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Affiliation(s)
- Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Risa Tona
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alessandra Brofferio
- Cardiology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rafal Olszewski
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Z.K. Assir
- Allama Iqbal Medical Research Centre, Jinnah Hospital Complex, Lahore 54550, Pakistan
| | - Akhtar A. Bandesha
- Cardiology Department, The Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Asma A. Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Atteeq U. Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carmen Brewer
- Audiology Unit, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD 20892, USA
| | - Wasim Ahmed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Suzanne M. Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sheikh Riazuddin
- Allama Iqbal Medical Research Centre, Jinnah Hospital Complex, Lahore 54550, Pakistan
| | - Steven E. Boyden
- Section on Genetics of Communication Disorders, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas B. Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
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23
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PKP2 and DSG2 genetic variations in Latvian arrhythmogenic right ventricular dysplasia/cardiomyopathy registry patients. Anatol J Cardiol 2018; 20:296-302. [PMID: 30391969 PMCID: PMC6280287 DOI: 10.14744/anatoljcardiol.2018.35984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Objective: The Latvian arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD-C) registry was established to determine the genetic background of ARVD-C for analyzing discovered genetic variation frequencies in the European and Latvian populations. Methods: In total, 38 patients with suspected ARVD-C were selected. The clinical parameters were defined according to the ARVD-C guidelines, PKP2 and DSG2 gene analysis was performed using the Sanger sequencing. Additionally, large deletions/duplications were analyzed using the multiplex ligation-dependent probe amplification (MLPA) analysis. Results: Twenty symptomatic patients were enrolled in the study. Typical ARVD abnormalities were found in electrocardiography for 10 (50%) patients, in Holter monitoring for 19 (95%), in transthoracic echocardiography for 20 (100%), and in cardiac magnetic resonance for 6 (30%). Different benign genetic variations were found. Three novel, unregistered, possibly benign variations were found in the PKP2 gene: c.2489+131G>A, c.2489+72delA, and c.1035-5T>C and three in the DSG2 gene: c.404G>A, c.1107G>A, and c.379-15A>G. Two genetic variations in the PKP2 gene: c.1592T>G, c.2489+1G>A are possibly pathogenic. For the first time, variation c.1592T>G, has been discovered in the homozygote form. Using the MLPA analysis, large deletions or duplications were not found. Conclusion: The prevalence of the majority of non-pathological genetic variations is similar in the Latvian ARVD-C patients and the European population. Possibly, pathogenic variations were found only in 10% of our registry patients, which could mean that PKP2 and DSG2 are not the most commonly affected genes in the Latvian population.
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24
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Fraser AG. A manifesto for cardiovascular imaging: addressing the human factor. Eur Heart J Cardiovasc Imaging 2018; 18:1311-1321. [PMID: 29029029 PMCID: PMC5837338 DOI: 10.1093/ehjci/jex216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/11/2017] [Indexed: 12/22/2022] Open
Abstract
Our use of modern cardiovascular imaging tools has not kept pace with their technological development. Diagnostic errors are common but seldom investigated systematically. Rather than more impressive pictures, our main goal should be more precise tests of function which we select because their appropriate use has therapeutic implications which in turn have a beneficial impact on morbidity or mortality. We should practise analytical thinking, use checklists to avoid diagnostic pitfalls, and apply strategies that will reduce biases and avoid overdiagnosis. We should develop normative databases, so that we can apply diagnostic algorithms that take account of variations with age and risk factors and that allow us to calculate pre-test probability and report the post-test probability of disease. We should report the imprecision of a test, or its confidence limits, so that reference change values can be considered in daily clinical practice. We should develop decision support tools to improve the quality and interpretation of diagnostic imaging, so that we choose the single best test irrespective of modality. New imaging tools should be evaluated rigorously, so that their diagnostic performance is established before they are widely disseminated; this should be a shared responsibility of manufacturers with clinicians, leading to cost-effective implementation. Trials should evaluate diagnostic strategies against independent reference criteria. We should exploit advances in machine learning to analyse digital data sets and identify those features that best predict prognosis or responses to treatment. Addressing these human factors will reap benefit for patients, while technological advances continue unpredictably.
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Affiliation(s)
- Alan G Fraser
- School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.,Department of Cardiology, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK.,Division of Cardiovascular Imaging and Dynamics, Department of Cardiovascular Sciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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25
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Lack of evidence for a causal role of CALR3 in monogenic cardiomyopathy. Eur J Hum Genet 2018; 26:1603-1610. [PMID: 29988065 PMCID: PMC6189092 DOI: 10.1038/s41431-018-0208-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 11/08/2022] Open
Abstract
The pathogenicity of previously published disease-associated genes and variants is sometimes questionable. Large-scale, population-based sequencing studies have uncovered numerous false assignments of pathogenicity. Misinterpretation of sequence variants may have serious implications for the patients and families involved, as genetic test results are increasingly being used in medical decision making. In this study, we assessed the role of the calreticulin-3 gene (CALR3) in cardiomyopathy. CALR3 has been included in several cardiomyopathy gene panels worldwide. Its inclusion is based on a single publication describing two missense variants in patients with hypertrophic cardiomyopathy. In our national cardiomyopathy cohort (n = 6154), we identified 17 unique, rare heterozygous CALR3 variants in 48 probands. Overall, our patient cohort contained a significantly higher number of rare CALR3 variants compared to the ExAC population (p = 0.0036). However, after removing a potential Dutch founder variant, no statistically significant difference was found (p = 0.89). In nine probands, the CALR3 variant was accompanied by a disease-causing variant in another, well-known cardiomyopathy gene. In three families, the CALR3 variant did not segregate with the disease. Furthermore, we could not demonstrate calreticulin-3 protein expression in myocardial tissues at various ages. On the basis of these findings, it seems highly questionable that variants in CALR3 are a monogenic cause of cardiomyopathy.
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26
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Stallmeyer B, Dittmann S, Schulze-Bahr E. Genetische Diagnostik zur Vermeidung des plötzlichen Herztods. Internist (Berl) 2018; 59:776-789. [DOI: 10.1007/s00108-018-0462-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Brodehl A, Gaertner-Rommel A, Milting H. Molecular insights into cardiomyopathies associated with desmin (DES) mutations. Biophys Rev 2018; 10:983-1006. [PMID: 29926427 DOI: 10.1007/s12551-018-0429-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/22/2018] [Indexed: 12/15/2022] Open
Abstract
Increasing usage of next-generation sequencing techniques pushed during the last decade cardiogenetic diagnostics leading to the identification of a huge number of genetic variants in about 170 genes associated with cardiomyopathies, channelopathies, or syndromes with cardiac involvement. Because of the biochemical and cellular complexity, it is challenging to understand the clinical meaning or even the relevant pathomechanisms of the majority of genetic sequence variants. However, detailed knowledge about the associated molecular pathomechanism is essential for the development of efficient therapeutic strategies in future and genetic counseling. Mutations in DES, encoding the muscle-specific intermediate filament protein desmin, have been identified in different kinds of cardiac and skeletal myopathies. Here, we review the functions of desmin in health and disease with a focus on cardiomyopathies. In addition, we will summarize the genetic and clinical literature about DES mutations and will explain relevant cell and animal models. Moreover, we discuss upcoming perspectives and consequences of novel experimental approaches like genome editing technology, which might open a novel research field contributing to the development of efficient and mutation-specific treatment options.
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Affiliation(s)
- Andreas Brodehl
- Erich and Hanna Klessmann Institute for Cardiovascular Research & Development, Heart and Diabetes Centre NRW, Ruhr-University Bochum, Georgstrasse 11, 32545, Bad Oeynhausen, Germany.
| | - Anna Gaertner-Rommel
- Erich and Hanna Klessmann Institute for Cardiovascular Research & Development, Heart and Diabetes Centre NRW, Ruhr-University Bochum, Georgstrasse 11, 32545, Bad Oeynhausen, Germany
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute for Cardiovascular Research & Development, Heart and Diabetes Centre NRW, Ruhr-University Bochum, Georgstrasse 11, 32545, Bad Oeynhausen, Germany.
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28
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Lawal TA, Lewis KL, Johnston JJ, Heidlebaugh AR, Ng D, Gaston-Johansson FG, Klein WMP, Biesecker BB, Biesecker LG. Disclosure of cardiac variants of uncertain significance results in an exome cohort. Clin Genet 2018; 93:1022-1029. [PMID: 29383714 DOI: 10.1111/cge.13220] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 01/19/2018] [Accepted: 01/25/2018] [Indexed: 01/26/2023]
Abstract
This study examined the impact of disclosing subclassifications of genetic variants of uncertain significance (VUS) on behavioral intentions. We studied return of VUS results to 79 individuals with a cardiomyopathy-associated VUS, subclassified into VUS-high or VUS-low. Primary outcomes were perceived risk (absolute and comparative), perceived severity, perceived value of information, self-efficacy, decision regret, and behavioral intentions to share results and change behaviors. There was no significant difference between the 2 subclasses in overall behavioral intentions (t = 0.023, P = .982) and each of the individual items on the behavioral intentions scale; absolute (t = -1.138, P = .259) or comparative (t = -0.463, P = .645) risk perceptions; perceived value of information (t = 0.582, P = .563) and self-efficacy (t = -0.733, P = .466). Decision regret was significantly different (t = 2.148, P = .035), with VUS-low (mean = 17.24, SD = 16.08) reporting greater regret. Combining the subclasses, perceived value of information was the strongest predictor of behavioral intentions (β = 0.524, P < .001). Participants generally understood the meaning of a genetic VUS result classification and reported satisfaction with result disclosure. No differences in behavioral intentions were found, but differences in decision regret suggest participants distinguish subclasses of VUS results. The perceived value of VUS may motivate recipients to pursue health-related behaviors.
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Affiliation(s)
- T A Lawal
- National Institute of Nursing Research, National Institutes of Health (NIH), Bethesda, Maryland
| | - K L Lewis
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - J J Johnston
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - A R Heidlebaugh
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - D Ng
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - F G Gaston-Johansson
- Department of Acute and Chronic Care, Johns Hopkins University School of Nursing, Baltimore, Maryland
| | - W M P Klein
- Behavioral Research Program, National Cancer Institute, NIH, Bethesda, Maryland
| | - B B Biesecker
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - L G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
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29
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Biesecker BB, Lewis KL, Umstead KL, Johnston JJ, Turbitt E, Fishler KP, Patton JH, Miller IM, Heidlebaugh AR, Biesecker LG. Web Platform vs In-Person Genetic Counselor for Return of Carrier Results From Exome Sequencing: A Randomized Clinical Trial. JAMA Intern Med 2018; 178:338-346. [PMID: 29356820 PMCID: PMC5885925 DOI: 10.1001/jamainternmed.2017.8049] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
IMPORTANCE A critical bottleneck in clinical genomics is the mismatch between large volumes of results and the availability of knowledgeable professionals to return them. OBJECTIVE To test whether a web-based platform is noninferior to a genetic counselor for educating patients about their carrier results from exome sequencing. DESIGN, SETTING, AND PARTICIPANTS A randomized noninferiority trial conducted in a longitudinal sequencing cohort at the National Institutes of Health from February 5, 2014, to December 16, 2016, was used to compare the web-based platform with a genetic counselor. Among the 571 eligible participants, 1 to 7 heterozygous variants were identified in genes that cause a phenotype that is recessively inherited. Surveys were administered after cohort enrollment, immediately following trial education, and 1 month and 6 months later to primarily healthy postreproductive participants who expressed interest in learning their carrier results. Both intention-to-treat and per-protocol analyses were applied. INTERVENTIONS A web-based platform that integrated education on carrier results with personal test results was designed to directly parallel disclosure education by a genetic counselor. The sessions took a mean (SD) time of 21 (10.6), and 27 (9.3) minutes, respectively. MAIN OUTCOMES AND MEASURES The primary outcomes and noninferiority margins (δNI) were knowledge (0 to 8, δNI = -1), test-specific distress (0 to 30, δNI = +1), and decisional conflict (15 to 75, δNI = +6). RESULTS After 462 participants (80.9%) provided consent and were randomized, all but 3 participants (n = 459) completed surveys following education and counseling; 398 (86.1%) completed 1-month surveys and 392 (84.8%) completed 6-month surveys. Participants were predominantly well-educated, non-Hispanic white, married parents; mean (SD) age was 63 (63.1) years and 246 (53.6%) were men. The web platform was noninferior to the genetic counselor on outcomes assessed at 1 and 6 months: knowledge (mean group difference, -0.18; lower limit of 97.5% CI, -0.63; δNI = -1), test-specific distress (median group difference, 0; upper limit of 97.5% CI, 0; δNI = +1), and decisional conflict about choosing to learn results (mean group difference, 1.18; upper limit of 97.5% CI, 2.66; δNI = +6). There were no significant differences between the genetic counselors and web-based platform detected between modes of education delivery in disclosure rates to spouses (151 vs 159; relative risk [RR], 1.04; 95% CI, 0.64-1.69; P > .99), children (103 vs 117; RR, 1.07; 95% CI, 0.85-1.36; P = .59), or siblings (91 vs 78; RR, 1.17; 95% CI, 0.94-1.46; P = .18). CONCLUSIONS AND RELEVANCE This trial demonstrates noninferiority of web-based return of carrier results among postreproductive, mostly healthy adults. Replication studies among younger and more diverse populations are needed to establish generalizability. Yet return of results via a web-based platform may be sufficient for subsets of test results, reserving genetic counselors for return of results with a greater health threat. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00410241.
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Affiliation(s)
- Barbara B Biesecker
- Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Katie L Lewis
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Kendall L Umstead
- Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Jennifer J Johnston
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Erin Turbitt
- Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Kristen P Fishler
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - John H Patton
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ilana M Miller
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Alexis R Heidlebaugh
- Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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30
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High proportion of genetic cases in patients with advanced cardiomyopathy including a novel homozygous Plakophilin 2-gene mutation. PLoS One 2017; 12:e0189489. [PMID: 29253866 PMCID: PMC5734774 DOI: 10.1371/journal.pone.0189489] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/27/2017] [Indexed: 11/19/2022] Open
Abstract
Cardiomyopathies might lead to end-stage heart disease with the requirement of drastic treatments like bridging up to transplant or heart transplantation. A not precisely known proportion of these diseases are genetically determined. We genotyped 43 index-patients (30 DCM, 10 ARVC, 3 RCM) with advanced or end stage cardiomyopathy using a gene panel which covered 46 known cardiomyopathy disease genes. Fifty-three variants with possible impact on disease in 33 patients were identified. Of these 27 (51%) were classified as likely pathogenic or pathogenic in the MYH7, MYL2, MYL3, NEXN, TNNC1, TNNI3, DES, LMNA, PKP2, PLN, RBM20, TTN, and CRYAB genes. Fifty-six percent (n = 24) of index-patients carried a likely pathogenic or pathogenic mutation. Of these 75% (n = 18) were familial and 25% (n = 6) sporadic cases. However, severe cardiomyopathy seemed to be not characterized by a specific mutation profile. Remarkably, we identified a novel homozygous PKP2-missense variant in a large consanguineous family with sudden death in early childhood and several members with heart transplantation in adolescent age.
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Lin Y, Zhang Q, Zhong ZA, Xu Z, He S, Rao F, Liu Y, Tang J, Wang F, Liu H, Xie J, Wu H, Wang S, Li X, Shan Z, Deng C, Liao Z, Deng H, Liao H, Xue Y, Chen W, Zhan X, Zhang B, Wu S. Whole Genome Sequence Identified a Rare Homozygous Pathogenic Mutation of the DSG2 Gene in a Familial Arrhythmogenic Cardiomyopathy Involving Both Ventricles. Cardiology 2017; 138:41-54. [PMID: 28578331 DOI: 10.1159/000462962] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/13/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND This study was designed to identify the pathogenic mutation in a Chinese family with arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D) using whole genome sequencing (WGS). METHODS AND RESULTS Probands II:1 and II:2 underwent routine examinations for diagnosis. Genomic DNA was extracted from the peripheral blood of family members and analyzed using WGS. A total of 60,285 single-nucleotide polymorphisms (SNP) and 13,918 insertions/deletions (InDel) occurring in the exonic regions of genes and predisposing to cardiomyopathies and arrhythmias were identified. When filtered using the 1000 Genomes Project (2014 version), NHLBI ESP6500, and ExAC databases, 12 missense SNP and 2 InDel in exonic regions remained, the allele frequencies of which were <0.01 or unknown. The potentially pathogenic mutations that occurred in the genes DSG2, PKP4, PRKAG2, FOXD4, CTTN, and DMD, which were identified by SIFT or PolyPhen-2 software as "damaging," were validated using Sanger sequencing. Probands II:1 and II:2 shared an extremely rare homozygous mutation in the DSG2 (p.F531C) gene, which was also demonstrated using intersection analysis of WGS data from probands II:1 and II:2. Electron microscopy and histological staining of myocardial biopsies showed widened and destroyed intercalated discs, and interrupted, atrophic, and disarranged myocardial fibers, and hyperplastic interstitial fibers, collagen fibers, and adipocytes were infiltrated and invaded. CONCLUSIONS A homozygous mutation of DSG2 p.F531C was identified as the pathogenic mutation in patients with ARVC/D involving both ventricles, as a result of widened and impaired intercalated discs, interrupted myocardial fibers, and abnormally hyperplastic interstitial fibers, collagen fibers, and adipocytes.
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Affiliation(s)
- Yubi Lin
- Guangdong Cardiovascular Institute, Guangdong Academy of Medical Sciences, Guangdong General Hospital, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Medical School of South China University of Technology, Guangzhou, China
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Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 2017. [PMID: 28349240 DOI: 10.1007/s00439‐017‐1779‐6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD ( http://www.hgmd.org ) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.
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Affiliation(s)
- Peter D Stenson
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katy Evans
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Hayden
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sally Heywood
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Michelle Hussain
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew D Phillips
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 2017; 136:665-677. [PMID: 28349240 PMCID: PMC5429360 DOI: 10.1007/s00439-017-1779-6] [Citation(s) in RCA: 912] [Impact Index Per Article: 130.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023]
Abstract
The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.
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Affiliation(s)
- Peter D Stenson
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katy Evans
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Hayden
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sally Heywood
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Michelle Hussain
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew D Phillips
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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de Gonzalo-Calvo D, Quezada M, Campuzano O, Perez-Serra A, Broncano J, Ayala R, Ramos M, Llorente-Cortes V, Blasco-Turrión S, Morales F, Gonzalez P, Brugada R, Mangas A, Toro R. Familial dilated cardiomyopathy: A multidisciplinary entity, from basic screening to novel circulating biomarkers. Int J Cardiol 2017; 228:870-880. [PMID: 27889554 DOI: 10.1016/j.ijcard.2016.11.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/23/2016] [Accepted: 11/05/2016] [Indexed: 12/11/2022]
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Genetic basis of dilated cardiomyopathy. Int J Cardiol 2016; 224:461-472. [PMID: 27736720 DOI: 10.1016/j.ijcard.2016.09.068] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/15/2016] [Accepted: 09/17/2016] [Indexed: 01/19/2023]
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Christiansen SL, Hertz CL, Ferrero-Miliani L, Dahl M, Weeke PE, LuCamp, Ottesen GL, Frank-Hansen R, Bundgaard H, Morling N. Genetic investigation of 100 heart genes in sudden unexplained death victims in a forensic setting. Eur J Hum Genet 2016; 24:1797-1802. [PMID: 27650965 DOI: 10.1038/ejhg.2016.118] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/12/2016] [Accepted: 08/05/2016] [Indexed: 11/09/2022] Open
Abstract
In forensic medicine, one-third of the sudden deaths remain unexplained after medico-legal autopsy. A major proportion of these sudden unexplained deaths (SUD) are considered to be caused by inherited cardiac diseases. Sudden cardiac death (SCD) may be the first manifestation of these diseases. The purpose of this study was to explore the yield of next-generation sequencing of genes associated with SCD in a cohort of SUD victims. We investigated 100 genes associated with cardiac diseases in 61 young (1-50 years) SUD cases. DNA was captured with the Haloplex target enrichment system and sequenced using an Illumina MiSeq. The identified genetic variants were evaluated and classified as likely, unknown or unlikely to have a functional effect. The criteria for this classification were based on the literature, databases, conservation and prediction of the effect of the variant. We found that 21 (34%) individuals carried variants with a likely functional effect. Ten (40%) of these variants were located in genes associated with cardiomyopathies and 15 (60%) of the variants in genes associated with cardiac channelopathies. Nineteen individuals carried variants with unknown functional effect. Our findings indicate that broad genetic investigation of SUD victims increases the diagnostic outcome, and the investigation should comprise genes involved in both cardiomyopathies and cardiac channelopathies.
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Affiliation(s)
- Sofie Lindgren Christiansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christin Løth Hertz
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura Ferrero-Miliani
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Dahl
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Peter Ejvin Weeke
- The Department of Cardiology, Laboratory of Molecular Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - LuCamp
- LuCamp, The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care, Copenhagen, Denmark
| | - Gyda Lolk Ottesen
- Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune Frank-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henning Bundgaard
- The Unit for Inherited Cardiac Diseases, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Assessing the capability of massively parallel sequencing for opportunistic pharmacogenetic screening. Genet Med 2016; 19:357-361. [PMID: 27537706 PMCID: PMC5316383 DOI: 10.1038/gim.2016.105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/16/2016] [Indexed: 12/21/2022] Open
Abstract
PURPOSE The aim of the study was to assess exome data for preemptive pharmacogenetic screening for 203 clinically relevant pharmacogenetic variant positions from the Pharmacogenomics Knowledgebase and Clinical Pharmacogenetics Implementation Consortium and identify copy-number variants (CNVs) in CYP2D6. METHODS We examined the coverage and genotype quality of 203 pharmacogenetic variant positions in 973 exomes compared with five genomes and with five genotyping chip data sets. Then, we determined the agreement of exome and chip genotypes by evaluating concordance in a three-way comparison of exome, genome, and chip-based genotyping at 1,929 variant positions in five individuals. Finally, we evaluated the utility of exomes for detecting CYP2D6 CNVs. RESULTS For 5 individuals examined for 203 pharmacogenetic variants (5 × 203 = 1,015), 998/1,015 were identified by genome, 849/1,015 were identified by exome, and 295/1,015 by genotyping chip. Thirty-six pharmacogenetic star allele variants with moderate to strong Clinical Pharmacogenetics Implementation Consortium (CPIC) therapeutic recommendations were identified in 973 exomes. Exomes had high (98%) genotype concordance with chip-based genotyping. CYP2D6 CNVs were identified in 57/973 exomes. CONCLUSIONS Exomes outperformed the current chip-based assay in detecting more important pharmacogenetic variant positions and CYP2D6 CNVs for preemptive pharmacogenetic screening. Tools should be developed to derive pharmacogenetic variants from exomes.Genet Med 19 3, 357-361.
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Hata Y, Yoshida K, Kinoshita K, Nishida N. Epilepsy-related sudden unexpected death: targeted molecular analysis of inherited heart disease genes using next-generation DNA sequencing. Brain Pathol 2016; 27:292-304. [PMID: 27135274 DOI: 10.1111/bpa.12390] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/11/2016] [Accepted: 04/21/2016] [Indexed: 11/27/2022] Open
Abstract
Inherited heart disease causing electric instability in the heart has been suggested to be a risk factor for sudden unexpected death in epilepsy (SUDEP). The purpose of this study was to reveal the correlation between epilepsy-related sudden unexpected death (SUD) and inherited heart disease. Twelve epilepsy-related SUD cases (seven males and five females, aged 11-78 years) were examined. Nine cases fulfilled the criteria of SUDEP, and three cases died by drowning. In addition to examining three major epilepsy-related genes, we used next-generation sequencing (NGS) to examine 73 inherited heart disease-related genes. We detected both known pathogenic variants and rare variants with minor allele frequencies of <0.5%. The pathogenicity of these variants was evaluated and graded by eight in silico predictive algorithms. Six known and six potential rare variants were detected. Among these, three known variants of LDB3, DSC2 and KCNE1 and three potential rare variants of MYH6, DSP and DSG2 were predicted by in silico analysis as possibly highly pathogenic in three of the nine SUDEP cases. Two of three cases with desmosome-related variants showed mild but possible significant right ventricular dysplasia-like pathology. A case with LDB3 and MYH6 variants showed hypertrabeculation of the left ventricle and severe fibrosis of the cardiac conduction system. In the three drowning death cases, one case with mild prolonged QT interval had two variants in ANK2. This study shows that inherited heart disease may be a significant risk factor for SUD in some epilepsy cases, even if pathological findings of the heart had not progressed to an advanced stage of the disease. A combination of detailed pathological examination of the heart and gene analysis using NGS may be useful for evaluating arrhythmogenic potential of epilepsy-related SUD.
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Affiliation(s)
- Yukiko Hata
- Department of Legal Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Koji Yoshida
- Department of Neurology, Toyama University Hospital, Toyama, Japan
| | - Koshi Kinoshita
- Department of Legal Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Naoki Nishida
- Department of Legal Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
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39
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Green RC, Goddard KAB, Jarvik GP, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Anan CF, Chinnaiyan AM, Chung WK, Clayton EW, Cooper GM, East K, Evans JP, Fullerton SM, Garraway LA, Garrett JR, Gray SW, Henderson GE, Hindorff LA, Holm IA, Lewis MH, Hutter CM, Janne PA, Joffe S, Kaufman D, Knoppers BM, Koenig BA, Krantz ID, Manolio TA, McCullough L, McEwen J, McGuire A, Muzny D, Myers RM, Nickerson DA, Ou J, Parsons DW, Petersen GM, Plon SE, Rehm HL, Roberts JS, Robinson D, Salama JS, Scollon S, Sharp RR, Shirts B, Spinner NB, Tabor HK, Tarczy-Hornoch P, Veenstra DL, Wagle N, Weck K, Wilfond BS, Wilhelmsen K, Wolf SM, Wynn J, Yu JH. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine. Am J Hum Genet 2016; 98:1051-1066. [PMID: 27181682 DOI: 10.1016/j.ajhg.2016.04.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/14/2016] [Indexed: 12/11/2022] Open
Abstract
Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.
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Affiliation(s)
- Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA.
| | - Katrina A B Goddard
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Laura M Amendola
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, NY 10032, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Barbara A Bernhardt
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sawona Biswas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carrie L Blout
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kyle B Brothers
- Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Wylie Burke
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA; Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Departments of Pathology and Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Ann Arbor, MI 48109, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10029, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Ellen W Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University, Nashville, TN 37203, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kelly East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Levi A Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jeremy R Garrett
- Children's Mercy Bioethics Center, Children's Mercy Hospital, Kansas City, MO 64108, USA; Departments of Pediatrics and Philosophy, University of Missouri - Kansas City, Kansas City, MO 64110, USA
| | - Stacy W Gray
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gail E Henderson
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ingrid A Holm
- Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Carolyn M Hutter
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Pasi A Janne
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Steven Joffe
- Department of Medical Ethics & Health Policy, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - David Kaufman
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Barbara A Koenig
- Institute for Health and Aging, University of California, San Francisco, San Francisco, CA 94118, USA
| | - Ian D Krantz
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Laurence McCullough
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean McEwen
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Amy McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey Ou
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Donald W Parsons
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sharon E Plon
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA; Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, MA 02139, USA
| | - J Scott Roberts
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
| | - Joseph S Salama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard R Sharp
- Biomedical Ethics Research Program, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Brian Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nancy B Spinner
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Holly K Tabor
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Peter Tarczy-Hornoch
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; University of Washington, Seattle, WA 98105, USA
| | - David L Veenstra
- Department of Pharmacy, University of Washington, Seattle, WA 98195, USA
| | - Nikhil Wagle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Karen Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Benjamin S Wilfond
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Kirk Wilhelmsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Susan M Wolf
- Law School, Medical School, and Consortium on Law and Values in Health, Environment, & the Life Sciences, Minneapolis, University of Minnesota, MN 55455, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY 10029, USA
| | - Joon-Ho Yu
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
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Maxwell K, Hart S, Vijai J, Schrader K, Slavin T, Thomas T, Wubbenhorst B, Ravichandran V, Moore R, Hu C, Guidugli L, Wenz B, Domchek S, Robson M, Szabo C, Neuhausen S, Weitzel J, Offit K, Couch F, Nathanson K. Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer. Am J Hum Genet 2016; 98:801-817. [PMID: 27153395 DOI: 10.1016/j.ajhg.2016.02.024] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/26/2016] [Indexed: 01/24/2023] Open
Abstract
Sequencing tests assaying panels of genes or whole exomes are widely available for cancer risk evaluation. However, methods for classification of variants resulting from this testing are not well studied. We evaluated the ability of a variant-classification methodology based on American College of Medical Genetics and Genomics (ACMG) guidelines to define the rate of mutations and variants of uncertain significance (VUS) in 180 medically relevant genes, including all ACMG-designated reportable cancer and non-cancer-associated genes, in individuals who met guidelines for hereditary cancer risk evaluation. We performed whole-exome sequencing in 404 individuals in 253 families and classified 1,640 variants. Potentially clinically actionable (likely pathogenic [LP] or pathogenic [P]) versus nonactionable (VUS, likely benign, or benign) calls were 95% concordant with locus-specific databases and Clinvar. LP or P mutations were identified in 12 of 25 breast cancer susceptibility genes in 26 families without identified BRCA1/2 mutations (11%). Evaluation of 84 additional genes associated with autosomal-dominant cancer susceptibility identified LP or P mutations in only two additional families (0.8%). However, individuals from 10 of 253 families (3.9%) had incidental LP or P mutations in 32 non-cancer-associated genes, and 9% of individuals were monoallelic carriers of a rare LP or P mutation in 39 genes associated with autosomal-recessive cancer susceptibility. Furthermore, 95% of individuals had at least one VUS. In summary, these data support the clinical utility of ACMG variant-classification guidelines. Additionally, evaluation of extended panels of cancer-associated genes in breast/ovarian cancer families leads to only an incremental clinical benefit but substantially increases the complexity of the results.
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Beck TF, Mullikin JC, Biesecker LG. Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants. Clin Chem 2016; 62:647-54. [PMID: 26847218 DOI: 10.1373/clinchem.2015.249623] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/07/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) data are used for both clinical care and clinical research. DNA sequence variants identified using NGS are often returned to patients/participants as part of clinical or research protocols. The current standard of care is to validate NGS variants using Sanger sequencing, which is costly and time-consuming. METHODS We performed a large-scale, systematic evaluation of Sanger-based validation of NGS variants using data from the ClinSeq® project. We first used NGS data from 19 genes in 5 participants, comparing them to high-throughput Sanger sequencing results on the same samples, and found no discrepancies among 234 NGS variants. We then compared NGS variants in 5 genes from 684 participants against data from Sanger sequencing. RESULTS Of over 5800 NGS-derived variants, 19 were not validated by Sanger data. Using newly designed sequencing primers, Sanger sequencing confirmed 17 of the NGS variants, and the remaining 2 variants had low quality scores from exome sequencing. Overall, we measured a validation rate of 99.965% for NGS variants using Sanger sequencing, which was higher than many existing medical tests that do not necessitate orthogonal validation. CONCLUSIONS A single round of Sanger sequencing is more likely to incorrectly refute a true-positive variant from NGS than to correctly identify a false-positive variant from NGS. Validation of NGS-derived variants using Sanger sequencing has limited utility, and best practice standards should not include routine orthogonal Sanger validation of NGS variants.
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Affiliation(s)
- Tyler F Beck
- National Human Genome Research Institute, NIH, Bethesda, MD
| | - James C Mullikin
- National Human Genome Research Institute, NIH, Bethesda, MD; NIH Intramural Sequencing Center, Rockville, MD
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Van Driest SL, Wells QS, Stallings S, Bush WS, Gordon A, Nickerson DA, Kim JH, Crosslin DR, Jarvik GP, Carrell DS, Ralston JD, Larson EB, Bielinski SJ, Olson JE, Ye Z, Kullo IJ, Abul-Husn NS, Scott SA, Bottinger E, Almoguera B, Connolly J, Chiavacci R, Hakonarson H, Rasmussen-Torvik LJ, Pan V, Persell SD, Smith M, Chisholm RL, Kitchner TE, He MM, Brilliant MH, Wallace JR, Doheny KF, Shoemaker MB, Li R, Manolio TA, Callis TE, Macaya D, Williams MS, Carey D, Kapplinger JD, Ackerman MJ, Ritchie MD, Denny JC, Roden DM. Association of Arrhythmia-Related Genetic Variants With Phenotypes Documented in Electronic Medical Records. JAMA 2016; 315:47-57. [PMID: 26746457 PMCID: PMC4758131 DOI: 10.1001/jama.2015.17701] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE Large-scale DNA sequencing identifies incidental rare variants in established Mendelian disease genes, but the frequency of related clinical phenotypes in unselected patient populations is not well established. Phenotype data from electronic medical records (EMRs) may provide a resource to assess the clinical relevance of rare variants. OBJECTIVE To determine the clinical phenotypes from EMRs for individuals with variants designated as pathogenic by expert review in arrhythmia susceptibility genes. DESIGN, SETTING, AND PARTICIPANTS This prospective cohort study included 2022 individuals recruited for nonantiarrhythmic drug exposure phenotypes from October 5, 2012, to September 30, 2013, for the Electronic Medical Records and Genomics Network Pharmacogenomics project from 7 US academic medical centers. Variants in SCN5A and KCNH2, disease genes for long QT and Brugada syndromes, were assessed for potential pathogenicity by 3 laboratories with ion channel expertise and by comparison with the ClinVar database. Relevant phenotypes were determined from EMRs, with data available from 2002 (or earlier for some sites) through September 10, 2014. EXPOSURES One or more variants designated as pathogenic in SCN5A or KCNH2. MAIN OUTCOMES AND MEASURES Arrhythmia or electrocardiographic (ECG) phenotypes defined by International Classification of Diseases, Ninth Revision (ICD-9) codes, ECG data, and manual EMR review. RESULTS Among 2022 study participants (median age, 61 years [interquartile range, 56-65 years]; 1118 [55%] female; 1491 [74%] white), a total of 122 rare (minor allele frequency <0.5%) nonsynonymous and splice-site variants in 2 arrhythmia susceptibility genes were identified in 223 individuals (11% of the study cohort). Forty-two variants in 63 participants were designated potentially pathogenic by at least 1 laboratory or ClinVar, with low concordance across laboratories (Cohen κ = 0.26). An ICD-9 code for arrhythmia was found in 11 of 63 (17%) variant carriers vs 264 of 1959 (13%) of those without variants (difference, +4%; 95% CI, -5% to +13%; P = .35). In the 1270 (63%) with ECGs, corrected QT intervals were not different in variant carriers vs those without (median, 429 vs 439 milliseconds; difference, -10 milliseconds; 95% CI, -16 to +3 milliseconds; P = .17). After manual review, 22 of 63 participants (35%) with designated variants had any ECG or arrhythmia phenotype, and only 2 had corrected QT interval longer than 500 milliseconds. CONCLUSIONS AND RELEVANCE Among laboratories experienced in genetic testing for cardiac arrhythmia disorders, there was low concordance in designating SCN5A and KCNH2 variants as pathogenic. In an unselected population, the putatively pathogenic genetic variants were not associated with an abnormal phenotype. These findings raise questions about the implications of notifying patients of incidental genetic findings.
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Affiliation(s)
| | - Quinn S Wells
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - William S Bush
- Vanderbilt University Medical Center, Nashville, Tennessee2Case Western Reserve University, Cleveland, Ohio
| | | | | | | | | | | | | | | | - Eric B Larson
- Group Health Research Institute, Seattle, Washington
| | | | | | - Zi Ye
- Mayo Clinic, Rochester, Minnesota
| | | | | | - Stuart A Scott
- Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Berta Almoguera
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - John Connolly
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Hakon Hakonarson
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania8Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | | | - Vivian Pan
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Stephen D Persell
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Maureen Smith
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rex L Chisholm
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | - Max M He
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin
| | | | | | | | | | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | | | | | - David Carey
- Geisinger Health System, Danville, Pennsylvania
| | | | | | - Marylyn D Ritchie
- Pennsylvania State University, University Park16Geisinger Health System, Danville, Pennsylvania
| | - Joshua C Denny
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, Tennessee
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Participant use and communication of findings from exome sequencing: a mixed-methods study. Genet Med 2015; 18:577-83. [PMID: 26540156 PMCID: PMC4860179 DOI: 10.1038/gim.2015.133] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/18/2015] [Indexed: 12/11/2022] Open
Abstract
Purpose This study investigated how genome sequencing results affect health behaviors, affect, and communication. Methods We report on 29 participants who received a sequence result in the ClinSeq® study, a cohort of well-educated, post-reproductive volunteers. A mixed methods design was used to explore respondents’ use, communication, and perceived utility of results. Results Most participants (72%) shared their result with at least one health care provider, and 31% reported changes to their health care. Participants scored high on the Positive Experiences subscale and low on the Distress subscale of a modified version of the Multidimensional Impact of Cancer Risk Assessment (MICRA). The majority (93%) shared their result with at least one family member. Participant’s described deriving personal utility from their results. Conclusions This paper is the first to describe research participants’ reactions to actionable sequencing results. Our findings suggest clinical and personal benefit from receiving sequencing results, both of which may contribute to improved health for the recipients. Given the participants’ largely positive or neutral affective responses and disclosure of their results to physicians and relatives, health care providers should redirect concern from the potential for distress and attend to motivating patients to follow their medical recommendations.
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Santori M, Blanco-Verea A, Gil R, Cortis J, Becker K, Schneider PM, Carracedo A, Brion M. Broad-based molecular autopsy: a potential tool to investigate the involvement of subtle cardiac conditions in sudden unexpected death in infancy and early childhood. Arch Dis Child 2015; 100:952-6. [PMID: 26272908 DOI: 10.1136/archdischild-2015-308200] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/01/2015] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Sudden unexplained death in children is a tragic and traumatic event, often worsened when the cause of death cannot be determined. This work aimed to investigate the presence of putative pathogenic genetic variants in a broad spectrum of cardiomyopathy, channelopathy and aortic disease associated genes that may have increased these children's vulnerability to sudden cardiac death. DESIGN We performed molecular autopsy of 41 cases of sudden unexplained death in infants and children through massive parallel sequencing of up to 86 sudden cardiac death-related genes. Multiple in silico analyses were conducted together with a thorough review of the literature in order to prioritise the putative pathogenic variants. RESULTS A total of 63 variants in 35 cases were validated. The largest proportion of these variants is located within cardiomyopathy genes although this would have been more expected of channelopathy gene variants. Subtle microscopic features of heart tissue may indicate the presence of an early onset cardiomyopathy as a predisposing condition to sudden unexpected death in some individuals. CONCLUSIONS Next-generation sequencing technologies reveal the existence of a wide spectrum of rare and novel genetic variants in sarcomere genes, compared with that of cardiac ion channels, in sudden unexplained death in infants and children. Our findings encourage further investigation of the role of early onset inherited cardiomyopathies and other diseases involving myocardial dysfunction in these deaths. Early detection of variants in these individuals could help to unmask subtle forms of disease within their relatives, who would eventually benefit from better counselling about their genetic history.
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Affiliation(s)
- Montserrat Santori
- Xenética de Enfermidades Cardiovasculares, Instituto de Investigación Sanitaria de Santiago, Red de Investigación Cardiovascular (RIC), Santiago De Compostela, Spain Grupo de Medicina Xenómica, University of Santiago de Compostela, Santiago de Compostela, Spain Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
| | - Alejandro Blanco-Verea
- Xenética de Enfermidades Cardiovasculares, Instituto de Investigación Sanitaria de Santiago, Red de Investigación Cardiovascular (RIC), Santiago De Compostela, Spain Grupo de Medicina Xenómica, University of Santiago de Compostela, Santiago de Compostela, Spain Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
| | - Rocio Gil
- Xenética de Enfermidades Cardiovasculares, Instituto de Investigación Sanitaria de Santiago, Red de Investigación Cardiovascular (RIC), Santiago De Compostela, Spain Grupo de Medicina Xenómica, University of Santiago de Compostela, Santiago de Compostela, Spain Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
| | - Judith Cortis
- Faculty of Medicine, Institute of Legal Medicine, University of Cologne, Cologne, Germany
| | - Katrin Becker
- Faculty of Medicine, Institute of Legal Medicine, University of Cologne, Cologne, Germany
| | - Peter M Schneider
- Faculty of Medicine, Institute of Legal Medicine, University of Cologne, Cologne, Germany
| | - Angel Carracedo
- Grupo de Medicina Xenómica, University of Santiago de Compostela, Santiago de Compostela, Spain Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain Center of Excellence in Genomic Medicine Research, King Abdulaziz University Jeddah, Kingdom of Saudi Arabia
| | - Maria Brion
- Xenética de Enfermidades Cardiovasculares, Instituto de Investigación Sanitaria de Santiago, Red de Investigación Cardiovascular (RIC), Santiago De Compostela, Spain Grupo de Medicina Xenómica, University of Santiago de Compostela, Santiago de Compostela, Spain Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
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Hertz CL, Christiansen SL, Ferrero-Miliani L, Dahl M, Weeke PE, Ottesen GL, Frank-Hansen R, Bundgaard H, Morling N. Next-generation sequencing of 100 candidate genes in young victims of suspected sudden cardiac death with structural abnormalities of the heart. Int J Legal Med 2015; 130:91-102. [PMID: 26383259 DOI: 10.1007/s00414-015-1261-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/03/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND In sudden, unexpected, non-traumatic death in young individuals, structural abnormalities of the heart are frequently identified at autopsy. However, the findings may be unspecific and cause of death may remain unclear. A significant proportion of these cases are most likely caused by inherited cardiac diseases, and the cases are categorized as sudden cardiac death (SCD). The purpose of this study was to explore the added diagnostic value of genetic testing by next-generation sequencing (NGS) of a broad gene panel, as a supplement to the traditional forensic investigation in cases with non-diagnostic structural abnormalities of the heart. METHODS AND RESULTS We screened 72 suspected SCD cases (<50 years) using the HaloPlex Target Enrichment System (Agilent) and NGS (Illumina MiSeq) for 100 genes previously associated with inherited cardiomyopathies and channelopathies. Fifty-two cases had non-diagnostic structural cardiac abnormalities and 20 cases, diagnosed with a cardiomyopathy post-mortem (ARVC = 14, HCM = 6), served as comparators. Fifteen (29%) of the deceased individuals with non-diagnostic findings had variants with likely functional effects based on conservation, computational prediction, allele-frequency and supportive literature. The corresponding frequency in deceased individuals with cardiomyopathies was 35% (p = 0.8). CONCLUSION The broad genetic screening revealed variants with likely functional effects at similar high rates, i.e. in 29 and 35% of the suspected SCD cases with non-diagnostic and diagnostic cardiac abnormalities, respectively. Although the interpretation of broad NGS screening is challenging, it can support the forensic investigation and help the cardiologist's decision to offer counselling and clinical evaluation to relatives of young SCD victims.
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Affiliation(s)
- C L Hertz
- The Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 11 Frederik V's Vej, 2100, Copenhagen, Denmark.
| | - S L Christiansen
- The Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 11 Frederik V's Vej, 2100, Copenhagen, Denmark
| | - L Ferrero-Miliani
- The Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 11 Frederik V's Vej, 2100, Copenhagen, Denmark
| | - M Dahl
- The Department of Clinical Biochemistry, Køge University Hospital, Køge, Denmark
| | - P E Weeke
- The Department of Cardiology, Laboratory of Molecular Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - G L Ottesen
- The Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - R Frank-Hansen
- The Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 11 Frederik V's Vej, 2100, Copenhagen, Denmark
| | - H Bundgaard
- The Unit for Inherited Cardiac Diseases, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - N Morling
- The Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 11 Frederik V's Vej, 2100, Copenhagen, Denmark
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Hertz CL, Christiansen SL, Larsen MK, Dahl M, Ferrero-Miliani L, Weeke PE, Pedersen O, Hansen T, Grarup N, Ottesen GL, Frank-Hansen R, Banner J, Morling N. Genetic investigations of sudden unexpected deaths in infancy using next-generation sequencing of 100 genes associated with cardiac diseases. Eur J Hum Genet 2015; 24:817-22. [PMID: 26350513 DOI: 10.1038/ejhg.2015.198] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/08/2015] [Accepted: 08/24/2015] [Indexed: 02/07/2023] Open
Abstract
Sudden infant death syndrome (SIDS) is the most frequent manner of post-perinatal death among infants. One of the suggested causes of the syndrome is inherited cardiac diseases, mainly channelopathies, that can trigger arrhythmias and sudden death. The purpose of this study was to investigate cases of sudden unexpected death in infancy (SUDI) for potential causative variants in 100 cardiac-associated genes. We investigated 47 SUDI cases of which 38 had previously been screened for variants in RYR2, KCNQ1, KCNH2 and SCN5A. Using the Haloplex Target Enrichment System (Agilent) and next-generation sequencing (NGS), the coding regions of 100 genes associated with inherited channelopathies and cardiomyopathies were captured and sequenced on the Illumina MiSeq platform. Sixteen (34%) of the SUDI cases had variants with likely functional effects, based on conservation, computational prediction and allele frequency, in one or more of the genes screened. The possible effects of the variants were not verified with family or functional studies. Eight (17%) of the SUDI cases had variants in genes affecting ion channel functions. The remaining eight cases had variants in genes associated with cardiomyopathies. In total, one third of the SUDI victims in a forensic setting had variants with likely functional effect that presumably contributed to the cause of death. The results support the assumption that channelopathies are important causes of SUDI. Thus, analysis of genes associated with cardiac diseases in SUDI victims is important in the forensic setting and a valuable supplement to the clinical investigation in all cases of sudden death.
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Affiliation(s)
- Christin Loeth Hertz
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sofie Lindgren Christiansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maiken Kudahl Larsen
- Department of Forensic Medicine, Faculty of Health Sciences, University of Aarhus, Aarhus, Denmark
| | - Morten Dahl
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Biochemistry, Køge, Copenhagen University Hospital, Copenhagen, Denmark
| | - Laura Ferrero-Miliani
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Ejvin Weeke
- Department of Cardiology, Laboratory of Molecular Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gyda Lolk Ottesen
- Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune Frank-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jytte Banner
- Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Identification of Medically Actionable Secondary Findings in the 1000 Genomes. PLoS One 2015; 10:e0135193. [PMID: 26332594 PMCID: PMC4558085 DOI: 10.1371/journal.pone.0135193] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/19/2015] [Indexed: 12/13/2022] Open
Abstract
The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.
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Brion M, Sobrino B, Martinez M, Blanco-Verea A, Carracedo A. Massive parallel sequencing applied to the molecular autopsy in sudden cardiac death in the young. Forensic Sci Int Genet 2015; 18:160-70. [PMID: 26243589 DOI: 10.1016/j.fsigen.2015.07.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 12/18/2022]
Abstract
Sudden cardiac death in the young is a very traumatic event that occurs often in apparently healthy individuals without an explainable cause of death after a comprehensive medico-legal investigation. Knowledge about the pathologies with a risk of sudden death is increasingly showing a greater underlying genetic heterogeneity, which provides one of the main handicaps for molecular autopsy. On the other hand the enormous technological advances in sequencing technologies, allow us to analyse as many genes as we want at a cost increasingly reduced. The sum of these two factors (increased knowledge of genetics and available technologies) allow us to make an individualized study of the causes of sudden cardiac death in young adults, through massive sequencing of all potential genes involved in the process. We define this approach as massive genomic autopsy, and with this review we will try to explain the possible scenarios and methods available for its implementation.
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Affiliation(s)
- M Brion
- Xenética de Enfermidades Cardiovasculares, Instituto de Investigación Sanitaria de Santiago, Red de Investigación Cardiovascular (RIC), Santiago De Compostela, Spain; Grupo de Medicina Xenómica, University of Santiago de Compostela. Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain.
| | - B Sobrino
- Grupo de Medicina Xenómica, University of Santiago de Compostela. Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
| | - M Martinez
- Xenética de Enfermidades Cardiovasculares, Instituto de Investigación Sanitaria de Santiago, Red de Investigación Cardiovascular (RIC), Santiago De Compostela, Spain; Grupo de Medicina Xenómica, University of Santiago de Compostela. Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
| | - A Blanco-Verea
- Xenética de Enfermidades Cardiovasculares, Instituto de Investigación Sanitaria de Santiago, Red de Investigación Cardiovascular (RIC), Santiago De Compostela, Spain; Grupo de Medicina Xenómica, University of Santiago de Compostela. Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, University of Santiago de Compostela. Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Rara (CIBERER), Spain; Center of Excellence in Genomic Medicine, King Abdulaziz University, Jeddah, KSA, Saudi Arabia
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Li MH, Abrudan JL, Dulik MC, Sasson A, Brunton J, Jayaraman V, Dugan N, Haley D, Rajagopalan R, Biswas S, Sarmady M, DeChene ET, Deardorff MA, Wilkens A, Noon SE, Scarano MI, Santani AB, White PS, Pennington J, Conlin LK, Spinner NB, Krantz ID, Vetter VL. Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death. Hum Genomics 2015; 9:15. [PMID: 26187847 PMCID: PMC4506570 DOI: 10.1186/s40246-015-0038-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/09/2015] [Indexed: 11/23/2022] Open
Abstract
Background Conditions associated with sudden cardiac arrest/death (SCA/D) in youth often have a genetic etiology. While SCA/D is uncommon, a pro-active family screening approach may identify these inherited structural and electrical abnormalities prior to symptomatic events and allow appropriate surveillance and treatment. This study investigated the diagnostic utility of exome sequencing (ES) by evaluating the capture and coverage of genes related to SCA/D. Methods Samples from 102 individuals (13 with known molecular etiologies for SCA/D, 30 individuals without known molecular etiologies for SCA/D and 59 with other conditions) were analyzed following exome capture and sequencing at an average read depth of 100X. Reads were mapped to human genome GRCh37 using Novoalign, and post-processing and analysis was done using Picard and GATK. A total of 103 genes (2,190 exons) related to SCA/D were used as a primary filter. An additional 100 random variants within the targeted genes associated with SCA/D were also selected and evaluated for depth of sequencing and coverage. Although the primary objective was to evaluate the adequacy of depth of sequencing and coverage of targeted SCA/D genes and not for primary diagnosis, all patients who had SCA/D (known or unknown molecular etiologies) were evaluated with the project’s variant analysis pipeline to determine if the molecular etiologies could be successfully identified. Results The majority of exons (97.6 %) were captured and fully covered on average at minimum of 20x sequencing depth. The proportion of unique genomic positions reported within poorly covered exons remained small (4 %). Exonic regions with less coverage reflect the need to enrich these areas to improve coverage. Despite limitations in coverage, we identified 100 % of cases with a prior known molecular etiology for SCA/D, and analysis of an additional 30 individuals with SCA/D but no known molecular etiology revealed a diagnostic answer in 5/30 (17 %). We also demonstrated 95 % of 100 randomly selected reported variants within our targeted genes would have been picked up on ES based on our coverage analysis. Conclusions ES is a helpful clinical diagnostic tool for SCA/D given its potential to successfully identify a molecular diagnosis, but clinicians should be aware of limitations of available platforms from technical and diagnostic perspectives. Electronic supplementary material The online version of this article (doi:10.1186/s40246-015-0038-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mindy H Li
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Jenica L Abrudan
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Matthew C Dulik
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Ariella Sasson
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Joshua Brunton
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Vijayakumar Jayaraman
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Noreen Dugan
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Danielle Haley
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Ramakrishnan Rajagopalan
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Sawona Biswas
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Mahdi Sarmady
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Elizabeth T DeChene
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Matthew A Deardorff
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Alisha Wilkens
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Sarah E Noon
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Maria I Scarano
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Avni B Santani
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Peter S White
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Present address: Department of Pediatrics, Cincinnati Children's Hospital and Medical Center, and Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
| | - Jeffrey Pennington
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Laura K Conlin
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Nancy B Spinner
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Ian D Krantz
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Victoria L Vetter
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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Abstract
With the wider deployment of massively-parallel, next-generation sequencing, it is now possible to survey human genome data for research and clinical purposes. The reduced cost of producing short-read sequencing has now shifted the burden to data analysis. Analysis of genome sequencing remains challenged by the complexity of the human genome, including redundancy and the repetitive nature of genome elements and the large amount of variation in individual genomes. Public databases of human genome sequences greatly facilitate interpretation of common and rare genetic variation, although linking database sequence information to detailed clinical information is limited by privacy and practical issues. Genetic variation is a rich source of knowledge for cardiovascular disease because many, if not all, cardiovascular disorders are highly heritable. The role of rare genetic variation in predicting risk and complications of cardiovascular diseases has been well established for hypertrophic and dilated cardiomyopathy, where the number of genes that are linked to these disorders is growing. Bolstered by family data, where genetic variants segregate with disease, rare variation can be linked to specific genetic variation that offers profound diagnostic information. Understanding genetic variation in cardiomyopathy is likely to help stratify forms of heart failure and guide therapy. Ultimately, genetic variation may be amenable to gene correction and gene editing strategies.
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Affiliation(s)
- Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine
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