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Venkat V, Abdelhalim H, DeGroat W, Zeeshan S, Ahmed Z. Investigating genes associated with heart failure, atrial fibrillation, and other cardiovascular diseases, and predicting disease using machine learning techniques for translational research and precision medicine. Genomics 2023; 115:110584. [PMID: 36813091 DOI: 10.1016/j.ygeno.2023.110584] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/06/2023] [Accepted: 02/11/2023] [Indexed: 02/22/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of mortality and loss of disability adjusted life years (DALYs) globally. CVDs like Heart Failure (HF) and Atrial Fibrillation (AF) are associated with physical effects on the heart muscles. As a result of the complex nature, progression, inherent genetic makeup, and heterogeneity of CVDs, personalized treatments are believed to be critical. Rightful application of artificial intelligence (AI) and machine learning (ML) approaches can lead to new insights into CVDs for providing better personalized treatments with predictive analysis and deep phenotyping. In this study we focused on implementing AI/ML techniques on RNA-seq driven gene-expression data to investigate genes associated with HF, AF, and other CVDs, and predict disease with high accuracy. The study involved generating RNA-seq data derived from the serum of consented CVD patients. Next, we processed the sequenced data using our RNA-seq pipeline and applied GVViZ for gene-disease data annotation and expression analysis. To achieve our research objectives, we developed a new Findable, Accessible, Intelligent, and Reproducible (FAIR) approach that includes a five-level biostatistical evaluation, primarily based on the Random Forest (RF) algorithm. During our AI/ML analysis, we have fitted, trained, and implemented our model to classify and distinguish high-risk CVD patients based on their age, gender, and race. With the successful execution of our model, we predicted the association of highly significant HF, AF, and other CVDs genes with demographic variables.
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Affiliation(s)
- Vignesh Venkat
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Habiba Abdelhalim
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - William DeGroat
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Saman Zeeshan
- Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany St, New Brunswick, NJ, USA
| | - Zeeshan Ahmed
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA; Department of Medicine, Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, 125 Paterson St, New Brunswick, NJ, USA.
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2
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Spurrell CH, Barozzi I, Kosicki M, Mannion BJ, Blow MJ, Fukuda-Yuzawa Y, Slaven N, Afzal SY, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Lee EA, Garvin TH, Pham QT, Kronshage AN, Lisgo S, Bristow J, Cappola TP, Morley MP, Margulies KB, Pennacchio LA, Dickel DE, Visel A. Genome-wide fetalization of enhancer architecture in heart disease. Cell Rep 2022; 40:111400. [PMID: 36130500 PMCID: PMC9534044 DOI: 10.1016/j.celrep.2022.111400] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/10/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Heart disease is associated with re-expression of key transcription factors normally active only during prenatal development of the heart. However, the impact of this reactivation on the regulatory landscape in heart disease is unclear. Here, we use RNA-seq and ChIP-seq targeting a histone modification associated with active transcriptional enhancers to generate genome-wide enhancer maps from left ventricle tissue from up to 26 healthy controls, 18 individuals with idiopathic dilated cardiomyopathy (DCM), and five fetal hearts. Healthy individuals have a highly reproducible epigenomic landscape, consisting of more than 33,000 predicted heart enhancers. In contrast, we observe reproducible disease-associated changes in activity at 6,850 predicted heart enhancers. Combined analysis of adult and fetal samples reveals that the heart disease epigenome and transcriptome both acquire fetal-like characteristics, with 3,400 individual enhancers sharing fetal regulatory properties. We also provide a comprehensive data resource (http://heart.lbl.gov) for the mechanistic exploration of DCM etiology.
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Affiliation(s)
- Cailyn H Spurrell
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Neil Slaven
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sarah Y Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elizabeth A Lee
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Quan T Pham
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anne N Kronshage
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - James Bristow
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas P Cappola
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael P Morley
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kenneth B Margulies
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA.
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3
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Alimohamed MZ, Westers H, Vos YJ, Van der Velde KJ, Sijmons RH, Van der Zwaag PA, Sikkema-Raddatz B, Jongbloed JDH. Validation of New Gene Variant Classification Methods: a Field-Test in Diagnostic Cardiogenetics. Front Genet 2022; 13:824510. [PMID: 35299955 PMCID: PMC8921548 DOI: 10.3389/fgene.2022.824510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background: In the molecular genetic diagnostics of Mendelian disorders, solutions are needed for the major challenge of dealing with the large number of variants of uncertain significance (VUSs) identified using next-generation sequencing (NGS). Recently, promising approaches using constraint metrics to calculate case excess scores (CE), etiological fractions (EF), and gnomAD-derived constraint scores have been reported that estimate the likelihood of rare variants in specific genes or regions that are pathogenic. Our objective is to study the usability of these constraint data into variant interpretation in a diagnostic setting, using our cardiomyopathy cohort.Methods and Results: Patients (N = 2002) referred for clinical genetic diagnostics underwent NGS testing of 55–61 genes associated with cardiomyopathies. Previously classified likely pathogenic (LP) and pathogenic (P) variants were used to validate the use of data from CE, EF, and gnomAD constraint analyses for (re)classification of associated variant types in specific cardiomyopathy subtype-related genes. The classifications corroborated in 94% (354/378) of cases. Next, we reclassified 23 unique VUSs to LP, increasing the diagnostic yield by 1.2%. In addition, 106 unique VUSs (5.3% of patients) were prioritized for co-segregation or functional analyses.Conclusions: Our analysis confirms that the use of constraint metrics data can improve variant interpretation, and we, therefore, recommend using constraint scores on other cohorts and disorders and its inclusion in variant interpretation protocols.
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Affiliation(s)
- Mohamed Z. Alimohamed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
- Department of Research and Training, Shree Hindu Mandal Hospital, Dar-es-salaam, Tanzania
- Tanzania Human Genetics Organization, Groningen, Netherlands
- *Correspondence: Mohamed Z. Alimohamed, ; Jan D. H. Jongbloed,
| | - Helga Westers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Yvonne J. Vos
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - K. Joeri Van der Velde
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Rolf H. Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paul A. Van der Zwaag
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jan D. H. Jongbloed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- *Correspondence: Mohamed Z. Alimohamed, ; Jan D. H. Jongbloed,
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Clinical Implication of Genetic Testing in Dilated Cardiomyopathy. INTERNATIONAL JOURNAL OF HEART FAILURE 2022; 4:1-11. [PMID: 36262197 PMCID: PMC9383343 DOI: 10.36628/ijhf.2021.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/29/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022]
Abstract
Dilated cardiomyopathy (DCM) is one of the important causes of heart failure (HF). With the rapidly evolving technologies for gene analysis and tremendous advances in knowledge of HF genetics, the importance of genetic testing in DCM is currently highlighted. Several genetic variants causing DCM have been identified and this information is used for diagnosis, risk stratification and family screening of DCM patients. However, there are still several challenges in applying genetic testing to real clinical practice. In this review, we will summarize recent understandings in DCM genetics and provide an evidence-based practical guide to the use of genetic testing for DCM patients.
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Fenix AM, Miyaoka Y, Bertero A, Blue SM, Spindler MJ, Tan KKB, Perez-Bermejo JA, Chan AH, Mayerl SJ, Nguyen TD, Russell CR, Lizarraga PP, Truong A, So PL, Kulkarni A, Chetal K, Sathe S, Sniadecki NJ, Yeo GW, Murry CE, Conklin BR, Salomonis N. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Nat Commun 2021; 12:6324. [PMID: 34732726 PMCID: PMC8566601 DOI: 10.1038/s41467-021-26623-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/22/2021] [Indexed: 12/16/2022] Open
Abstract
Mutations in the cardiac splicing factor RBM20 lead to malignant dilated cardiomyopathy (DCM). To understand the mechanism of RBM20-associated DCM, we engineered isogenic iPSCs with DCM-associated missense mutations in RBM20 as well as RBM20 knockout (KO) iPSCs. iPSC-derived engineered heart tissues made from these cell lines recapitulate contractile dysfunction of RBM20-associated DCM and reveal greater dysfunction with missense mutations than KO. Analysis of RBM20 RNA binding by eCLIP reveals a gain-of-function preference of mutant RBM20 for 3' UTR sequences that are shared with amyotrophic lateral sclerosis (ALS) and processing-body associated RNA binding proteins (FUS, DDX6). Deep RNA sequencing reveals that the RBM20 R636S mutant has unique gene, splicing, polyadenylation and circular RNA defects that differ from RBM20 KO. Super-resolution microscopy verifies that mutant RBM20 maintains very limited nuclear localization potential; rather, the mutant protein associates with cytoplasmic processing bodies (DDX6) under basal conditions, and with stress granules (G3BP1) following acute stress. Taken together, our results highlight a pathogenic mechanism in cardiac disease through splicing-dependent and -independent pathways.
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Affiliation(s)
- Aidan M Fenix
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Yuichiro Miyaoka
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Alessandro Bertero
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, Stem Cell Program, and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Kenneth K B Tan
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | | | - Amanda H Chan
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Steven J Mayerl
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Trieu D Nguyen
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | | | | | - Annie Truong
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Po-Lin So
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA
| | - Aishwarya Kulkarni
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, Stem Cell Program, and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nathan J Sniadecki
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
- Department of Mechanical Engineering, University of Washington, 3720 15th Avenue NE, Seattle, WA, 98105, USA
- Department of Bioengineering, University of Washington, 3720 15th Avenue NE, Seattle, WA, 98105, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program, and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Charles E Murry
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
- Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.
- Department of Bioengineering, University of Washington, 3720 15th Avenue NE, Seattle, WA, 98105, USA.
- Department of Medicine/Cardiology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
- Sana Biotechnology, 188 E Blaine Street, Seattle, WA, 98102, USA.
| | - Bruce R Conklin
- Gladstone Institutes, 1650 Owens St, San Francisco, CA, 94158, USA.
- Department of Medicine, Cellular and Molecular Pharmacology, and Ophthalmology, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45229, USA.
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6
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Zhang L, Shi J, Ouyang J, Zhang R, Tao Y, Yuan D, Lv C, Wang R, Ning B, Roberts R, Tong W, Liu Z, Shi T. X-CNV: genome-wide prediction of the pathogenicity of copy number variations. Genome Med 2021; 13:132. [PMID: 34407882 PMCID: PMC8375180 DOI: 10.1186/s13073-021-00945-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/30/2021] [Indexed: 01/04/2023] Open
Abstract
Background Gene copy number variations (CNVs) contribute to genetic diversity and disease prevalence across populations. Substantial efforts have been made to decipher the relationship between CNVs and pathogenesis but with limited success. Results We have developed a novel computational framework X-CNV (www.unimd.org/XCNV), to predict the pathogenicity of CNVs by integrating more than 30 informative features such as allele frequency (AF), CNV length, CNV type, and some deleterious scores. Notably, over 14 million CNVs across various ethnic groups, covering nearly 93% of the human genome, were unified to calculate the AF. X-CNV, which yielded area under curve (AUC) values of 0.96 and 0.94 in training and validation sets, was demonstrated to outperform other available tools in terms of CNV pathogenicity prediction. A meta-voting prediction (MVP) score was developed to quantitively measure the pathogenic effect, which is based on the probabilistic value generated from the XGBoost algorithm. The proposed MVP score demonstrated a high discriminative power in determining pathogenetic CNVs for inherited traits/diseases in different ethnic groups. Conclusions The ability of the X-CNV framework to quantitatively prioritize functional, deleterious, and disease-causing CNV on a genome-wide basis outperformed current CNV-annotation tools and will have broad utility in population genetics, disease-association studies, and diagnostic screening. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00945-4.
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Affiliation(s)
- Li Zhang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai, 200062, China
| | - Jingru Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jian Ouyang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Riquan Zhang
- School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai, 200062, China
| | - Yiran Tao
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dongsheng Yuan
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Chengkai Lv
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Ruiyuan Wang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Ruth Roberts
- ApconiX Ltd, Alderley Park, Alderley Edge, SK10 4TG, UK.,University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Weida Tong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
| | - Zhichao Liu
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China. .,School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai, 200062, China. .,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
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Sex Differences, Genetic and Environmental Influences on Dilated Cardiomyopathy. J Clin Med 2021; 10:jcm10112289. [PMID: 34070351 PMCID: PMC8197492 DOI: 10.3390/jcm10112289] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is characterized by dilatation of the left ventricle and impaired systolic function and is the second most common cause of heart failure after coronary heart disease. The etiology of DCM is diverse including genetic pathogenic variants, infection, inflammation, autoimmune diseases, exposure to chemicals/toxins as well as endocrine and neuromuscular causes. DCM is inherited in 20–50% of cases where more than 30 genes have been implicated in the development of DCM with pathogenic variants in TTN (Titin) most frequently associated with disease. Even though male sex is a risk factor for heart failure, few studies have examined sex differences in the pathogenesis of DCM. We searched the literature for studies examining idiopathic or familial/genetic DCM that reported data by sex in order to determine the sex ratio of disease. We found 31 studies that reported data by sex for non-genetic DCM with an average overall sex ratio of 2.5:1 male to female and 7 studies for familial/genetic DCM with an overall average sex ratio of 1.7:1 male to female. No manuscripts that we found had more females than males in their studies. We describe basic and clinical research findings that may explain the increase in DCM in males over females based on sex differences in basic physiology and the immune and fibrotic response to damage caused by mutations, infections, chemotherapy agents and autoimmune responses.
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8
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Subaran RL, Stewart WCL. FREQMAX provides an alternative approach for determining high-resolution allele frequency thresholds in carrier screening. Hum Mutat 2020; 41:2078-2086. [PMID: 33032373 DOI: 10.1002/humu.24123] [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: 07/31/2019] [Revised: 06/26/2020] [Accepted: 10/01/2020] [Indexed: 11/08/2022]
Abstract
As whole-genome data become available for increasing numbers of individuals across diverse populations, the list of genomic variants of unknown significance (VOUS) continues to grow. One powerful tool in VOUS interpretation is determining whether an allele is too common to be considered pathogenic. As genetic and epidemiological parameters vary across disease models, so too does the pathogenic allele frequency threshold for each disease gene. One threshold-setting approach is the maximum credible allele frequency (MCAF) method. However, estimating some of the input values MCAF requires, especially those involving heterogeneity, can present nontrivial statistical challenges. Here, we introduce FREQMAX, our alternative approach for determining allele frequency thresholds in carrier screening. FREQMAX makes efficient use of the data available for well-studied traits and exhibits flexibility for traits where information may be less complete. For cystic fibrosis, more alleles are excluded as benign by FREQMAX than by MCAF. For less-comprehensively characterized traits like ciliary dyskinesia and Smith-Lemli-Opitz syndrome, FREQMAX is able to set the allele frequency threshold without requiring a priori estimates of maximum genetic and allelic contributions. Furthermore, though we describe FREQMAX in the context of carrier screening, its classical population genetics framework also provides context for adaptation to other trait models.
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Affiliation(s)
- Ryan L Subaran
- Bioinformatics R&D, Sema4, a Mount Sinai Venture, Stamford, Connecticut, USA
| | - William C L Stewart
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
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Park KJ, Lee W, Chun S, Min WK. The Frequency of Discordant Variant Classification in the Human Gene Mutation Database: A Comparison of the American College of Medical Genetics and Genomics Guidelines and ClinVar. Lab Med 2020; 52:250-259. [PMID: 32926152 DOI: 10.1093/labmed/lmaa072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE Discordant variant classifications among public databases is one of the well-documented limitations when interpreting the pathogenicity of variants. The aim of this study is to investigate the level of germline variant misannotation from the Human Gene Mutation Database (HGMD) and the annotation concordance between databases. METHODS We used a total of 188,106 classified variants (disease-causing mutations [n = 179,454] and polymorphisms [n = 8652]) in 6466 genes from the HGMD. All variants were reanalyzed based on the American College of Medical Genetics and Genomics (ACMG) guidelines and compared to ClinVar database variants. RESULTS When variants were classified based on the ACMG guidelines, misclassification was observed in 3.47% (2289/65,896) of variants. The overall concordance between HGMD and ClinVar was 97.62% (52,499/53,780) of variants studied. CONCLUSION Variants in databases must be used with caution when variant pathogenicity is interpreted. This study reveals the frequency of misannotation of the HGMD variants and annotation concordance between databases in depth.
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Affiliation(s)
- Kyoung-Jin Park
- Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang-Si, Gyeonggi-Do, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sail Chun
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Won-Ki Min
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Abstract
In the absence of contemporary, population-based epidemiological studies, estimates of the incidence and prevalence of the inherited cardiomyopathies have been derived from screening studies, most often of young adult populations, to assess cardiovascular risk or to detect the presence of disease in athletes or military recruits. The global estimates for hypertrophic cardiomyopathy (1/500 individuals), dilated cardiomyopathy (1/250) and arrhythmogenic right ventricular cardiomyopathy (1/5,000) are probably conservative given that only individuals who fulfil diagnostic criteria would have been included. This caveat is highly relevant because a substantial minority or even a majority of individuals who carry disease-causing genetic variants and are at risk of disease complications have incomplete and/or late-onset disease expression. The genetic literature on cardiomyopathy, which is often focused on the identification of genetic variants, has been biased in favour of pedigrees with higher penetrance. In clinical practice, an abnormal electrocardiogram with normal or non-diagnostic imaging results is a common finding for the sarcomere variants that cause hypertrophic cardiomyopathy, the titin and sarcomere variants that cause dilated cardiomyopathy and the desmosomal variants that cause either arrhythmogenic right ventricular cardiomyopathy or dilated cardiomyopathy. Therefore, defining the genetic epidemiology is also challenging given the overlapping phenotypes, incomplete and age-related expression, and highly variable penetrance even within individual families carrying the same genetic variant.
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Affiliation(s)
- William J McKenna
- Institute of Cardiovascular Science, University College London, London, UK. .,Heart Hospital, Hamad Medical Corporation, Doha, Qatar.
| | - Daniel P Judge
- Section of Advanced HF & Transplant Cardiology, Medical University of South Carolina, Charleston, SC, USA
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11
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Jinqiang Zhuang MD, Ruijun Yuan MD, Yizeng MD, Congliang Miao MD, Dandan Zhou MD, Anli Na MD, Xinying Yang MD, Hui Xu MD, Hong J. The CnB1 p.D102A variant is linked to dilated cardiomyopathy via impaired Calcineurin activity. J Mol Cell Cardiol 2020; 148:15-24. [PMID: 32882262 DOI: 10.1016/j.yjmcc.2020.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/30/2020] [Accepted: 08/18/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The role of calcineurin (protein phosphatase 2B (PP2B)) in the pathogenesis of human dilated cardiomyopathy (DCM) has not been fully elucidated. We determined the potential involvement of calcineurin in the pathogenesis of DCM caused by mutations in CnB1, a subunit of calcineurin. METHODS By whole-exome sequencing, we identified a new CnB1 variant in a Han Chinese proband with cardiomyopathy from a 3-generation family with 2 normal individuals and 3 individuals with familial dilated cardiomyopathy. The potential pathogenic variant was validated by Sanger sequencing. We performed functional and mechanistic experiments in a CnB1-knockin (KI) mouse model and at the cellular level. RESULTS We detected a rare heterozygous CnB1 variant (p.D102A) in a proband with dilated cardiomyopathy. This variant was localized to the EF hand 3 region of CnB1, where no variants have been previously reported. KI mice harboring the p.D102A variant exhibited decreased cardiac function and cardiac dilatation. Immunoblotting, RT-PCR and immunofluorescence results showed decreased cardiomyocyte size and heart failure-related protein expression. A calcineurin activity assay demonstrated decreased calcineurin activity in the KI mice, accompanied by the decreased ability of CnB1 to bind CnA. CONCLUSIONS CnB1 p.D102A is a disease-associated variant that confers susceptibility to cardiac dilatation. This variant is associated with impaired calcineurin activity and a subsequent decrease in the ability of CnB1 to bind CnA.
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Affiliation(s)
- M D Jinqiang Zhuang
- Department of Internal and Emergency Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China
| | - M D Ruijun Yuan
- Department of Cardiovascular Surgery, Changhai Hospital, Second Military Medical University. Shanghai, China
| | - M D Yizeng
- Department of Critical Care Medicine, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Shangcheng District, Hangzhou, 310003, China
| | - M D Congliang Miao
- Department of Internal and Emergency Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China
| | - M D Dandan Zhou
- Department of Internal and Emergency Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China
| | - M D Anli Na
- Department of Internal and Emergency Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China
| | - M D Xinying Yang
- Department of Internal and Emergency Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China
| | - M D Hui Xu
- Department of Internal and Emergency Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China
| | - Jiang Hong
- Department of Internal and Emergency Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China.
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12
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Bayona-Bafaluy MP, Iglesias E, López-Gallardo E, Emperador S, Pacheu-Grau D, Labarta L, Montoya J, Ruiz-Pesini E. Genetic aspects of the oxidative phosphorylation dysfunction in dilated cardiomyopathy. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 786:108334. [PMID: 33339579 DOI: 10.1016/j.mrrev.2020.108334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/27/2022]
Abstract
Dilated cardiomyopathy is a frequent and extremely heterogeneous medical condition. Deficits in the oxidative phosphorylation system have been described in patients suffering from dilated cardiomyopathy. Hence, mutations in proteins related to this biochemical pathway could be etiological factors for some of these patients. Here, we review the clinical phenotypes of patients harboring pathological mutations in genes related to the oxidative phosphorylation system, either encoded in the mitochondrial or in the nuclear genome, presenting with dilated cardiomyopathy. In addition to the clinical heterogeneity of these patients, the large genetic heterogeneity has contributed to an improper allocation of pathogenicity for many candidate mutations. We suggest criteria to avoid incorrect assignment of pathogenicity to newly found mutations and discuss possible therapies targeting the oxidative phosphorylation function.
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Affiliation(s)
- M Pilar Bayona-Bafaluy
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - Eldris Iglesias
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain.
| | - Ester López-Gallardo
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - Sonia Emperador
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center, Georg-August University,Humboldtalle, 23., 37073, Göttingen, Germany.
| | - Lorenzo Labarta
- Unidad de Cuidados Intensivos, Hospital San Jorge, Av. Martínez de Velasco, 36., 22004, Huesca, Spain.
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain; Fundación ARAID, Av. de Ranillas, 1-D., 50018, Zaragoza, Spain.
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13
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Popa-Fotea NM, Cojocaru C, Scafa-Udriste A, Micheu MM, Dorobantu M. The Multifaced Perspectives of Genetic Testing in Pediatric Cardiomyopathies and Channelopathies. J Clin Med 2020; 9:E2111. [PMID: 32635562 PMCID: PMC7408669 DOI: 10.3390/jcm9072111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 12/22/2022] Open
Abstract
Pediatric inherited cardiomyopathies (CMPs) and channelopathies (CNPs) remain important causes of death in this population, therefore, there is a need for prompt diagnosis and tailored treatment. Conventional evaluation fails to establish the diagnosis of pediatric CMPs and CNPs in a significant proportion, prompting further, more complex testing to make a diagnosis that could influence the implementation of lifesaving strategies. Genetic testing in CMPs and CNPs may help unveil the underlying cause, but needs to be carried out with caution given the lack of uniform recommendations in guidelines about the precise time to start the genetic evaluation or the type of targeted testing or whole-genome sequencing. A very diverse etiology and the scarce number of randomized studies of pediatric CMPs and CNPs make genetic testing of these maladies far more particular than their adult counterpart. The genetic diagnosis is even more puzzling if the psychological impact point of view is taken into account. This review aims to put together different perspectives, state-of-the art recommendations-synthetizing the major indications from European and American guidelines-and psychosocial outlooks to construct a comprehensive genetic assessment of pediatric CMPs and CNPs.
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Affiliation(s)
- Nicoleta-Monica Popa-Fotea
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Floreasca Street 8, 014461 Bucharest, Romania; (N.-M.P.-F.); (C.C.); (A.S.-U.); (M.D.)
- Department 4—Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
| | - Cosmin Cojocaru
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Floreasca Street 8, 014461 Bucharest, Romania; (N.-M.P.-F.); (C.C.); (A.S.-U.); (M.D.)
| | - Alexandru Scafa-Udriste
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Floreasca Street 8, 014461 Bucharest, Romania; (N.-M.P.-F.); (C.C.); (A.S.-U.); (M.D.)
- Department 4—Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
| | - Miruna Mihaela Micheu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Floreasca Street 8, 014461 Bucharest, Romania; (N.-M.P.-F.); (C.C.); (A.S.-U.); (M.D.)
| | - Maria Dorobantu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Floreasca Street 8, 014461 Bucharest, Romania; (N.-M.P.-F.); (C.C.); (A.S.-U.); (M.D.)
- Department 4—Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
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14
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Affiliation(s)
- Diane Fatkin
- Molecular Cardiology Division Victor Chang Cardiac Research Institute Darlinghurst Australia.,Cardiology Department St. Vincent's Hospital Darlinghurst Australia.,Faculty of Medicine UNSW Sydney Kensington Australia
| | - Renee Johnson
- Molecular Cardiology Division Victor Chang Cardiac Research Institute Darlinghurst Australia
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15
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Ramchand J, Wallis M, Macciocca I, Lynch E, Farouque O, Martyn M, Phelan D, Chong B, Lockwood S, Weintraub R, Thompson T, Trainer A, Zentner D, Vohra J, Chetrit M, Hare DL, James P. Prospective Evaluation of the Utility of Whole Exome Sequencing in Dilated Cardiomyopathy. J Am Heart Assoc 2020; 9:e013346. [PMID: 31931689 PMCID: PMC7033851 DOI: 10.1161/jaha.119.013346] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background Dilated cardiomyopathy may be heritable but shows extensive genetic heterogeneity. The utility of whole exome sequencing as a first-line genetic test for patients with dilated cardiomyopathy in a contemporary "real-world" setting has not been specifically established. Using whole exome sequencing with rigorous, evidence-based variant interpretation, we aimed to identify the prevalence of a molecular diagnosis in patients with dilated cardiomyopathy in a clinical setting. Methods and Results Whole exome sequencing was performed in eligible patients (n=83) with idiopathic or familial dilated cardiomyopathy. Variants were prioritized for curation in up to 247 genes and classified using American College of Medical Genetics and Genomics-based criteria. Ten (12%) had a pathogenic or likely pathogenic variant. Eight (10%) participants had truncating TTN variants classified as variants of uncertain significance. Five (6%) participants had variants of unknown significance according to strict American College of Medical Genetics and Genomics criteria but classified as either pathogenic or likely pathogenic by other clinical laboratories. Pathogenic or likely pathogenic variants were found in 8 genes (all within tier 1 genes), 2 (20%) of which are not included in a standard commercially available dilated cardiomyopathy panel. Using our bioinformatics pipeline, there was an average of 0.74 variants of uncertain significance per case with ≈0.75 person-hours needed to interpret each of these variants. Conclusions Whole exome sequencing is an effective diagnostic tool for patients with dilated cardiomyopathy. With stringent classification using American College of Medical Genetics and Genomics criteria, the rate of detection of pathogenic variants is lower than previous reports. Efforts to improve adherence to these guidelines will be important to prevent erroneous misclassification of nonpathogenic variants in dilated cardiomyopathy genetic testing and inappropriate cascade screening.
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Affiliation(s)
- Jay Ramchand
- Department of Medicine Austin Health The University of Melbourne Heidelberg Victoria Australia.,Department of Cardiology Austin Health Heidelberg Victoria Australia
| | - Mathew Wallis
- Department of Genetics Austin Health Heidelberg Victoria Australia
| | - Ivan Macciocca
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia
| | - Elly Lynch
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia.,Melbourne Genomics Health Alliance Melbourne Victoria Australia
| | - Omar Farouque
- Department of Medicine Austin Health The University of Melbourne Heidelberg Victoria Australia.,Department of Cardiology Austin Health Heidelberg Victoria Australia
| | - Melissa Martyn
- Melbourne Genomics Health Alliance Melbourne Victoria Australia.,Department of Paediatrics University of Melbourne Parkville Victoria Australia.,Murdoch Children's Research Institute Parkville Victoria Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia
| | - Siobhan Lockwood
- Monash Cardiovascular Research Centre and Monash Heart Monash University and Monash Health Melbourne Australia
| | - Robert Weintraub
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia
| | - Tina Thompson
- Genetic Medicine Melbourne Health Parkville Victoria Australia
| | - Alison Trainer
- Genetic Medicine Melbourne Health Parkville Victoria Australia
| | - Dominica Zentner
- Department of Cardiology Melbourne Health Parkville Victoria Australia.,Genetic Medicine Melbourne Health Parkville Victoria Australia.,Royal Melbourne Hospital Clinical School Faculty of Medicine Dentistry and Health Sciences University of Melbourne Parkville Victoria Australia
| | - Jitendra Vohra
- Department of Cardiology Melbourne Health Parkville Victoria Australia.,Genetic Medicine Melbourne Health Parkville Victoria Australia.,Royal Melbourne Hospital Clinical School Faculty of Medicine Dentistry and Health Sciences University of Melbourne Parkville Victoria Australia
| | | | - David L Hare
- Department of Medicine Austin Health The University of Melbourne Heidelberg Victoria Australia.,Department of Cardiology Austin Health Heidelberg Victoria Australia
| | - Paul James
- Genetic Medicine Melbourne Health Parkville Victoria Australia
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16
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Johnston JR, Landim-Vieira M, Marques MA, de Oliveira GAP, Gonzalez-Martinez D, Moraes AH, He H, Iqbal A, Wilnai Y, Birk E, Zucker N, Silva JL, Chase PB, Pinto JR. The intrinsically disordered C terminus of troponin T binds to troponin C to modulate myocardial force generation. J Biol Chem 2019; 294:20054-20069. [PMID: 31748410 PMCID: PMC6937556 DOI: 10.1074/jbc.ra119.011177] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/13/2019] [Indexed: 12/15/2022] Open
Abstract
Aberrant regulation of myocardial force production represents an early biomechanical defect associated with sarcomeric cardiomyopathies, but the molecular mechanisms remain poorly defined. Here, we evaluated the pathogenicity of a previously unreported sarcomeric gene variant identified in a pediatric patient with sporadic dilated cardiomyopathy, and we determined a molecular mechanism. Trio whole-exome sequencing revealed a de novo missense variant in TNNC1 that encodes a p.I4M substitution in the N-terminal helix of cardiac troponin C (cTnC). Reconstitution of this human cTnC variant into permeabilized porcine cardiac muscle preparations significantly decreases the magnitude and rate of isometric force generation at physiological Ca2+-activation levels. Computational modeling suggests that this inhibitory effect can be explained by a decrease in the rates of cross-bridge attachment and detachment. For the first time, we show that cardiac troponin T (cTnT), in part through its intrinsically disordered C terminus, directly binds to WT cTnC, and we find that this cardiomyopathic variant displays tighter binding to cTnT. Steady-state fluorescence and NMR spectroscopy studies suggest that this variant propagates perturbations in cTnC structural dynamics to distal regions of the molecule. We propose that the intrinsically disordered C terminus of cTnT directly interacts with the regulatory N-domain of cTnC to allosterically modulate Ca2+ activation of force, perhaps by controlling the troponin I switching mechanism of striated muscle contraction. Alterations in cTnC-cTnT binding may compromise contractile performance and trigger pathological remodeling of the myocardium.
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Affiliation(s)
- Jamie R Johnston
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Mayra A Marques
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - David Gonzalez-Martinez
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Huan He
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
| | - Anwar Iqbal
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Yael Wilnai
- Department of Pediatrics, Dana-Dwek ChildrenγÇÖs Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel 6423906
| | - Einat Birk
- Department of Cardiology, Schneider ChildrenγÇÖs Medical Center, Tel Aviv University, Petah Tikva, Israel 4920235
| | - Nili Zucker
- Department of Cardiology, Schneider ChildrenγÇÖs Medical Center, Tel Aviv University, Petah Tikva, Israel 4920235
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - P Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - Jose Renato Pinto
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
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17
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Fatkin D, Huttner IG, Kovacic JC, Seidman J, Seidman CE. Precision Medicine in the Management of Dilated Cardiomyopathy. J Am Coll Cardiol 2019; 74:2921-2938. [DOI: 10.1016/j.jacc.2019.10.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/25/2019] [Accepted: 10/10/2019] [Indexed: 01/16/2023]
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18
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Hata Y, Hirono K, Yamaguchi Y, Ichida F, Oku Y, Nishida N. Minimal inflammatory foci of unknown etiology may be a tentative sign of early stage inherited cardiomyopathy. Mod Pathol 2019; 32:1281-1290. [PMID: 31024045 DOI: 10.1038/s41379-019-0274-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 01/18/2023]
Abstract
Although relatively uncommon, pathologists may encounter minimal inflammatory foci in the absence of typical structural heart disease; however, the clinicopathological significance of minimal inflammatory foci, including correlation with sudden unexpected death, is unexplored. From 1072 serial autopsy subjects, cases with unexplained minimal inflammatory foci, the extent of which was under 1% of the whole examined ventricle, were extracted to exclude cases with borderline/focal myocarditis resulting from local, systemic infection, or autoimmune mechanisms. Immunohistochemistry and genetic analysis targeting viral genomes and heart disease-related genes using next generation sequencing were performed. We detected 10 cases with unexplained minimal inflammatory foci (five males, five females, aged 15-68 years). The cause and/or manner of death were sudden unexpected death (6 cases, 60%), sudden unexpected death with epilepsy (1 case, 10%), drowning in a hot bath (1 case, 10%), and suicide (2 cases, 20%). In none of these cases was pathogen-derived DNA or RNA detected. In 8 of the 10 cases (80%), 17 possible pathogenic genetic variants causative for arrhythmogenic right ventricular cardiomyopathy or dilated cardiomyopathy; DSP was the most frequently involved gene (three cases with two different variants), followed by LAMA4 and MYBPC3 (two cases, two variants for each gene), LDB3 (two cases, one variant), and the remaining 10 variants occurred in seven cases (DSC2, RYR2, SOS1, SCN5A, SGCD, LPL, PKP2, MYH11, GATA6, and DSG2). All mutations were missense mutations. DSP_Lys1581Glu and DSC2_p.Thr275Met were classified according to American College of Medical Genetics and Genomics consensus statement guidelines as pathogenic or likely pathogenic for arrhythmogenic cardiomyopathy in three patients (30%). The remaining 15 variants were classified as potentially pathogenic variants. Unexplained minimal inflammatory foci may be an early sign of inherited cardiomyopathy, and such cases might already have arrhythmogenic potential that can lead to sudden unexpected death. Detection of minimal inflammatory foci by careful pathological examination may indicate the value of conducting comprehensive genetic analysis, even if significant structural abnormalities are not evident.
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Affiliation(s)
- Yukiko Hata
- Department of Legal Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Keiichi Hirono
- Department of Pediatrics, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yoshiaki Yamaguchi
- Second Department of Internal Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Fukiko Ichida
- Department of Pediatrics, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yuko Oku
- 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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19
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Kim YE, Ki CS, Jang MA. Challenges and Considerations in Sequence Variant Interpretation for Mendelian Disorders. Ann Lab Med 2019; 39:421-429. [PMID: 31037860 PMCID: PMC6502951 DOI: 10.3343/alm.2019.39.5.421] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/28/2018] [Accepted: 04/09/2019] [Indexed: 11/23/2022] Open
Abstract
In 2015, the American College of Medical Genetics and Genomics (ACMG), together with the Association for Molecular Pathology (AMP), published the latest guidelines for the interpretation of sequence variants, which have been widely adopted into clinical practice. Despite these standardized efforts, the degrees of subjectivity and uncertainty allowed by the guidelines can lead to inconsistent variant classification across clinical laboratories, making it difficult to assess the pathogenicity of identified variants. We describe the critical elements of variant interpretation processes and potential pitfalls through practical examples and provide updated information based on a review of recent literature. The variant classification we describe is meant to be applicable to sequence variants for Mendelian disorders, whether identified by single-gene tests, multi-gene panels, exome sequencing, or genome sequencing. Continuing efforts to improve the reproducibility and objectivity of sequence variant interpretation across individuals and laboratories are needed.
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Affiliation(s)
- Young Eun Kim
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
| | | | - Mi Ae Jang
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea.
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20
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Affiliation(s)
- Diane Fatkin
- From the Molecular Cardiology Division, Victor Chang Cardiac Research Institute (D.F., R.J.); Cardiology Department, St. Vincent's Hospital (D.F.); and Faculty of Medicine, University of New South Wales; Sydney, Australia (D.F.).
| | - Renee Johnson
- From the Molecular Cardiology Division, Victor Chang Cardiac Research Institute (D.F., R.J.); Cardiology Department, St. Vincent's Hospital (D.F.); and Faculty of Medicine, University of New South Wales; Sydney, Australia (D.F.)
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21
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García-Molina E, Sabater-Molina M, López-Cuenca D, Olmo MC, Pérez I, Muñoz Esparza C, Gimeno Blanes JR. A study of the pathogenicity of variants in familial heart disease. The value of cosegregation. Am J Transl Res 2019; 11:1724-1735. [PMID: 30972196 PMCID: PMC6456527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/16/2018] [Indexed: 06/09/2023]
Abstract
With the development of deep sequencing, a significant proportion of mutations already listed in studies have inconclusive pathogenicity. We aim to establish the proportion of cases in which familial studies are possible and cosegregation analysis is informative. We also compare cosegregation analysis with in silico software and a proposed pathogenicity score. 204 consecutive positive tests were reviewed. 4 different in silico software programs were used. Spaendonck-Zwarts' pathogenicity score was also calculated. A total of 73 of the missense variants could be classified by the score as being likely or definitively pathogenic. A high percentage of nonsense variants were found in desmosomal genes and missense variants in sarcomeric genes. 36.3% of the missense variants in our cohort classified as very likely or definitively pathogenic were novel. Cosegregation analysis was positive in 19.5% and could be discarded in 15.6%. There was a significant discrepancy between the in silico tools used in the setting of inherited heart disease. Multiparametric scoring systems which include cosegregation and functional studies seem to perform better than individual prediction software.
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Affiliation(s)
- Esperanza García-Molina
- Cardiogenetics Laboratory, Inherited Cardiac Disease Unit, IMIB University Hospital Virgen de la ArrixacaMurcia (Spain)
- Department of Genetic and Microbiology, Murcia UniversityMurcia, Spain
| | - María Sabater-Molina
- Cardiogenetics Laboratory, Inherited Cardiac Disease Unit, IMIB University Hospital Virgen de la ArrixacaMurcia (Spain)
- Department of Genetic and Microbiology, Murcia UniversityMurcia, Spain
| | - David López-Cuenca
- Inherited Cardiac Disease Unit, Department of Cardiology, University Hospital Virgen de la ArrixacaMurcia, Spain
| | - María C Olmo
- Inherited Cardiac Disease Unit, Department of Cardiology, University Hospital Virgen de la ArrixacaMurcia, Spain
| | - Inmaculada Pérez
- Cardiogenetics Laboratory, Inherited Cardiac Disease Unit, IMIB University Hospital Virgen de la ArrixacaMurcia (Spain)
| | | | - Juan R Gimeno Blanes
- Inherited Cardiac Disease Unit, Department of Cardiology, University Hospital Virgen de la ArrixacaMurcia, Spain
- Department of Internal Medicine, Murcia UniversityMurcia, Spain
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22
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Bondue A, Arbustini E, Bianco A, Ciccarelli M, Dawson D, De Rosa M, Hamdani N, Hilfiker-Kleiner D, Meder B, Leite-Moreira AF, Thum T, Tocchetti CG, Varricchi G, Van der Velden J, Walsh R, Heymans S. Complex roads from genotype to phenotype in dilated cardiomyopathy: scientific update from the Working Group of Myocardial Function of the European Society of Cardiology. Cardiovasc Res 2018; 114:1287-1303. [PMID: 29800419 PMCID: PMC6054212 DOI: 10.1093/cvr/cvy122] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/05/2018] [Accepted: 05/16/2018] [Indexed: 12/14/2022] Open
Abstract
Dilated cardiomyopathy (DCM) frequently affects relatively young, economically, and socially active adults, and is an important cause of heart failure and transplantation. DCM is a complex disease and its pathological architecture encounters many genetic determinants interacting with environmental factors. The old perspective that every pathogenic gene mutation would lead to a diseased heart, is now being replaced by the novel observation that the phenotype depends not only on the penetrance-malignancy of the mutated gene-but also on epigenetics, age, toxic factors, pregnancy, and a diversity of acquired diseases. This review discusses how gene mutations will result in mutation-specific molecular alterations in the heart including increased mitochondrial oxidation (sarcomeric gene e.g. TTN), decreased calcium sensitivity (sarcomeric genes), fibrosis (e.g. LMNA and TTN), or inflammation. Therefore, getting a complete picture of the DCM patient will include genomic data, molecular assessment by preference from cardiac samples, stratification according to co-morbidities, and phenotypic description. Those data will help to better guide the heart failure and anti-arrhythmic treatment, predict response to therapy, develop novel siRNA-based gene silencing for malignant gene mutations, or intervene with mutation-specific altered gene pathways in the heart.This article is part of the Mini Review Series from the Varenna 2017 meeting of the Working Group of Myocardial Function of the European Society of Cardiology.
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Affiliation(s)
- Antoine Bondue
- Department of Cardiology, CUB Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Eloisa Arbustini
- Centre for Inherited Cardiovascular Diseases, IRCCS Foundation, University Hospital Policlinico San Matteo, Pavia, Italy
| | - Anna Bianco
- Department of Translational Medical Sciences, Federico II University, Naples, Italy
- Department of Cardiology, Maastricht University Medical Center & CARIM, Maastricht University, Maastricht, The Netherlands
| | - Michele Ciccarelli
- School of Medicine, Surgery and Dentistry, University of Salerno, Salerno, Italy
| | - Dana Dawson
- School of Medicine and Dentistry, University of Aberdeen, Aberdeen, UK
| | - Matteo De Rosa
- School of Medicine, Surgery and Dentistry, University of Salerno, Salerno, Italy
| | - Nazha Hamdani
- Department of Systems Physiology, Ruhr University Bochum, Bochum, Germany
| | - Denise Hilfiker-Kleiner
- Molecular Cardiology, Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Benjamin Meder
- Department of Cardiology, Heidelberg University, Heidelberg, Germany
- Department of Genetics, Stanford University School of Medicine, Genome Technology Center, Palo Alto, CA, USA
| | - Adelino F Leite-Moreira
- Cardiovascular R&D Unit, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, Porto, Portugal
- Department of Cardiothoracic Surgery, Hospital of S. João, Porto, Portugal
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Carlo G Tocchetti
- Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Gilda Varricchi
- Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Jolanda Van der Velden
- Department of Physiology, VU University Medical Centre, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Roddy Walsh
- Cardiovascular Research Center, Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London, UK
| | - Stephane Heymans
- Department of Cardiology, Maastricht University Medical Center & CARIM, Maastricht University, Maastricht, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
- Department of Cardiovascular Sciences, Leuven University, Leuven, Belgium
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23
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A gene-centric strategy for identifying disease-causing rare variants in dilated cardiomyopathy. Genet Med 2018; 21:133-143. [PMID: 29892087 DOI: 10.1038/s41436-018-0036-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/27/2018] [Indexed: 12/19/2022] Open
Abstract
PURPOSE We evaluated strategies for identifying disease-causing variants in genetic testing for dilated cardiomyopathy (DCM). METHODS Cardiomyopathy gene panel testing was performed in 532 DCM patients and 527 healthy control subjects. Rare variants in 41 genes were stratified using variant-level and gene-level characteristics. RESULTS A majority of DCM cases and controls carried rare protein-altering cardiomyopathy gene variants. Variant-level characteristics alone had limited discriminative value. Differentiation between groups was substantially improved by addition of gene-level information that incorporated ranking of genes based on literature evidence for disease association. The odds of DCM were increased to nearly 9-fold for truncating variants or high-impact missense variants in the subset of 14 genes that had the strongest biological links to DCM (P <0.0001). For some of these genes, DCM-associated variants appeared to be clustered in key protein functional domains. Multiple rare variants were present in many family probands, however, there was generally only one "driver" pathogenic variant that cosegregated with disease. CONCLUSION Rare variants in cardiomyopathy genes can be effectively stratified by combining variant-level and gene-level information. Prioritization of genes based on their a priori likelihood of disease causation is a key factor in identifying clinically actionable variants in cardiac genetic testing.
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24
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Bakalakos A, Ritsatos K, Anastasakis A. Current perspectives on the diagnosis and management of dilated cardiomyopathy Beyond heart failure: a Cardiomyopathy Clinic Doctor's point of view. Hellenic J Cardiol 2018; 59:254-261. [PMID: 29807197 DOI: 10.1016/j.hjc.2018.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/12/2018] [Accepted: 05/18/2018] [Indexed: 01/01/2023] Open
Abstract
Left ventricular enlargement and dysfunction are fundamental components of dilated cardiomyopathy (DCM). DCM is a major cause of heart failure and cardiac transplantation. A wide variety of etiologies underlie acquired and familial DCM. Familial disease is reported in 20% to 35% of cases. A genetic substrate is recognized in at least 30% of familial cases. A recently proposed scheme defines DCM as a continuum of subclinical and clinical phenotypes. The evolution of classification systems permitted use of effective treatment strategies in disorders sharing the same structural and functional characteristics and common clinical expression. The major causes of death are progressive heart failure and sudden cardiac death secondary to ventricular arrhythmias or less commonly bradyarrhythmias. Remarkable progress has been made in survival owing to well-defined evidence-based therapies and appropriate guidelines for risk stratification and sudden cardiac death prevention measures. Neurohormonal antagonists and device therapy decreased all-cause mortality in adult patients with DCM. However, additional red flags in diagnosis have to be addressed in everyday practice, and cardiologists have to be aware of the subsequent effect on risk stratification and treatment plan. Genetic substrate cannot be modified, but the presence of a peculiar type of gene mutation modifies thresholds for implantable cardioverter defibrillator (ICD) implantation. DCM is part of the spectrum of heart failure which is a syndrome with certain morphological and functional characteristics. Although significant progress has been achieved in the management of patients with DCM, it seems that the future treatments of this entity will be related to the specific pathological substrate.
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MESH Headings
- Arrhythmias, Cardiac/epidemiology
- Arrhythmias, Cardiac/etiology
- Arrhythmias, Cardiac/prevention & control
- Cardiomyopathy, Dilated/diagnosis
- Cardiomyopathy, Dilated/drug therapy
- Cardiomyopathy, Dilated/epidemiology
- Cardiomyopathy, Dilated/genetics
- Connectin/metabolism
- Cytoskeleton/metabolism
- Death, Sudden, Cardiac/epidemiology
- Death, Sudden, Cardiac/prevention & control
- Defibrillators, Implantable/standards
- Female
- Genetic Testing/methods
- Heart Failure/complications
- Humans
- Male
- Mutation/genetics
- Prevalence
- Risk Assessment
- Sarcomeres/metabolism
- Troponin T/metabolism
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Affiliation(s)
- Athanasios Bakalakos
- Unit of Inherited and Rare Cardiovascular Diseases, Onassis Cardiac Surgery Centre, 356 Sygrou Avenue 17674, Kallithea Athens, Greece.
| | - Konstantinos Ritsatos
- Unit of Inherited and Rare Cardiovascular Diseases, Onassis Cardiac Surgery Centre, 356 Sygrou Avenue 17674, Kallithea Athens, Greece
| | - Aris Anastasakis
- Unit of Inherited and Rare Cardiovascular Diseases, Onassis Cardiac Surgery Centre, 356 Sygrou Avenue 17674, Kallithea Athens, Greece
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25
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Genome-wide association study of cardiotoxicity in the NCCTG N9831 (Alliance) adjuvant trastuzumab trial. Pharmacogenet Genomics 2018; 27:378-385. [PMID: 28763429 DOI: 10.1097/fpc.0000000000000302] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVES The major clinical side effect of the ERBB2-targeted breast cancer therapy, trastuzumab, is a decline in the left ventricular ejection fraction (LVEF). Improved markers are needed to better identify patients susceptible to cardiotoxicity. METHODS The NCCTG N9831 trial compared adjuvant doxorubicin and cyclophosphamide followed by either weekly paclitaxel (arm A); paclitaxel then trastuzumab (arm B); or concurrent paclitaxel and trastuzumab (arm C) in patients with HER2-positive breast cancer. A genome-wide association study was performed on all patients with available DNA (N=1446). We used linear regression to identify single nucleotide polymorphisms (SNPs) associated with decline in LVEF, adjusting for age, baseline LVEF, antihypertensive medications, and the first two principle components. RESULTS In total, 618 863 SNPs passed quality control and DNA from 1191 patients passed genotyping quality control and were identified as Whites of non-Hispanic origin. SNPs at six loci were associated with a decline in LVEF (P=7.73×10 to 8.93×10), LDB2, BRINP1, chr6 intergenic, RAB22A, TRPC6, and LINC01060, in patients who received chemotherapy plus trastuzumab (arms BC, N=800). None of these loci were significant in patients who received chemotherapy only (arm A, N=391) and did not increase in significance in the combined analysis of all patients. We did not observe association, P<0.05, with SNPs previously associated with trastuzumab-induced cardiotoxicity at ERBB2, I655V, and P1170A. We replicated association, P<0.05, with SNPs previously associated with anthracycline-induced cardiotoxicity at CBR3 and ABCB1. CONCLUSION Our study identified six putative novel cardiotoxicity loci in patients treated with combination chemotherapy and trastuzumab that require further investigation and confirmed known associations of anthracycline-induced cardiotoxicity.
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26
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Zhou P, He N, Zhang JW, Lin ZJ, Wang J, Yan LM, Meng H, Tang B, Li BM, Liu XR, Shi YW, Zhai QX, Yi YH, Liao WP. Novel mutations and phenotypes of epilepsy-associated genes in epileptic encephalopathies. GENES BRAIN AND BEHAVIOR 2018; 17:e12456. [PMID: 29314583 DOI: 10.1111/gbb.12456] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/13/2017] [Accepted: 12/30/2017] [Indexed: 12/30/2022]
Abstract
Epileptic encephalopathies are severe epilepsy disorders with strong genetic bases. We performed targeted next-generation sequencing (NGS) in 70 patients with epileptic encephalopathies. The likely pathogenicity of variants in candidate genes was evaluated by American College of Medical Genetics and Genomics (ACMG) scoring taken together with the accepted clinical presentation. Thirty-three candidate variants were detected after population filtration and computational prediction. According to ACMG, 21 candidate variants, including 18 de novo variants, were assessed to be pathogenic/likely pathogenic with clinical concordance. Twelve variants were initially assessed as uncertain significance by ACMG, among which 3 were considered causative and 3 others were considered possibly causative after analysis of clinical concordance. In total, 24 variants were identified as putatively causative, among which 19 were novel findings. SCN1A mutations were identified in 50% of patients with Dravet syndrome. TSC1/TSC2 mutations were detected in 66.7% of patients with tuberous sclerosis. STXBP1 mutations were the main findings in patients with West syndrome. Mutations in SCN2A, KCNT1, KCNQ2 and CLCN4 were identified in patients with epileptic infantile with migrating focal seizures; among them, KCNQ2 and CLCN4 were first identified as potential causative genes. Only one CHD2 mutation was detected in patients with Lennox-Gastaut syndrome. This study highlighted the utility of targeted NGS in genetic diagnoses of epileptic encephalopathies and a comprehensive evaluation of the pathogenicity of variants based on ACMG scoring and assessment of clinical concordance. Epileptic encephalopathies differ in genetic causes, and the genotype-phenotype correlations would provide insights into the underlying pathogenic mechanisms.
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Affiliation(s)
- P Zhou
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - N He
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - J-W Zhang
- Department of Pediatrics, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Z-J Lin
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - J Wang
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - L-M Yan
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - H Meng
- Department of Neurology, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Clinical Neuroscience Institute, Jinan University, Guangzhou, China
| | - B Tang
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - B-M Li
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - X-R Liu
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Y-W Shi
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Q-X Zhai
- Department of Pediatrics, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Y-H Yi
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - W-P Liao
- Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Institute of Neuroscience, Guangzhou, China.,Key Laboratory of Neurogenetics, Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
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27
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Donahue JK. Sequencing of uncertain significance. J Cardiovasc Electrophysiol 2017; 29:105-106. [PMID: 29120076 DOI: 10.1111/jce.13384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/06/2017] [Indexed: 11/30/2022]
Affiliation(s)
- J Kevin Donahue
- Division of Cardiology, University of Massachusetts Medical School, Worcester, MA, USA
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28
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Position Statement on the Diagnosis and Management of Familial Dilated Cardiomyopathy. Heart Lung Circ 2017; 26:1127-1132. [DOI: 10.1016/j.hlc.2017.04.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/14/2017] [Indexed: 11/24/2022]
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29
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Goldfeder RL, Wall DP, Khoury MJ, Ioannidis JPA, Ashley EA. Human Genome Sequencing at the Population Scale: A Primer on High-Throughput DNA Sequencing and Analysis. Am J Epidemiol 2017; 186:1000-1009. [PMID: 29040395 DOI: 10.1093/aje/kww224] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/02/2016] [Indexed: 12/30/2022] Open
Abstract
Most human diseases have underlying genetic causes. To better understand the impact of genes on disease and its implications for medicine and public health, researchers have pursued methods for determining the sequences of individual genes, then all genes, and now complete human genomes. Massively parallel high-throughput sequencing technology, where DNA is sheared into smaller pieces, sequenced, and then computationally reordered and analyzed, enables fast and affordable sequencing of full human genomes. As the price of sequencing continues to decline, more and more individuals are having their genomes sequenced. This may facilitate better population-level disease subtyping and characterization, as well as individual-level diagnosis and personalized treatment and prevention plans. In this review, we describe several massively parallel high-throughput DNA sequencing technologies and their associated strengths, limitations, and error modes, with a focus on applications in epidemiologic research and precision medicine. We detail the methods used to computationally process and interpret sequence data to inform medical or preventative action.
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30
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Simmons MA, Brueckner M. The genetics of congenital heart disease… understanding and improving long-term outcomes in congenital heart disease: a review for the general cardiologist and primary care physician. Curr Opin Pediatr 2017; 29:520-528. [PMID: 28872494 PMCID: PMC5665656 DOI: 10.1097/mop.0000000000000538] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW This review has two purposes: to provide an updated review of the genetic causes of congenital heart disease (CHD) and the clinical implications of these genetic mutations, and to provide a clinical algorithm for clinicians considering a genetics evaluation of a CHD patient. RECENT FINDINGS A large portion of congenital heart disease is thought to have a significant genetic contribution, and at this time a genetic cause can be identified in approximately 35% of patients. Through the advances made possible by next generation sequencing, many of the comorbidities that are frequently seen in patients with genetic congenital heart disease patients can be attributed to the genetic mutation that caused the congenital heart disease. These comorbidities are both cardiac and noncardiac and include: neurodevelopmental disability, pulmonary disease, heart failure, renal dysfunction, arrhythmia and an increased risk of malignancy. Identification of the genetic cause of congenital heart disease helps reduce patient morbidity and mortality by improving preventive and early intervention therapies to address these comorbidities. SUMMARY Through an understanding of the clinical implications of the genetic underpinning of congenital heart disease, clinicians can provide care tailored to an individual patient and continue to improve the outcomes of congenital heart disease patients.
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Affiliation(s)
- M. Abigail Simmons
- Department of Pediatrics (Cardiology), Yale University School of Medicine
| | - Martina Brueckner
- Department of Pediatrics (Cardiology), Yale University School of Medicine
- Department of Genetics, Yale University School of Medicine
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31
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Kesselheim A, Ashton E, Bockenhauer D. Potential and pitfalls in the genetic diagnosis of kidney diseases. Clin Kidney J 2017; 10:581-585. [PMID: 28980668 PMCID: PMC5622903 DOI: 10.1093/ckj/sfx075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing has dramatically decreased the cost of gene sequencing, facilitating the simultaneous analysis of multiple genes at the same time; obtaining a genetic result for an individual patient has become much easier. The article by Ars and Torra in this issue of the Clinical Kidney Journal provides examples of the ever-increasing ability to understand a given patient's disease on the molecular level, so that in some cases not only the causative variants in a disease gene are identified, but also potential modifiers in other genes. Yet, with increased sequencing, a large number of variants are discovered that are difficult to interpret. These so-called 'variants of uncertain significance' raise important questions: when and how can pathogenicity be clearly attributed? This is of critical importance, as there are potentially serious consequences attached: decisions about various forms of treatment and even about life and death, such as termination of pregnancy, may hinge on the answer to these questions. Geneticists, thus, need to use the utmost care in the interpretation of identified variants and clinicians must be aware of this problem. We here discuss the potential of genetics to facilitate personalized treatment, but also the pitfalls and how to deal with them.
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Affiliation(s)
- Anne Kesselheim
- Centre for Nephrology, University College London, London, UK
| | - Emma Ashton
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- North East Thames Regional Genetics Service, Molecular Genetics, London, UK
| | - Detlef Bockenhauer
- Centre for Nephrology, University College London, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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32
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Araco M, Merlo M, Carr-White G, Sinagra G. Genetic bases of dilated cardiomyopathy. J Cardiovasc Med (Hagerstown) 2017; 18:123-130. [PMID: 27661610 DOI: 10.2459/jcm.0000000000000432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cardiomyopathies represent a wide and heterogeneous group of diseases wherein a genetic cause has been consistently identified.Dilated cardiomyopathy (DCM) is characterized by ventricular dilation and progressive systolic dysfunction, and it is the most common form of cardiomyopathy.Causative genetic mutations have been identified in more than 40 genes encoding proteins belonging to different cellular structures and pathways.A great diversity of pathways has been implied in the pathogenesis of DCM, depending on the affected genes and on the dislodged intracellular structures or mechanisms.This review describes the major genes and focus on the pathophysiologic mechanisms of DCM, with a special consideration of the most recent discoveries in the field.
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Affiliation(s)
- Marco Araco
- aDepartment of Cardiology, Guys and St Thomas NHS Trust, London, United Kingdom bDivision of Cardiology, Cardiovascular Department, Ospedali Riuniti and University of Trieste, Trieste, Italy
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33
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Gradishar W, Johnson K, Brown K, Mundt E, Manley S. Clinical Variant Classification: A Comparison of Public Databases and a Commercial Testing Laboratory. Oncologist 2017; 22:797-803. [PMID: 28408614 PMCID: PMC5507641 DOI: 10.1634/theoncologist.2016-0431] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/05/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND There is a growing move to consult public databases following receipt of a genetic test result from a clinical laboratory; however, the well-documented limitations of these databases call into question how often clinicians will encounter discordant variant classifications that may introduce uncertainty into patient management. Here, we evaluate discordance in BRCA1 and BRCA2 variant classifications between a single commercial testing laboratory and a public database commonly consulted in clinical practice. MATERIALS AND METHODS BRCA1 and BRCA2 variant classifications were obtained from ClinVar and compared with the classifications from a reference laboratory. Full concordance and discordance were determined for variants whose ClinVar entries were of the same pathogenicity (pathogenic, benign, or uncertain). Variants with conflicting ClinVar classifications were considered partially concordant if ≥1 of the listed classifications agreed with the reference laboratory classification. RESULTS Four thousand two hundred and fifty unique BRCA1 and BRCA2 variants were available for analysis. Overall, 73.2% of classifications were fully concordant and 12.3% were partially concordant. The remaining 14.5% of variants had discordant classifications, most of which had a definitive classification (pathogenic or benign) from the reference laboratory compared with an uncertain classification in ClinVar (14.0%). CONCLUSION Here, we show that discrepant classifications between a public database and single reference laboratory potentially account for 26.7% of variants in BRCA1 and BRCA2. The time and expertise required of clinicians to research these discordant classifications call into question the practicality of checking all test results against a database and suggest that discordant classifications should be interpreted with these limitations in mind. IMPLICATIONS FOR PRACTICE With the increasing use of clinical genetic testing for hereditary cancer risk, accurate variant classification is vital to ensuring appropriate medical management. There is a growing move to consult public databases following receipt of a genetic test result from a clinical laboratory; however, we show that up to 26.7% of variants in BRCA1 and BRCA2 have discordant classifications between ClinVar and a reference laboratory. The findings presented in this paper serve as a note of caution regarding the utility of database consultation.
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Affiliation(s)
- William Gradishar
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
| | - KariAnne Johnson
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
| | - Krystal Brown
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
| | - Erin Mundt
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
| | - Susan Manley
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
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34
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Burke MA, Cook SA, Seidman JG, Seidman CE. Clinical and Mechanistic Insights Into the Genetics of Cardiomyopathy. J Am Coll Cardiol 2017; 68:2871-2886. [PMID: 28007147 DOI: 10.1016/j.jacc.2016.08.079] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 08/01/2016] [Accepted: 08/02/2016] [Indexed: 12/19/2022]
Abstract
Over the last quarter-century, there has been tremendous progress in genetics research that has defined molecular causes for cardiomyopathies. More than a thousand mutations have been identified in many genes with varying ontologies, therein indicating the diverse molecules and pathways that cause hypertrophic, dilated, restrictive, and arrhythmogenic cardiomyopathies. Translation of this research to the clinic via genetic testing can precisely group affected patients according to molecular etiology, and identify individuals without evidence of disease who are at high risk for developing cardiomyopathy. These advances provide insights into the earliest manifestations of cardiomyopathy and help to define the molecular pathophysiological basis for cardiac remodeling. Although these efforts remain incomplete, new genomic technologies and analytic strategies provide unparalleled opportunities to fully explore the genetic architecture of cardiomyopathies. Such data hold the promise that mutation-specific pathophysiology will uncover novel therapeutic targets, and herald the beginning of precision therapy for cardiomyopathy patients.
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Affiliation(s)
- Michael A Burke
- Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia; Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Stuart A Cook
- National Heart & Lung Institute, Imperial College London, London, United Kingdom; National Heart Centre Singapore, Singapore; Duke-National University of Singapore, Singapore
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Howard Hughes Medical Institute, Chevy Chase, Maryland.
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Szabadosova V, Boronova I, Ferenc P, Tothova I, Bernasovska J, Zigova M, Kmec J, Bernasovsky I. Analysis of selected genes associated with cardiomyopathy by next-generation sequencing. J Clin Lab Anal 2017; 32. [PMID: 28594148 DOI: 10.1002/jcla.22254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/14/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND As the leading cause of congestive heart failure, cardiomyopathy represents a heterogenous group of heart muscle disorders. Despite considerable progress being made in the genetic diagnosis of cardiomyopathy by detection of the mutations in the most prevalent cardiomyopathy genes, the cause remains unsolved in many patients. High-throughput mutation screening in the disease genes for cardiomyopathy is now possible because of using target enrichment followed by next-generation sequencing. The aim of the study was to analyze a panel of genes associated with dilated or hypertrophic cardiomyopathy based on previously published results in order to identify the subjects at risk. METHODS The method of next-generation sequencing by IlluminaHiSeq 2500 platform was used to detect sequence variants in 16 individuals diagnosed with dilated or hypertrophic cardiomyopathy. Detected variants were filtered and the functional impact of amino acid changes was predicted by computational programs. RESULTS DNA samples of the 16 patients were analyzed by whole exome sequencing. We identified six nonsynonymous variants that were shown to be pathogenic in all used prediction softwares: rs3744998 (EPG5), rs11551768 (MGME1), rs148374985 (MURC), rs78461695 (PLEC), rs17158558 (RET) and rs2295190 (SYNE1). Two of the analyzed sequence variants had minor allele frequency (MAF)<0.01: rs148374985 (MURC), rs34580776 (MYBPC3). CONCLUSION Our data support the potential role of the detected variants in pathogenesis of dilated or hypertrophic cardiomyopathy; however, the possibility that these variants might not be true disease-causing variants but are susceptibility alleles that require additional mutations or injury to cause the clinical phenotype of disease must be considered.
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Affiliation(s)
- Viktoria Szabadosova
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Iveta Boronova
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Peter Ferenc
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Iveta Tothova
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Jarmila Bernasovska
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Michaela Zigova
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Presov, Slovakia
| | - Jan Kmec
- Cardiocentre, Faculty Hospital of J.A. Reiman, Presov, Slovakia
| | - Ivan Bernasovsky
- Center of Languages and Cultures of National Minorities, University of Presov, Presov, Slovakia
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Serie DJ, Crook JE, Necela BM, Axenfeld BC, Dockter TJ, Colon-Otero G, Perez EA, Thompson EA, Norton N. Breast Cancer Clinical Trial of Chemotherapy and Trastuzumab: Potential Tool to Identify Cardiac Modifying Variants of Dilated Cardiomyopathy. J Cardiovasc Dev Dis 2017; 4:jcdd4020006. [PMID: 29367538 PMCID: PMC5715703 DOI: 10.3390/jcdd4020006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
Doxorubicin and the ERBB2 targeted therapy, trastuzumab, are routinely used in the treatment of HER2+ breast cancer. In mouse models, doxorubicin is known to cause cardiomyopathy and conditional cardiac knock out of Erbb2 results in dilated cardiomyopathy and increased sensitivity to doxorubicin-induced cell death. In humans, these drugs also result in cardiac phenotypes, but severity and reversibility is highly variable. We examined the association of decline in left ventricular ejection fraction (LVEF) at 15,204 single nucleotide polymorphisms (SNPs) spanning 72 cardiomyopathy genes, in 800 breast cancer patients who received doxorubicin and trastuzumab. For 7033 common SNPs (minor allele frequency (MAF) > 0.01) we performed single marker linear regression. For all SNPs, we performed gene-based testing with SNP-set (Sequence) Kernel Association Tests: SKAT, SKAT-O and SKAT-common/rare under rare variant non-burden; rare variant optimized burden and non-burden tests; and a combination of rare and common variants respectively. Single marker analyses identified seven missense variants in OBSCN (p = 0.0045-0.0009, MAF = 0.18-0.50) and two in TTN (both p = 0.04, MAF = 0.22). Gene-based rare variant analyses, SKAT and SKAT-O, performed very similarly (ILK, TCAP, DSC2, VCL, FXN, DSP and KCNQ1, p = 0.042-0.006). Gene-based tests of rare/common variants were significant at the nominal 5% level for OBSCN as well as TCAP, DSC2, VCL, NEXN, KCNJ2 and DMD (p = 0.044-0.008). Our results suggest that rare and common variants in OBSCN, as well as in other genes, could have modifying effects in cardiomyopathy.
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Affiliation(s)
- Daniel J Serie
- Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA.
| | - Julia E Crook
- Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA.
| | - Brian M Necela
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA.
| | - Bianca C Axenfeld
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA.
| | - Travis J Dockter
- Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
| | | | - Edith A Perez
- Hematology/Oncology, Mayo Clinic, Jacksonville, FL 32224, USA.
| | - E Aubrey Thompson
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA.
| | - Nadine Norton
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA.
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Dal Ferro M, Stolfo D, Altinier A, Gigli M, Perrieri M, Ramani F, Barbati G, Pivetta A, Brun F, Monserrat L, Giacca M, Mestroni L, Merlo M, Sinagra G. Association between mutation status and left ventricular reverse remodelling in dilated cardiomyopathy. Heart 2017; 103:1704-1710. [DOI: 10.1136/heartjnl-2016-311017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/10/2017] [Accepted: 03/16/2017] [Indexed: 01/22/2023] Open
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Nguyen AL, Marin D, Zhou A, Gentilello AS, Smoak EM, Cao Z, Fedick A, Wang Y, Taylor D, Scott RT, Xing J, Treff N, Schindler K. Identification and characterization of Aurora kinase B and C variants associated with maternal aneuploidy. Mol Hum Reprod 2017; 23:406-416. [PMID: 28369513 PMCID: PMC9915067 DOI: 10.1093/molehr/gax018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 03/20/2017] [Indexed: 12/16/2022] Open
Abstract
STUDY QUESTION Are single nucleotide variants (SNVs) in Aurora kinases B and C (AURKB, AURKC) associated with risk of aneuploid conception? SUMMARY ANSWER Two SNVs were found in patients with extreme aneuploid concepti rates with respect to their age; one variant, AURKC p.I79V, is benign, while another, AURKB p.L39P, is a potential gain-of-function mutant with increased efficiency in promoting chromosome alignment. WHAT IS KNOWN ALREADY Maternal age does not always predict aneuploidy risk, and rare gene variants can be drivers of disease. The AURKB and AURKC regulate chromosome segregation, and are associated with reproductive impairments in mouse and human. STUDY DESIGN, SIZE, DURATION An extreme phenotype sample selection scheme was performed for variant discovery. Ninety-six DNA samples were from young patients with higher than average embryonic aneuploidy rates and an additional 96 DNA samples were from older patients with lower than average aneuploidy rates. PARTICIPANTS/MATERIALS, SETTING, METHODS Using the192 DNA samples, the coding regions of AURKB and AURKC were sequenced using next generation sequencing. To assess biological significance, we expressed complementary RNA encoding the human variants in mouse oocytes. Assays such as determining subcellular localization and assessing catalytic activity were performed to determine alterations in protein function during meiosis. MAIN RESULTS AND THE ROLE OF CHANCE Ten SNVs were identified using three independent variant-calling methods. Two of the SNVs (AURKB p.L39P and AURKC p.I79V) were non-synonymous and identified by at least two variant-identification methods. The variant encoding AURKC p.I79V, identified in a young woman with a higher than average rate of aneuploid embryos, showed wild-type localization pattern and catalytic activity. On the other hand, the variant encoding AURKB p.L39P, identified in an older woman with lower than average rates of aneuploid embryos, increased the protein's ability to regulate alignment of chromosomes at the metaphase plate. These experiments were repeated three independent times using 2-3 mice for each trial. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION Biological significance of the human variants was assessed in an in vitro mouse oocyte model where the variants are over-expressed. Therefore, the human protein may not function identically to the mouse homolog, or the same in mouse oocytes as in human oocytes. Furthermore, supraphysiological expression levels may not accurately reflect endogenous activity. Moreover, the evaluated variants were identified in one patient each, and no trial linking the SNV to pregnancy outcomes was conducted. Finally, the patient aneuploidy rates were established by performing comprehensive chromosome screening in blastocysts, and because of the link between female gamete aneuploidy giving rise to aneuploid embryos, we evaluate the role of the variants in Meiosis I. However, it is possible that the chromosome segregation mistake arose during Meiosis II or in mitosis in the preimplantation embryo. Their implications in human female meiosis and aneuploidy risk remain to be determined. WIDER IMPLICATIONS OF THE FINDINGS The data provide evidence that gene variants exist in reproductively younger or advanced aged women that are predictive of the risk of producing aneuploid concepti in humans. Furthermore, a single amino acid in the N-terminus of AURKB is a gain-of-function mutant that could be protective of euploidy. STUDY FUNDING/COMPETING INTERESTS This work was supported by a Research Grant from the American Society of Reproductive Medicine and support from the Charles and Johanna Busch Memorial Fund at Rutgers, the State University of NJ to K.S. and the Foundation for Embryonic Competence, Inc to N.T. The authors declare no conflicts of interest.
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Affiliation(s)
| | | | - Anbo Zhou
- Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Rd. Piscataway, NJ 08854, USA
| | - Amanda S. Gentilello
- Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Rd. Piscataway, NJ 08854, USA
| | - Evan M. Smoak
- Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Rd. Piscataway, NJ 08854, USA
| | - Zubing Cao
- Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Rd. Piscataway, NJ 08854, USA
| | - Anastasia Fedick
- Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Rd. Piscataway, NJ 08854, USA,Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, NJ 07920, USA
| | - Yujue Wang
- Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Rd. Piscataway, NJ 08854, USA,Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, NJ 07920, USA
| | - Deanne Taylor
- Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, NJ 07920, USA,
Present address: Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Richard T. Scott
- Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, NJ 07920, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Rd. Piscataway, NJ 08854, USA
| | - Nathan Treff
- Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, NJ 07920, USA
| | - Karen Schindler
- Correspondence address. Department of Genetics, Rutgers, The State University of New Jersey, NJ, USA. E-mail:
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GeneImp: Fast Imputation to Large Reference Panels Using Genotype Likelihoods from Ultralow Coverage Sequencing. Genetics 2017; 206:91-104. [PMID: 28348060 DOI: 10.1534/genetics.117.200063] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/20/2017] [Indexed: 01/14/2023] Open
Abstract
We address the task of genotype imputation to a dense reference panel given genotype likelihoods computed from ultralow coverage sequencing as inputs. In this setting, the data have a high-level of missingness or uncertainty, and are thus more amenable to a probabilistic representation. Most existing imputation algorithms are not well suited for this situation, as they rely on prephasing for computational efficiency, and, without definite genotype calls, the prephasing task becomes computationally expensive. We describe GeneImp, a program for genotype imputation that does not require prephasing and is computationally tractable for whole-genome imputation. GeneImp does not explicitly model recombination, instead it capitalizes on the existence of large reference panels-comprising thousands of reference haplotypes-and assumes that the reference haplotypes can adequately represent the target haplotypes over short regions unaltered. We validate GeneImp based on data from ultralow coverage sequencing (0.5×), and compare its performance to the most recent version of BEAGLE that can perform this task. We show that GeneImp achieves imputation quality very close to that of BEAGLE, using one to two orders of magnitude less time, without an increase in memory complexity. Therefore, GeneImp is the first practical choice for whole-genome imputation to a dense reference panel when prephasing cannot be applied, for instance, in datasets produced via ultralow coverage sequencing. A related future application for GeneImp is whole-genome imputation based on the off-target reads from deep whole-exome sequencing.
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Kobayashi Y, Yang S, Nykamp K, Garcia J, Lincoln SE, Topper SE. Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Genome Med 2017; 9:13. [PMID: 28166811 PMCID: PMC5295186 DOI: 10.1186/s13073-017-0403-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/13/2017] [Indexed: 12/25/2022] Open
Abstract
Background The frequency of a variant in the general population is a key criterion used in the clinical interpretation of sequence variants. With certain exceptions, such as founder mutations, the rarity of a variant is a prerequisite for pathogenicity. However, defining the threshold at which a variant should be considered “too common” is challenging and therefore diagnostic laboratories have typically set conservative allele frequency thresholds. Methods Recent publications of large population sequencing data, such as the Exome Aggregation Consortium (ExAC) database, provide an opportunity to characterize with accuracy and precision the frequency distributions of very rare disease-causing alleles. Allele frequencies of pathogenic variants in ClinVar, as well as variants expected to be pathogenic through the nonsense-mediated decay (NMD) pathway, were analyzed to study the burden of pathogenic variants in 79 genes of clinical importance. Results Of 1364 BRCA1 and BRCA2 variants that are well characterized as pathogenic or that are expected to lead to NMD, 1350 variants had an allele frequency of less than 0.0025%. The remaining 14 variants were previously published founder mutations. Importantly, we observed no difference in the distributions of pathogenic variants expected to be lead to NMD compared to those that are not. Therefore, we expanded the analysis to examine the distributions of NMD expected variants in 77 additional genes. These 77 genes were selected to represent a broad set of clinical areas, modes of inheritance, and penetrance. Among these variants, most (97.3%) had an allele frequency of less than 0.01%. Furthermore, pathogenic variants with allele frequencies greater than 0.01% were well characterized in publications and included many founder mutations. Conclusions The observations made in this study suggest that, with certain caveats, a very low allele frequency threshold can be adopted to more accurately interpret sequence variants. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0403-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuya Kobayashi
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA.
| | - Shan Yang
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| | - Keith Nykamp
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| | - John Garcia
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| | | | - Scott E Topper
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
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Dalin MG, Engström PG, Ivarsson EG, Unneberg P, Light S, Schaufelberger M, Gilljam T, Andersson B, Bergo MO. Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy. Int J Cardiol 2017; 228:742-748. [DOI: 10.1016/j.ijcard.2016.11.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/05/2016] [Indexed: 01/13/2023]
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Hoskinson DC, Dubuc AM, Mason-Suares H. The current state of clinical interpretation of sequence variants. Curr Opin Genet Dev 2017; 42:33-39. [PMID: 28157586 DOI: 10.1016/j.gde.2017.01.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/20/2016] [Accepted: 01/09/2017] [Indexed: 01/19/2023]
Abstract
Accurate and consistent variant classification is required for Precision Medicine. But clinical variant classification remains in its infancy. While recent guidelines put forth jointly by the American College of Medical Genetics and Genomics (ACMG) and Association of Molecular Pathology (AMP) for the classification of Mendelian variants has advanced the field, the degree of subjectivity allowed by these guidelines can still lead to inconsistent classification across clinical molecular genetic laboratories. In addition, there are currently no such guidelines for somatic cancer variants, only published institutional practices. Additional variant classification guidelines, including disease- or gene-specific criteria, along with inter-laboratory data sharing is critical for accurate and consistent variant interpretation.
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Affiliation(s)
- Derick C Hoskinson
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, 65 Landsdowne Str., Cambridge, MA 02115 USA
| | - Adrian M Dubuc
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, 75 Francis Str., Boston, MA 02115 USA
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, 65 Landsdowne Str., Cambridge, MA 02115 USA; Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, 75 Francis Str., Boston, MA 02115 USA.
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Shim H, Kim JH, Kim CY, Hwang S, Kim H, Yang S, Lee JE, Lee I. Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource. Nucleic Acids Res 2016; 44:9611-9623. [PMID: 27903883 PMCID: PMC5175370 DOI: 10.1093/nar/gkw897] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/23/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022] Open
Abstract
Whole exome sequencing (WES) accelerates disease gene discovery using rare genetic variants, but further statistical and functional evidence is required to avoid false-discovery. To complement variant-driven disease gene discovery, here we present function-driven disease gene discovery in zebrafish (Danio rerio), a promising human disease model owing to its high anatomical and genomic similarity to humans. To facilitate zebrafish-based function-driven disease gene discovery, we developed a genome-scale co-functional network of zebrafish genes, DanioNet (www.inetbio.org/danionet), which was constructed by Bayesian integration of genomics big data. Rigorous statistical assessment confirmed the high prediction capacity of DanioNet for a wide variety of human diseases. To demonstrate the feasibility of the function-driven disease gene discovery using DanioNet, we predicted genes for ciliopathies and performed experimental validation for eight candidate genes. We also validated the existence of heterozygous rare variants in the candidate genes of individuals with ciliopathies yet not in controls derived from the UK10K consortium, suggesting that these variants are potentially involved in enhancing the risk of ciliopathies. These results showed that an integrated genomics big data for a model animal of diseases can expand our opportunity for harnessing WES data in disease gene discovery.
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Affiliation(s)
- Hongseok Shim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Ji Hyun Kim
- Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Chan Yeong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sohyun Hwang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hyojin Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sunmo Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Ji Eun Lee
- Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea .,Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
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Nouhravesh N, Ahlberg G, Ghouse J, Andreasen C, Svendsen JH, Haunsø S, Bundgaard H, Weeke PE, Olesen MS. Analyses of more than 60,000 exomes questions the role of numerous genes previously associated with dilated cardiomyopathy. Mol Genet Genomic Med 2016; 4:617-623. [PMID: 27896284 PMCID: PMC5118206 DOI: 10.1002/mgg3.245] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/05/2016] [Accepted: 08/09/2016] [Indexed: 12/24/2022] Open
Abstract
Background Hundreds of genetic variants have been described as disease causing in dilated cardiomyopathy (DCM). Some of these associations are now being questioned. We aimed to identify the prevalence of previously DCM associated variants in the Exome Aggregation Consortium (ExAC), in order to identify potentially false‐positive DCM variants. Methods Variants listed as DCM disease‐causing variants in the Human Gene Mutation Database were extracted from ExAC. Pathogenicity predictions for these variants were mined from dbNSFP v 2.9 database. Results Of the 473 DCM variants listed in HGMD, 148 (31%) were found in ExAC. The expected number of individuals with DCM in ExAC is 25 based on the prevalence in the general population. Yet, 35 variants were found in more than 25 individuals. In 13 genes, we identified all variants previously associated with DCM; four genes contained variants above our estimated cut‐off. Prediction tools found ExAC variants to be significantly more tolerated when compared to variants not found in ExAC (P = 0.004). Conclusion In ExAC, we identified a higher genotype prevalence of variants considered disease‐causing than expected. More importantly, we found 13 genes in which all variants previously associated with DCM were identified in ExAC, questioning the association of these genes with the monogenic form of DCM.
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Affiliation(s)
- Nina Nouhravesh
- Laboratory of Molecular Cardiology Department of Cardiology The Heart Centre University Hospital of Copenhagen Rigshospitalet Copenhagen Denmark
| | - Gustav Ahlberg
- Laboratory of Molecular Cardiology Department of Cardiology The Heart Centre University Hospital of Copenhagen Rigshospitalet Copenhagen Denmark
| | - Jonas Ghouse
- Laboratory of Molecular Cardiology Department of Cardiology The Heart Centre University Hospital of Copenhagen Rigshospitalet Copenhagen Denmark
| | - Charlotte Andreasen
- Laboratory of Molecular Cardiology Department of Cardiology The Heart Centre University Hospital of Copenhagen Rigshospitalet Copenhagen Denmark
| | - Jesper H Svendsen
- Laboratory of Molecular CardiologyDepartment of CardiologyThe Heart CentreUniversity Hospital of CopenhagenRigshospitaletCopenhagenDenmark; Department of Clinical MedicineFaculty of Medicine and Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Stig Haunsø
- Laboratory of Molecular Cardiology Department of Cardiology The Heart Centre University Hospital of Copenhagen Rigshospitalet Copenhagen Denmark
| | - Henning Bundgaard
- Unit for Inherited Cardiac Diseases The Heart Center National University Hospitals Rigshospitalet Copenhagen Denmark
| | - Peter E Weeke
- Laboratory of Molecular Cardiology Department of Cardiology The Heart Centre University Hospital of Copenhagen Rigshospitalet Copenhagen Denmark
| | - Morten S Olesen
- Laboratory of Molecular Cardiology Department of Cardiology The Heart Centre University Hospital of Copenhagen Rigshospitalet Copenhagen Denmark
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Taudien S, Lausser L, Giamarellos-Bourboulis EJ, Sponholz C, Schöneweck F, Felder M, Schirra LR, Schmid F, Gogos C, Groth S, Petersen BS, Franke A, Lieb W, Huse K, Zipfel PF, Kurzai O, Moepps B, Gierschik P, Bauer M, Scherag A, Kestler HA, Platzer M. Genetic Factors of the Disease Course After Sepsis: Rare Deleterious Variants Are Predictive. EBioMedicine 2016; 12:227-238. [PMID: 27639823 PMCID: PMC5078585 DOI: 10.1016/j.ebiom.2016.08.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 12/20/2022] Open
Abstract
Sepsis is a life-threatening organ dysfunction caused by dysregulated host response to infection. For its clinical course, host genetic factors are important and rare genomic variants are suspected to contribute. We sequenced the exomes of 59 Greek and 15 German patients with bacterial sepsis divided into two groups with extremely different disease courses. Variant analysis was focusing on rare deleterious single nucleotide variants (SNVs). We identified significant differences in the number of rare deleterious SNVs per patient between the ethnic groups. Classification experiments based on the data of the Greek patients allowed discrimination between the disease courses with estimated sensitivity and specificity > 75%. By application of the trained model to the German patients we observed comparable discriminatory properties despite lower population-specific rare SNV load. Furthermore, rare SNVs in genes of cell signaling and innate immunity related pathways were identified as classifiers discriminating between the sepsis courses. Sepsis patients with favorable disease course after sepsis, even in the case of unfavorable preconditions, seem to be affected more often by rare deleterious SNVs in cell signaling and innate immunity related pathways, suggesting a protective role of impairments in these processes against a poor disease course. Rare SNV load is higher in the Greek vs. German population. Subsets of rare deleterious SNVs are predictive for the disease course after sepsis. Patients with favorable disease course seem to carry protective deleterious variants in sepsis related pathways.
Sepsis is a life-threatening disease caused by improper response to infection. Only little is known about the role of genetic factors. From > 4000 patients we selected the most extreme cases showing either a favorable or adverse disease course. We determined rare (< 1/200) protein-damaging genetic variants, as they may have a large effect. Using a computational model that includes knowledge on genes we can predict the disease course with > 75% accuracy. Surprisingly, favorable courses can be expected if defense mechanisms are damaged and prevented from overshooting. This underlines the relevance of rare variants for better understanding of sepsis and may offer new treatment options.
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Affiliation(s)
- Stefan Taudien
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Ludwig Lausser
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Institute of Medical Systems Biology, Ulm University, Germany
| | - Evangelos J Giamarellos-Bourboulis
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Christoph Sponholz
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - Franziska Schöneweck
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Marius Felder
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | | | - Florian Schmid
- Institute of Medical Systems Biology, Ulm University, Germany
| | - Charalambos Gogos
- Department of Internal Medicine, University of Patras, Medical School, Greece
| | - Susann Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Klaus Huse
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Peter F Zipfel
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany; Friedrich Schiller University Jena, Jena, Germany
| | - Oliver Kurzai
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Septomics Research Center Jena, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Barbara Moepps
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Peter Gierschik
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Michael Bauer
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - André Scherag
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Hans A Kestler
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Institute of Medical Systems Biology, Ulm University, Germany; Friedrich Schiller University Jena, Jena, Germany.
| | - Matthias Platzer
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany.
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Bogomolovas J, Fleming JR, Anderson BR, Williams R, Lange S, Simon B, Khan MM, Rudolf R, Franke B, Bullard B, Rigden DJ, Granzier H, Labeit S, Mayans O. Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I. Open Biol 2016; 6:160114. [PMID: 27683155 PMCID: PMC5043576 DOI: 10.1098/rsob.160114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/01/2016] [Indexed: 02/06/2023] Open
Abstract
Missense single-nucleotide polymorphisms (mSNPs) in titin are emerging as a main causative factor of heart failure. However, distinguishing between benign and disease-causing mSNPs is a substantial challenge. Here, we research the question of whether a single mSNP in a generic domain of titin can affect heart function as a whole and, if so, how. For this, we studied the mSNP T2850I, seemingly linked to arrhythmogenic right ventricular cardiomyopathy (ARVC). We used structural biology, computational simulations and transgenic muscle in vivo methods to track the effect of the mutation from the molecular to the organismal level. The data show that the T2850I exchange is compatible with the domain three-dimensional fold, but that it strongly destabilizes it. Further, it induces a change in the conformational dynamics of the titin chain that alters its reactivity, causing the formation of aberrant interactions in the sarcomere. Echocardiography of knock-in mice indicated a mild diastolic dysfunction arising from increased myocardial stiffness. In conclusion, our data provide evidence that single mSNPs in titin's I-band can alter overall muscle behaviour. Our suggested mechanisms of disease are the development of non-native sarcomeric interactions and titin instability leading to a reduced I-band compliance. However, understanding the T2850I-induced ARVC pathology mechanistically remains a complex problem and will require a deeper understanding of the sarcomeric context of the titin region affected.
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Affiliation(s)
- Julius Bogomolovas
- Department of Integrative Pathophysiology, Medical Faculty Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Jennifer R Fleming
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Brian R Anderson
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ 85724, USA
| | - Rhys Williams
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Stephan Lange
- School of Medicine, University of California San Diego, 9500 Gilman Drive, MC-0613C, La Jolla, CA 92093, USA
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Muzamil M Khan
- Institute of Molecular and Cell Biology, Mannheim University of Applied Sciences, Paul-Wittsackstraße 110, 68163 Mannheim, Germany Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rüdiger Rudolf
- Institute of Molecular and Cell Biology, Mannheim University of Applied Sciences, Paul-Wittsackstraße 110, 68163 Mannheim, Germany Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Barbara Franke
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Belinda Bullard
- Department of Biology, University of York, York YO10 5DD, UK
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Henk Granzier
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ 85724, USA
| | - Siegfried Labeit
- Department of Integrative Pathophysiology, Medical Faculty Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Olga Mayans
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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Manrai AK, Funke BH, Rehm HL, Olesen MS, Maron BA, Szolovits P, Margulies DM, Loscalzo J, Kohane IS. Genetic Misdiagnoses and the Potential for Health Disparities. N Engl J Med 2016; 375:655-65. [PMID: 27532831 PMCID: PMC5292722 DOI: 10.1056/nejmsa1507092] [Citation(s) in RCA: 495] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND For more than a decade, risk stratification for hypertrophic cardiomyopathy has been enhanced by targeted genetic testing. Using sequencing results, clinicians routinely assess the risk of hypertrophic cardiomyopathy in a patient's relatives and diagnose the condition in patients who have ambiguous clinical presentations. However, the benefits of genetic testing come with the risk that variants may be misclassified. METHODS Using publicly accessible exome data, we identified variants that have previously been considered causal in hypertrophic cardiomyopathy and that are overrepresented in the general population. We studied these variants in diverse populations and reevaluated their initial ascertainments in the medical literature. We reviewed patient records at a leading genetic-testing laboratory for occurrences of these variants during the near-decade-long history of the laboratory. RESULTS Multiple patients, all of whom were of African or unspecified ancestry, received positive reports, with variants misclassified as pathogenic on the basis of the understanding at the time of testing. Subsequently, all reported variants were recategorized as benign. The mutations that were most common in the general population were significantly more common among black Americans than among white Americans (P<0.001). Simulations showed that the inclusion of even small numbers of black Americans in control cohorts probably would have prevented these misclassifications. We identified methodologic shortcomings that contributed to these errors in the medical literature. CONCLUSIONS The misclassification of benign variants as pathogenic that we found in our study shows the need for sequencing the genomes of diverse populations, both in asymptomatic controls and the tested patient population. These results expand on current guidelines, which recommend the use of ancestry-matched controls to interpret variants. As additional populations of different ancestry backgrounds are sequenced, we expect variant reclassifications to increase, particularly for ancestry groups that have historically been less well studied. (Funded by the National Institutes of Health.).
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Affiliation(s)
- Arjun K Manrai
- From the Departments of Biomedical Informatics (A.K.M., D.M.M., I.S.K.), Pathology (B.H.F.), and Medicine (B.A.M., J.L.), Harvard Medical School, the Departments of Pathology, Massachusetts General Hospital (B.H.F.), and the Department of Pathology (H.L.R.), Division of Cardiovascular Medicine (B.A.M.), and Department of Medicine (B.A.M., J.L.), Brigham and Women's Hospital, Boston, and the Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology (MIT) (A.K.M., I.S.K.), the Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine (B.H.F., H.L.R.), and the Computer Science and Artificial Intelligence Laboratory, MIT (P.S.), Cambridge - all in Massachusetts; and the Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Center, University Hospital of Copenhagen, Rigshospitalet, and the Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (M.S.O.) - both in Copenhagen
| | - Birgit H Funke
- From the Departments of Biomedical Informatics (A.K.M., D.M.M., I.S.K.), Pathology (B.H.F.), and Medicine (B.A.M., J.L.), Harvard Medical School, the Departments of Pathology, Massachusetts General Hospital (B.H.F.), and the Department of Pathology (H.L.R.), Division of Cardiovascular Medicine (B.A.M.), and Department of Medicine (B.A.M., J.L.), Brigham and Women's Hospital, Boston, and the Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology (MIT) (A.K.M., I.S.K.), the Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine (B.H.F., H.L.R.), and the Computer Science and Artificial Intelligence Laboratory, MIT (P.S.), Cambridge - all in Massachusetts; and the Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Center, University Hospital of Copenhagen, Rigshospitalet, and the Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (M.S.O.) - both in Copenhagen
| | - Heidi L Rehm
- From the Departments of Biomedical Informatics (A.K.M., D.M.M., I.S.K.), Pathology (B.H.F.), and Medicine (B.A.M., J.L.), Harvard Medical School, the Departments of Pathology, Massachusetts General Hospital (B.H.F.), and the Department of Pathology (H.L.R.), Division of Cardiovascular Medicine (B.A.M.), and Department of Medicine (B.A.M., J.L.), Brigham and Women's Hospital, Boston, and the Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology (MIT) (A.K.M., I.S.K.), the Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine (B.H.F., H.L.R.), and the Computer Science and Artificial Intelligence Laboratory, MIT (P.S.), Cambridge - all in Massachusetts; and the Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Center, University Hospital of Copenhagen, Rigshospitalet, and the Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (M.S.O.) - both in Copenhagen
| | - Morten S Olesen
- From the Departments of Biomedical Informatics (A.K.M., D.M.M., I.S.K.), Pathology (B.H.F.), and Medicine (B.A.M., J.L.), Harvard Medical School, the Departments of Pathology, Massachusetts General Hospital (B.H.F.), and the Department of Pathology (H.L.R.), Division of Cardiovascular Medicine (B.A.M.), and Department of Medicine (B.A.M., J.L.), Brigham and Women's Hospital, Boston, and the Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology (MIT) (A.K.M., I.S.K.), the Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine (B.H.F., H.L.R.), and the Computer Science and Artificial Intelligence Laboratory, MIT (P.S.), Cambridge - all in Massachusetts; and the Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Center, University Hospital of Copenhagen, Rigshospitalet, and the Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (M.S.O.) - both in Copenhagen
| | - Bradley A Maron
- From the Departments of Biomedical Informatics (A.K.M., D.M.M., I.S.K.), Pathology (B.H.F.), and Medicine (B.A.M., J.L.), Harvard Medical School, the Departments of Pathology, Massachusetts General Hospital (B.H.F.), and the Department of Pathology (H.L.R.), Division of Cardiovascular Medicine (B.A.M.), and Department of Medicine (B.A.M., J.L.), Brigham and Women's Hospital, Boston, and the Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology (MIT) (A.K.M., I.S.K.), the Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine (B.H.F., H.L.R.), and the Computer Science and Artificial Intelligence Laboratory, MIT (P.S.), Cambridge - all in Massachusetts; and the Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Center, University Hospital of Copenhagen, Rigshospitalet, and the Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (M.S.O.) - both in Copenhagen
| | - Peter Szolovits
- From the Departments of Biomedical Informatics (A.K.M., D.M.M., I.S.K.), Pathology (B.H.F.), and Medicine (B.A.M., J.L.), Harvard Medical School, the Departments of Pathology, Massachusetts General Hospital (B.H.F.), and the Department of Pathology (H.L.R.), Division of Cardiovascular Medicine (B.A.M.), and Department of Medicine (B.A.M., J.L.), Brigham and Women's Hospital, Boston, and the Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology (MIT) (A.K.M., I.S.K.), the Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine (B.H.F., H.L.R.), and the Computer Science and Artificial Intelligence Laboratory, MIT (P.S.), Cambridge - all in Massachusetts; and the Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Center, University Hospital of Copenhagen, Rigshospitalet, and the Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (M.S.O.) - both in Copenhagen
| | - David M Margulies
- From the Departments of Biomedical Informatics (A.K.M., D.M.M., I.S.K.), Pathology (B.H.F.), and Medicine (B.A.M., J.L.), Harvard Medical School, the Departments of Pathology, Massachusetts General Hospital (B.H.F.), and the Department of Pathology (H.L.R.), Division of Cardiovascular Medicine (B.A.M.), and Department of Medicine (B.A.M., J.L.), Brigham and Women's Hospital, Boston, and the Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology (MIT) (A.K.M., I.S.K.), the Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine (B.H.F., H.L.R.), and the Computer Science and Artificial Intelligence Laboratory, MIT (P.S.), Cambridge - all in Massachusetts; and the Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Center, University Hospital of Copenhagen, Rigshospitalet, and the Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (M.S.O.) - both in Copenhagen
| | - Joseph Loscalzo
- From the Departments of Biomedical Informatics (A.K.M., D.M.M., I.S.K.), Pathology (B.H.F.), and Medicine (B.A.M., J.L.), Harvard Medical School, the Departments of Pathology, Massachusetts General Hospital (B.H.F.), and the Department of Pathology (H.L.R.), Division of Cardiovascular Medicine (B.A.M.), and Department of Medicine (B.A.M., J.L.), Brigham and Women's Hospital, Boston, and the Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology (MIT) (A.K.M., I.S.K.), the Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine (B.H.F., H.L.R.), and the Computer Science and Artificial Intelligence Laboratory, MIT (P.S.), Cambridge - all in Massachusetts; and the Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Center, University Hospital of Copenhagen, Rigshospitalet, and the Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (M.S.O.) - both in Copenhagen
| | - Isaac S Kohane
- From the Departments of Biomedical Informatics (A.K.M., D.M.M., I.S.K.), Pathology (B.H.F.), and Medicine (B.A.M., J.L.), Harvard Medical School, the Departments of Pathology, Massachusetts General Hospital (B.H.F.), and the Department of Pathology (H.L.R.), Division of Cardiovascular Medicine (B.A.M.), and Department of Medicine (B.A.M., J.L.), Brigham and Women's Hospital, Boston, and the Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology (MIT) (A.K.M., I.S.K.), the Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine (B.H.F., H.L.R.), and the Computer Science and Artificial Intelligence Laboratory, MIT (P.S.), Cambridge - all in Massachusetts; and the Laboratory of Molecular Cardiology, Department of Cardiology, the Heart Center, University Hospital of Copenhagen, Rigshospitalet, and the Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen (M.S.O.) - both in Copenhagen
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EFHC1 variants in juvenile myoclonic epilepsy: reanalysis according to NHGRI and ACMG guidelines for assigning disease causality. Genet Med 2016; 19:144-156. [PMID: 27467453 DOI: 10.1038/gim.2016.86] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/09/2016] [Indexed: 12/12/2022] Open
Abstract
PURPOSE EFHC1 variants are the most common mutations in inherited myoclonic and grand mal clonic-tonic-clonic (CTC) convulsions of juvenile myoclonic epilepsy (JME). We reanalyzed 54 EFHC1 variants associated with epilepsy from 17 cohorts based on National Human Genome Research Institute (NHGRI) and American College of Medical Genetics and Genomics (ACMG) guidelines for interpretation of sequence variants. METHODS We calculated Bayesian LOD scores for variants in coinheritance, unconditional exact tests and odds ratios (OR) in case-control associations, allele frequencies in genome databases, and predictions for conservation/pathogenicity. We reviewed whether variants damage EFHC1 functions, whether efhc1-/- KO mice recapitulate CTC convulsions and "microdysgenesis" neuropathology, and whether supernumerary synaptic and dendritic phenotypes can be rescued in the fly model when EFHC1 is overexpressed. We rated strengths of evidence and applied ACMG combinatorial criteria for classifying variants. RESULTS Nine variants were classified as "pathogenic," 14 as "likely pathogenic," 9 as "benign," and 2 as "likely benign." Twenty variants of unknown significance had an insufficient number of ancestry-matched controls, but ORs exceeded 5 when compared with racial/ethnic-matched Exome Aggregation Consortium (ExAC) controls. CONCLUSIONS NHGRI gene-level evidence and variant-level evidence establish EFHC1 as the first non-ion channel microtubule-associated protein whose mutations disturb R-type VDCC and TRPM2 calcium currents in overgrown synapses and dendrites within abnormally migrated dislocated neurons, thus explaining CTC convulsions and "microdysgenesis" neuropathology of JME.Genet Med 19 2, 144-156.
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Sampson MG, Gillies CE, Robertson CC, Crawford B, Vega-Warner V, Otto EA, Kretzler M, Kang HM. Using Population Genetics to Interrogate the Monogenic Nephrotic Syndrome Diagnosis in a Case Cohort. J Am Soc Nephrol 2016; 27:1970-83. [PMID: 26534921 PMCID: PMC4926977 DOI: 10.1681/asn.2015050504] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/06/2015] [Indexed: 01/02/2023] Open
Abstract
To maximize clinical benefits of genetic screening of patients with nephrotic syndrome (NS) to diagnose monogenic causes, reliably distinguishing NS-causing variants from the background of rare, noncausal variants prevalent in all genomes is vital. To determine the prevalence of monogenic NS in a North American case cohort while accounting for background prevalence of genetic variation, we sequenced 21 implicated monogenic NS genes in 312 participants from the Nephrotic Syndrome Study Network and 61 putative controls from the 1000 Genomes Project (1000G). These analyses were extended to available sequence data from approximately 2500 subjects from the 1000G. A typical pathogenicity filter identified causal variants for NS in 4.2% of patients and 5.8% of subjects from the 1000G. We devised a more stringent pathogenicity filtering strategy, reducing background prevalence of causal variants to 1.5%. When applying this stringent filter to patients, prevalence of monogenic NS was 2.9%; of these patients, 67% were pediatric, and 44% had FSGS on biopsy. The rate of complete remission did not associate with monogenic classification. Thus, we identified factors contributing to inaccurate monogenic classification of NS and developed a more accurate variant filtering strategy. The prevalence and clinical correlates of monogenic NS in this sporadically affected cohort differ substantially from those reported for patients referred for genetic analysis. Particularly in unselected, population-based cases, considering putative causal variants in known NS genes from a probabilistic rather than a deterministic perspective may be more precise. We also introduce GeneVetter, a web tool for monogenic assessment of rare disease.
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Affiliation(s)
| | | | | | | | | | - Edgar A Otto
- Departments of Pediatrics and Communicable Diseases, and
| | - Matthias Kretzler
- Internal Medicine, Division of Nephrology and Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, Michigan; and
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
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50
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Perrot A, Tomasov P, Villard E, Faludi R, Melacini P, Lossie J, Lohmann N, Richard P, De Bortoli M, Angelini A, Varga-Szemes A, Sperling SR, Simor T, Veselka J, Özcelik C, Charron P. Mutations in NEBL encoding the cardiac Z-disk protein nebulette are associated with various cardiomyopathies. Arch Med Sci 2016; 12:263-78. [PMID: 27186169 PMCID: PMC4848357 DOI: 10.5114/aoms.2016.59250] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/29/2015] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Transgenic mice overexpressing mutated NEBL, encoding the cardiac-specific Z-disk protein nebulette, develop severe cardiac phenotypes. Since cardiomyopathies are commonly familial and because mutations in a single gene may result in variable phenotypes, we tested the hypothesis that NEBL mutations are associated with cardiomyopathy. MATERIAL AND METHODS We analyzed 389 patients, including cohorts of patients with dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy (HCM), and left ventricular non-compaction cardiomyopathy (LVNC). The 28 coding exons of the NEBL gene were sequenced. Further bioinformatic analysis was used to distinguish variants. RESULTS In total, we identified six very rare heterozygous missense mutations in NEBL in 7 different patients (frequency 1.8%) in highly conserved codons. The mutations were not detectable in 320 Caucasian sex-matched unrelated individuals without cardiomyopathy and 192 Caucasian sex-matched blood donors without heart disease. Known cardiomyopathy genes were excluded in these patients. The mutations p.H171R and p.I652L were found in 2 HCM patients. Further, p.Q581R and p.S747L were detected in 2 DCM patients, while the mutation p.A175T was identified independently in two unrelated patients with DCM. One LVNC patient carried the mutation p.P916L. All HCM and DCM related mutations were located in the nebulin-like repeats, domains responsible for actin binding. Interestingly, the mutation associated with LVNC was located in the C-terminal serine-rich linker region. CONCLUSIONS Our data suggest that NEBL mutations may cause various cardiomyopathies. We herein describe the first NEBL mutations in HCM and LVNC. Our findings underline the notion that the cardiomyopathies are true allelic diseases.
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Affiliation(s)
- Andreas Perrot
- Charité-Universitätsmedizin Berlin, Cardiovascular Genetics, Experimental and Clinical Research Center, Berlin, Germany
| | - Pavol Tomasov
- Department of Cardiology, 2 Medical School, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Eric Villard
- AP-HP, Département de Génétique et Département de Cardiologie et Inserm UMR 1166, Hopital Pitié-Salpêtrière, Paris, France
| | - Reka Faludi
- Heart Institute, Faculty of Medicine, University of Pécs, Pécs, Hungary
| | - Paola Melacini
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy
| | - Janine Lossie
- Charité-Universitätsmedizin Berlin, Cardiovascular Genetics, Experimental and Clinical Research Center, Berlin, Germany
| | - Nadine Lohmann
- Charité-Universitätsmedizin Berlin, Cardiovascular Genetics, Experimental and Clinical Research Center, Berlin, Germany
| | - Pascale Richard
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, UF Cardiogénétique et Myogénétique, Service de Biochimie Métabolique, Paris, France
| | - Marzia De Bortoli
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy
| | - Annalisa Angelini
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy
| | - Akos Varga-Szemes
- Heart Institute, Faculty of Medicine, University of Pécs, Pécs, Hungary
| | - Silke R. Sperling
- Charité-Universitätsmedizin Berlin, Cardiovascular Genetics, Experimental and Clinical Research Center, Berlin, Germany
| | - Tamás Simor
- Heart Institute, Faculty of Medicine, University of Pécs, Pécs, Hungary
| | - Josef Veselka
- Department of Cardiology, 2 Medical School, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Cemil Özcelik
- Charité-Universitätsmedizin Berlin, Cardiovascular Genetics, Experimental and Clinical Research Center, Berlin, Germany
- Knappschaftskrankenhaus Recklinghausen, Medizinischen Klinik I Kardiologie, Gastroenterologie und Diabetologie, Recklinghausen, Germany
| | - Philippe Charron
- AP-HP, Département de Génétique et Département de Cardiologie et Inserm UMR 1166, Hopital Pitié-Salpêtrière, Paris, France
- Université de Versailles Saint Quentin en Yvelines, Versailles, France
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