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Slavotinek AM, Thompson ML, Martin LJ, Gelb BD. Diagnostic yield after next-generation sequencing in pediatric cardiovascular disease. HGG ADVANCES 2024; 5:100286. [PMID: 38521975 PMCID: PMC11024993 DOI: 10.1016/j.xhgg.2024.100286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024] Open
Abstract
Genetic testing with exome sequencing and genome sequencing is increasingly offered to infants and children with cardiovascular diseases. However, the rates of positive diagnoses after genetic testing within the different categories of cardiac disease and phenotypic subtypes of congenital heart disease (CHD) have been little studied. We report the diagnostic yield after next-generation sequencing in 500 patients with CHD from diverse population subgroups that were enrolled at three different sites in the Clinical Sequencing Evidence-Generating Research consortium. Patients were ascertained due to a primary cardiovascular issue comprising arrhythmia, cardiomyopathy, and/or CHD, and corresponding human phenotype ontology terms were selected to describe the cardiac and extracardiac findings. We examined the diagnostic yield for patients with arrhythmia, cardiomyopathy, and/or CHD and phenotypic subtypes of CHD comprising conotruncal defects, heterotaxy, left ventricular outflow tract obstruction, septal defects, and "other" heart defects. We found a significant increase in the frequency of positive findings for patients who underwent genome sequencing compared to exome sequencing and for syndromic cardiac defects compared to isolated cardiac defects. We also found significantly higher diagnostic rates for patients who presented with isolated cardiomyopathy compared to isolated CHD. For patients with syndromic presentations who underwent genome sequencing, there were significant differences in the numbers of positive diagnoses for phenotypic subcategories of CHD, ranging from 31.7% for septal defects to 60% for "other". Despite variation in the diagnostic yield at each site, our results support genetic testing in pediatric patients with syndromic and isolated cardiovascular issues and in all subtypes of CHD.
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Affiliation(s)
- Anne M Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
| | - Michelle L Thompson
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lisa J Martin
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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2
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Stanley KJ, Kalbfleisch KJ, Moran OM, Chaturvedi RR, Roifman M, Chen X, Manshaei R, Martin N, McDermott S, McNiven V, Myles-Reid D, Nield LE, Reuter MS, Schwartz MLB, Shannon P, Silver R, Somerville C, Teitelbaum R, Zahavich L, Bassett AS, Kim RH, Mital S, Chitayat D, Jobling RK. Expanding the phenotypic spectrum of NOTCH1 variants: clinical manifestations in families with congenital heart disease. Eur J Hum Genet 2024; 32:795-803. [PMID: 38778082 PMCID: PMC11219983 DOI: 10.1038/s41431-024-01629-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/28/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
Pathogenic variants in NOTCH1 are associated with non-syndromic congenital heart disease (CHD) and Adams-Oliver syndrome (AOS). The clinical presentation of individuals with damaging NOTCH1 variants is characterized by variable expressivity and incomplete penetrance; however, data on systematic phenotypic characterization are limited. We report the genotype and phenotype of a cohort of 33 individuals (20 females, 13 males; median age 23.4 years, range 2.5-68.3 years) from 11 families with causative NOTCH1 variants (9 inherited, 2 de novo; 9 novel), ascertained from a proband with CHD. We describe the cardiac and extracardiac anomalies identified in these 33 individuals, only four of whom met criteria for AOS. The most common CHD identified was tetralogy of Fallot, though various left- and right-sided lesions and septal defects were also present. Extracardiac anomalies identified include cutis aplasia (5/33), cutaneous vascular anomalies (7/33), vascular anomalies of the central nervous system (2/10), Poland anomaly (1/33), pulmonary hypertension (2/33), and structural brain anomalies (3/14). Identification of these findings in a cardiac proband cohort supports NOTCH1-associated CHD and NOTCH1-associated AOS lying on a phenotypic continuum. Our findings also support (1) Broad indications for NOTCH1 molecular testing (any familial CHD, simplex tetralogy of Fallot or hypoplastic left heart); (2) Cascade testing in all at-risk relatives; and (3) A thorough physical exam, in addition to cardiac, brain (structural and vascular), abdominal, and ophthalmologic imaging, in all gene-positive individuals. This information is important for guiding the medical management of these individuals, particularly given the high prevalence of NOTCH1 variants in the CHD population.
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Affiliation(s)
- Kaitlin J Stanley
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kelsey J Kalbfleisch
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Olivia M Moran
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rajiv R Chaturvedi
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Maian Roifman
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Xin Chen
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Roozbeh Manshaei
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nicole Martin
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Simina McDermott
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Vanda McNiven
- Division of Genetics, Department of Pediatrics, McMaster Children's Hospital, Hamilton, ON, Canada
| | - Diane Myles-Reid
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Lynne E Nield
- Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Miriam S Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marci L B Schwartz
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Rachel Silver
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Cherith Somerville
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ronni Teitelbaum
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Laura Zahavich
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anne S Bassett
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Raymond H Kim
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- Fred A. Litwin Family Centre in Genetic Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Seema Mital
- Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- Ted Rogers Centre for Heart Research, Toronto, ON, Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Rebekah K Jobling
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada.
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada.
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3
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Pidaparti M, Geddes GC, Durbin MD. Clinical Genetic and Genomic Testing in Congenital Heart Disease and Cardiomyopathy. J Clin Med 2024; 13:2544. [PMID: 38731073 PMCID: PMC11084871 DOI: 10.3390/jcm13092544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
Congenital heart disease (CHD) and cardiomyopathies are the leading cause of morbidity and mortality worldwide. These conditions are often caused by genetic factors, and recent research has shown that genetic and genomic testing can provide valuable information for patient care. By identifying genetic causes, healthcare providers can screen for other related health conditions, offer early interventions, estimate prognosis, select appropriate treatments, and assess the risk for family members. Genetic and genomic testing is now the standard of care in patients with CHD and cardiomyopathy. However, rapid advances in technology and greater availability of testing options have led to changes in recommendations for the most appropriate testing method. Several recent studies have investigated the utility of genetic testing in this changing landscape. This review summarizes the literature surrounding the clinical utility of genetic evaluation in patients with CHD and cardiomyopathy.
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Affiliation(s)
- Mahati Pidaparti
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Gabrielle C. Geddes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Matthew D. Durbin
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Herman B Wells Center for Pediatric Research, 1044 W. Walnut, Indianapolis, IN 46202, USA
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4
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Helm BM, Ware SM. Clinical Decision Analysis of Genetic Evaluation and Testing in 1013 Intensive Care Unit Infants with Congenital Heart Defects Supports Universal Genetic Testing. Genes (Basel) 2024; 15:505. [PMID: 38674439 PMCID: PMC11050575 DOI: 10.3390/genes15040505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Extracardiac anomalies (ECAs) are strong predictors of genetic disorders in infants with congenital heart disease (CHD), but there are no prior studies assessing performance of ECA status as a screen for genetic diagnoses in CHD patients. This retrospective cohort study assessed this in our comprehensive inpatient CHD genetics service focusing on neonates and infants admitted to the intensive care unit (ICU). The performance and diagnostic utility of using ECA status to screen for genetic disorders was assessed using decision curve analysis, a statistical tool to assess clinical utility, determining the threshold of phenotypic screening by ECA versus a Test-All approach. Over 24% of infants had genetic diagnoses identified (n = 244/1013), and ECA-positive status indicated a 4-fold increased risk of having a genetic disorder. However, ECA status had low-moderate screening performance based on predictive summary index, a compositive measure of positive and negative predictive values. For those with genetic diagnoses, nearly one-third (32%, 78/244) were ECA-negative but had cytogenetic and/or monogenic disorders identified by genetic testing. Thus, if the presence of multiple congenital anomalies is the phenotypic driver to initiate genetic testing, 13.4% (78/580) of infants with isolated CHD with identifiable genetic causes will be missed. Given the prevalence of genetic disorders and limited screening performance of ECA status, this analysis supports genetic testing in all CHD infants in intensive care settings rather than screening based on ECA.
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Affiliation(s)
- Benjamin M. Helm
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202, USA
| | - Stephanie M. Ware
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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5
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Baker EK, Shikany A, Winlaw DS, Weaver KN. Phenotypes and genotypes in a cohort of children with single-ventricle CHD. Cardiol Young 2024; 34:815-821. [PMID: 37850440 DOI: 10.1017/s1047951123003505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
OBJECTIVE CHD is known to be associated with increased risk for neurodevelopmental disorders. The combination of CHD with neurodevelopmental disorders and/or extra-cardiac anomalies increases the chance for an underlying genetic diagnosis. Over the last 15 years, there has been a dramatic increase in the use of broad-scale genetic testing. We sought to determine if neurodevelopmental disorders in children with single-ventricle CHD born prior to the genetic testing revolution are associated with genetic diagnosis. METHODS We identified 74 5-12-year-old patients with single-ventricle CHD post-Fontan procedure. We retrospectively evaluated genetic testing performed and neurodevelopmental status of these patients. RESULTS In this cohort, there was an overall higher rate of neurodevelopmental disorders (80%) compared to the literature (50%). More of the younger (5-7-year-old) patients were seen by genetic counsellors compared to the older (8-12-year-old) cohort (46% versus 19% p value = 0.01). In the younger cohort, the average age of initial consultation was 7.7 days compared to 251 days in the older cohort. The overall rate of achieving a molecular diagnosis was 12% and 8% in the younger and older cohorts, respectively; however, the vast majority of did not have broad genetic testing. CONCLUSION The minority of patients in our cohort achieved a genetic diagnosis. Given a large increase in the number of genes associated with monogenic CHD and neurodevelopmental disorders in the last decade, comprehensive testing and consultation with clinical genetics should be considered in this age range, since current testing standards did not exist during their infancy.
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Affiliation(s)
- Elizabeth K Baker
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Amy Shikany
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - David S Winlaw
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Heart Institute, Cardiothoracic Surgery, Cincinnati Children's Hospital Medicine, Cincinnati, OH, USA
| | - K Nicole Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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6
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Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
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Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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7
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Vahab N, Bonu T, Kuhlmann L, Ramialison M, Tyagi S. Uncovering co-regulatory modules and gene regulatory networks in the heart through machine learning-based analysis of large-scale epigenomic data. Comput Biol Med 2024; 171:108068. [PMID: 38354497 DOI: 10.1016/j.compbiomed.2024.108068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/30/2023] [Accepted: 01/27/2024] [Indexed: 02/16/2024]
Abstract
The availability of large-scale epigenomic data from various cell types and conditions has yielded valuable insights for evaluating and learning features predicting the co-binding of transcription factors (TF). However, prior attempts to develop models predicting motif co-occurrence lacked scalability for globally analyzing any motif combination or making cross-species predictions. Moreover, mapping co-regulatory modules (CRM) to gene regulatory networks (GRN) is crucial for understanding underlying function. Currently, no comprehensive pipeline exists for large-scale, rapid, and accurate CRM and GRN identification. In this study, we analyzed and evaluated different TF binding characteristics facilitating biologically significant co-binding to identify all potential clusters of co-binding TFs. We curated the UniBind database, containing ChIP-Seq data from over 1983 samples and 232 TFs, and implemented two machine learning models to predict CRMs and the potential regulatory networks they operate on. Two machine learning models, Convolution Neural Networks (CNN) and Random Forest Classifier(RFC), used to predict co-binding between TFs, were compared using precision-recall Receiver Operating Characteristic (ROC) curves. CNN outperformed RFC (AUC 0.94 vs. 0.88) and achieved higher F1 scores (0.938 vs. 0.872). The CRMs generated by the clustering algorithm were validated against ChipAtlas and MCOT, revealing additional motifs forming CRMs. We predicted 200k CRMs for 50k+ human genes, validated against recent CRM prediction methods with 100% overlap. Further, we narrowed our focus to study heart-related regulatory motifs, filtering the generated CRMs to report 1784 Cardiac CRMs containing at least four cardiac TFs. Identified cardiac CRMs revealed potential novel regulators like ARID3A and RXRB for SCAD, including known TFs like PPARG for F11R. Our findings highlight the importance of the NKX family of transcription factors in cardiac development and provide potential targets for further investigation in cardiac disease.
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Affiliation(s)
- Naima Vahab
- School of Computational Technologies, RMIT University, Melbourne VIC 3000, Australia; Department of Infectious Diseases, Alfred Hospital, Prahran VIC 3008, Australia
| | - Tarun Bonu
- Faculty of Information Technology, Monash University, Clayton VIC 3800, Australia
| | - Levin Kuhlmann
- Faculty of Information Technology, Monash University, Clayton VIC 3800, Australia
| | | | - Sonika Tyagi
- School of Computational Technologies, RMIT University, Melbourne VIC 3000, Australia; Department of Infectious Diseases, Alfred Hospital, Prahran VIC 3008, Australia.
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Amdani S, Auerbach SR, Bansal N, Chen S, Conway J, Silva JPDA, Deshpande SR, Hoover J, Lin KY, Miyamoto SD, Puri K, Price J, Spinner J, White R, Rossano JW, Bearl DW, Cousino MK, Catlin P, Hidalgo NC, Godown J, Kantor P, Masarone D, Peng DM, Rea KE, Schumacher K, Shaddy R, Shea E, Tapia HV, Valikodath N, Zafar F, Hsu D. Research Gaps in Pediatric Heart Failure: Defining the Gaps and Then Closing Them Over the Next Decade. J Card Fail 2024; 30:64-77. [PMID: 38065308 DOI: 10.1016/j.cardfail.2023.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 01/13/2024]
Abstract
Given the numerous opportunities and the wide knowledge gaps in pediatric heart failure, an international group of pediatric heart failure experts with diverse backgrounds were invited and tasked with identifying research gaps in each pediatric heart failure domain that scientists and funding agencies need to focus on over the next decade.
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Affiliation(s)
- Shahnawaz Amdani
- Department of Pediatric Cardiology, Cleveland Clinic Children's, Cleveland, Ohio.
| | - Scott R Auerbach
- Division of Pediatric Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Neha Bansal
- Division of Pediatric Cardiology, Mount Sinai Kravis Children's Hospital, Icahn School of Medicine, New York, New York
| | - Sharon Chen
- Division of Pediatric Cardiology, Lucile Packard Children's Hospital, Stanford University School of Medicine, Palo Alto, California
| | - Jennifer Conway
- Division of Pediatric Cardiology, Stollery Children's Hospital, Edmonton, Alberta, Canada
| | - Julie Pires DA Silva
- Division of Pediatric Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | - Jessica Hoover
- Department of Pediatric Cardiology, Cleveland Clinic Children's, Cleveland, Ohio
| | - Kimberly Y Lin
- Division of Cardiology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Shelley D Miyamoto
- Division of Pediatric Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kriti Puri
- Department of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine/Texas Children's Hospital, Houston, Texas
| | - Jack Price
- Department of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine/Texas Children's Hospital, Houston, Texas
| | - Joseph Spinner
- Department of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine/Texas Children's Hospital, Houston, Texas
| | - Rachel White
- Division of Cardiology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Joseph W Rossano
- Division of Cardiology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - David W Bearl
- Department of Pediatric Cardiology, Monroe Carell Jr. Children's Hospital, Nashville, Tennessee
| | - Melissa K Cousino
- Department of Pediatrics, University of Michigan, C. S. Mott Children's Hospital, Ann Arbor, Michigan
| | - Perry Catlin
- Department of Psychology, Marquette University, Milwaukee, Wisconsin
| | - Nicolas Corral Hidalgo
- Division of Pediatric Cardiology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York
| | - Justin Godown
- Department of Pediatric Cardiology, Monroe Carell Jr. Children's Hospital, Nashville, Tennessee
| | - Paul Kantor
- Children's Hospital Los Angeles and the Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Daniele Masarone
- Heart Failure Unit, Department of Cardiology, AORN dei Colli-Monaldi Hospital Naples, Naples, Italy
| | - David M Peng
- Department of Pediatrics, University of Michigan, C. S. Mott Children's Hospital, Ann Arbor, Michigan
| | - Kelly E Rea
- Department of Pediatrics, University of Michigan, C. S. Mott Children's Hospital, Ann Arbor, Michigan
| | - Kurt Schumacher
- Department of Pediatrics, University of Michigan, C. S. Mott Children's Hospital, Ann Arbor, Michigan
| | - Robert Shaddy
- Children's Hospital Los Angeles and the Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Erin Shea
- Heart Failure Unit, Department of Cardiology, AORN dei Colli-Monaldi Hospital Naples, Naples, Italy
| | - Henry Valora Tapia
- Division of Pediatric Cardiology, University of Utah. Salt Lake City, Utah
| | - Nishma Valikodath
- Department of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine/Texas Children's Hospital, Houston, Texas
| | - Farhan Zafar
- The Heart Institute, Cincinnati Children's Hospital Medical Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Daphne Hsu
- Division of Pediatric Cardiology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York
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9
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Chhatwal K, Smith JJ, Bola H, Zahid A, Venkatakrishnan A, Brand T. Uncovering the Genetic Basis of Congenital Heart Disease: Recent Advancements and Implications for Clinical Management. CJC PEDIATRIC AND CONGENITAL HEART DISEASE 2023; 2:464-480. [PMID: 38205435 PMCID: PMC10777202 DOI: 10.1016/j.cjcpc.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/13/2023] [Indexed: 01/12/2024]
Abstract
Congenital heart disease (CHD) is the most prevalent hereditary disorder, affecting approximately 1% of all live births. A reduction in morbidity and mortality has been achieved with advancements in surgical intervention, yet challenges in managing complications, extracardiac abnormalities, and comorbidities still exist. To address these, a more comprehensive understanding of the genetic basis underlying CHD is required to establish how certain variants are associated with the clinical outcomes. This will enable clinicians to provide personalized treatments by predicting the risk and prognosis, which might improve the therapeutic results and the patient's quality of life. We review how advancements in genome sequencing are changing our understanding of the genetic basis of CHD, discuss experimental approaches to determine the significance of novel variants, and identify barriers to use this knowledge in the clinics. Next-generation sequencing technologies are unravelling the role of oligogenic inheritance, epigenetic modification, genetic mosaicism, and noncoding variants in controlling the expression of candidate CHD-associated genes. However, clinical risk prediction based on these factors remains challenging. Therefore, studies involving human-induced pluripotent stem cells and single-cell sequencing help create preclinical frameworks for determining the significance of novel genetic variants. Clinicians should be aware of the benefits and implications of the responsible use of genomics. To facilitate and accelerate the clinical integration of these novel technologies, clinicians should actively engage in the latest scientific and technical developments to provide better, more personalized management plans for patients.
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Affiliation(s)
- Karanjot Chhatwal
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Jacob J. Smith
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Harroop Bola
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Abeer Zahid
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Ashwin Venkatakrishnan
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Thomas Brand
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
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10
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Zhu W, Lo CW. Insights into the genetic architecture of congenital heart disease from animal modeling. Zool Res 2023; 44:577-590. [PMID: 37147909 PMCID: PMC10236297 DOI: 10.24272/j.issn.2095-8137.2022.463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
Congenital heart disease (CHD) is observed in up to 1% of live births and is one of the leading causes of mortality from birth defects. While hundreds of genes have been implicated in the genetic etiology of CHD, their role in CHD pathogenesis is still poorly understood. This is largely a reflection of the sporadic nature of CHD, as well as its variable expressivity and incomplete penetrance. We reviewed the monogenic causes and evidence for oligogenic etiology of CHD, as well as the role of de novo mutations, common variants, and genetic modifiers. For further mechanistic insight, we leveraged single-cell data across species to investigate the cellular expression characteristics of genes implicated in CHD in developing human and mouse embryonic hearts. Understanding the genetic etiology of CHD may enable the application of precision medicine and prenatal diagnosis, thereby facilitating early intervention to improve outcomes for patients with CHD.
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Affiliation(s)
- Wenjuan Zhu
- Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology-Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201 USA. E-mail:
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11
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Griffin EL, Nees SN, Morton SU, Wynn J, Patel N, Jobanputra V, Robinson S, Kochav SM, Tao A, Andrews C, Cross N, Geva J, Lanzilotta K, Ritter A, Taillie E, Thompson A, Meyer C, Akers R, King EC, Cnota JF, Kim RW, Porter GA, Brueckner M, Seidman CE, Shen Y, Gelb BD, Goldmuntz E, Newburger JW, Roberts AE, Chung WK. Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:e003791. [PMID: 36803080 PMCID: PMC10121846 DOI: 10.1161/circgen.122.003791] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/28/2022] [Indexed: 02/23/2023]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common major congenital anomaly and causes significant morbidity and mortality. Epidemiologic evidence supports a role of genetics in the development of CHD. Genetic diagnoses can inform prognosis and clinical management. However, genetic testing is not standardized among individuals with CHD. We sought to develop a list of validated CHD genes using established methods and to evaluate the process of returning genetic results to research participants in a large genomic study. METHODS Two-hundred ninety-five candidate CHD genes were evaluated using a ClinGen framework. Sequence and copy number variants involving genes in the CHD gene list were analyzed in Pediatric Cardiac Genomics Consortium participants. Pathogenic/likely pathogenic results were confirmed on a new sample in a clinical laboratory improvement amendments-certified laboratory and disclosed to eligible participants. Adult probands and parents of probands who received results were asked to complete a post-disclosure survey. RESULTS A total of 99 genes had a strong or definitive clinical validity classification. Diagnostic yields for copy number variants and exome sequencing were 1.8% and 3.8%, respectively. Thirty-one probands completed clinical laboratory improvement amendments-confirmation and received results. Participants who completed postdisclosure surveys reported high personal utility and no decision regret after receiving genetic results. CONCLUSIONS The application of ClinGen criteria to CHD candidate genes yielded a list that can be used to interpret clinical genetic testing for CHD. Applying this gene list to one of the largest research cohorts of CHD participants provides a lower bound for the yield of genetic testing in CHD.
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Affiliation(s)
- Emily L. Griffin
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Shannon N. Nees
- Nemours Cardiac Center, Nemours Children’s Hospital, Delaware. Wilmington, DE
| | - Sarah U. Morton
- Division of Newborn Medicine, Dept of Medicine, Boston Children’s Hospital
- Dept of Pediatrics, Harvard Medical School, Boston, MA
| | - Julia Wynn
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Nihir Patel
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vaidehi Jobanputra
- Dept of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Scott Robinson
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Stephanie M. Kochav
- Division of Cardiology, Dept of Medicine, Columbia University Vagelos College of Physicians & Surgeons, New York, NY
| | - Alice Tao
- Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Carli Andrews
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Nancy Cross
- Division of Pediatric Cardiology, Yale School of Medicine, New Haven, CT
| | - Judith Geva
- Dept of Cardiology, Boston Children’s Hospital
| | - Kristen Lanzilotta
- Division of Cardiology, Children’s Hospital of Philadelphia, Dept of Pediatrics, Perelman School of Medicine, University of Pennsylvania
| | - Alyssa Ritter
- Division of Cardiology, Children’s Hospital of Philadelphia, Dept of Pediatrics, Perelman School of Medicine, University of Pennsylvania
- Division of Human Genetics, Dept of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Eileen Taillie
- Dept of Pediatrics, Golisano Children’s Hospital, University of Rochester Medical Center, Rochester, NY
| | - Alexandra Thompson
- Division of Cardiothoracic Surgery, Children’s Hospital of Los Angeles, Los Angeles, CA
| | | | - Rachel Akers
- Division of Biostatistics & Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Eileen C. King
- Division of Biostatistics & Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - James F Cnota
- The Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Richard W. Kim
- Pediatric Cardiac Surgery, Children's Hospital of Los Angeles, Los Angeles, CA
| | - George A. Porter
- Dept of Pediatrics, University of Rochester Medical Center, The School of Medicine & Dentistry, Rochester, NY
| | - Martina Brueckner
- Dept of Genetics & Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Christine E. Seidman
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA
- Dept of Genetics, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Yufeng Shen
- Depts of Systems Biology & Biomedical Informatics, Columbia University, New York, NY
| | - Bruce D. Gelb
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Depts of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia, Dept of Pediatrics, Perelman School of Medicine, University of Pennsylvania
| | - Jane W. Newburger
- Dept of Pediatrics, Harvard Medical School, Boston, MA
- Dept of Cardiology, Boston Children’s Hospital
| | - Amy E. Roberts
- Dept of Cardiology, Boston Children’s Hospital
- Division of Genetics, Dept of Pediatrics, Boston Children’s Hospital
| | - Wendy K. Chung
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
- Dept of Medicine, Columbia University Irving Medical Center, New York, NY
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12
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Engwerda A, Kerstjens-Frederikse WS, Corsten-Janssen N, Dijkhuizen T, van Ravenswaaij-Arts CMA. The phenotypic spectrum of terminal 6q deletions based on a large cohort derived from social media and literature: a prominent role for DLL1. Orphanet J Rare Dis 2023; 18:59. [PMID: 36935482 PMCID: PMC10024851 DOI: 10.1186/s13023-023-02658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/27/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Terminal 6q deletions are rare, and the number of well-defined published cases is limited. Since parents of children with these aberrations often search the internet and unite via international social media platforms, these dedicated platforms may hold valuable knowledge about additional cases. The Chromosome 6 Project is a collaboration between researchers and clinicians at the University Medical Center Groningen and members of a Chromosome 6 support group on Facebook. The aim of the project is to improve the surveillance of patients with chromosome 6 aberrations and the support for their families by increasing the available information about these rare aberrations. This parent-driven research project makes use of information collected directly from parents via a multilingual online questionnaire. Here, we report our findings on 93 individuals with terminal 6q deletions and 11 individuals with interstitial 6q26q27 deletions, a cohort that includes 38 newly identified individuals. RESULTS Using this cohort, we can identify a common terminal 6q deletion phenotype that includes microcephaly, dysplastic outer ears, hypertelorism, vision problems, abnormal eye movements, dental abnormalities, feeding problems, recurrent infections, respiratory problems, spinal cord abnormalities, abnormal vertebrae, scoliosis, joint hypermobility, brain abnormalities (ventriculomegaly/hydrocephaly, corpus callosum abnormality and cortical dysplasia), seizures, hypotonia, ataxia, torticollis, balance problems, developmental delay, sleeping problems and hyperactivity. Other frequently reported clinical characteristics are congenital heart defects, kidney problems, abnormalities of the female genitalia, spina bifida, anal abnormalities, positional foot deformities, hypertonia and self-harming behaviour. The phenotypes were comparable up to a deletion size of 7.1 Mb, and most features could be attributed to the terminally located gene DLL1. Larger deletions that include QKI (> 7.1 Mb) lead to a more severe phenotype that includes additional clinical characteristics. CONCLUSIONS Terminal 6q deletions cause a common but highly variable phenotype. Most clinical characteristics can be linked to the smallest terminal 6q deletions that include the gene DLL1 (> 500 kb). Based on our findings, we provide recommendations for clinical follow-up and surveillance of individuals with terminal 6q deletions.
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Affiliation(s)
- Aafke Engwerda
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Nicole Corsten-Janssen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Trijnie Dijkhuizen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Conny M A van Ravenswaaij-Arts
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- ATN/Jonx, Groningen, The Netherlands.
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13
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Erbs E, Brasen CL, Lund AM, Rasmussen M. Adult patient diagnosed with NADSYN1 associated congenital NAD deficiency and analysis of NAD levels to be published in: European Journal of Medical Genetics. Eur J Med Genet 2023; 66:104698. [PMID: 36649848 DOI: 10.1016/j.ejmg.2023.104698] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/19/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Nicotinamide adenine dinucleotide (NAD) is an essential cosubstrate/coenzyme in multiple cellular redox processes and a substrate in several non-redox reactions. NADSYN1 encodes NAD synthetase 1, an enzyme in the NAD de novo synthesis pathway and the Preiss-Handler pathway, and biallelic pathogenic variants causes NAD deficiency associated with vertebral, cardiac, renal and limb defects. Szot et al. and Kortbawi et al. have reported a total of seven patients with NADSYN1 associated congenital NAD deficiency disorder with the oldest patient being seven years old. PATIENT DATA We present a male patient age 30 with a height of 130 cm and numerous skeletal malformations including segmentation defects of the spine, rib anomalies and unequal leg length as well as bilateral ptosis, cleft palate and asymmetric dysmorphic facial features. The patient underwent surgery for an aortic stenosis due to a bicuspid valve. No malformations of the kidneys or urinary tract were identified. RESULTS Trio exome sequencing revealed a homozygous missense variant in NADSYN1 c.1717G > A (p.Ala573Thr). Both parents were unaffected carriers of the variant. Analysis of NAD levels showed that the patient had a lower NAD pool compared to his unaffected siblings. The NAD pool rose approximately 25% after supplementation with nicotinamide, a NAD precursor for the salvage pathway. CONCLUSION The variant was previously reported in four patients and functional analyses by Szot et al. support the pathogenicity of the variant. We report an adult patient with NADSYN1 associated congenital NAD deficiency disorder and expand the phenotypic spectrum. We also present analysis of the NAD levels before and after supplementation with nicotinamide.
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Affiliation(s)
- Emilie Erbs
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark.
| | - Claus Lohman Brasen
- Department of Biochemistry and Immunology, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark; Department of Regional Health Research, University of Southern Denmark, Odense M, Denmark
| | - Allan Meldgaard Lund
- Center for Inherited Metabolic Disorders, Departments of Clinical Genetics and Pediatrics, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maria Rasmussen
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark; Department of Regional Health Research, University of Southern Denmark, Odense M, Denmark
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14
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Chui MMC, Mak CCY, Yu MHC, Wong SYY, Lun KS, Yung TC, Kwong AKY, Chow PC, Chung BHY. Evaluating High-Confidence Genes in Conotruncal Cardiac Defects by Gene Burden Analyses. J Am Heart Assoc 2023; 12:e028226. [PMID: 36789878 PMCID: PMC10111484 DOI: 10.1161/jaha.122.028226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background In nonsyndromic conotruncal cardiac defects, the use of next-generation sequencing for clinical diagnosis is increasingly adopted, but gene-disease associations in research are only partially translated to diagnostic panels, suggesting a need for evidence-based consensus. Methods and Results In an exome data set of 245 patients with conotruncal cardiac defects, we performed burden analysis on a high-confidence congenital heart disease gene list (n=132) with rare (<0.01%) and ultrarare (absent in the Genome Aggregation Database) protein-altering variants. Overall, we confirmed an excess of rare variants compared with ethnicity-matched controls and identified 2 known genes (GATA6, NOTCH1) and 4 candidate genes supported by the literature (ANKRD11, DOCK6, NPHP4, and STRA6). Ultrarare variant analysis was performed in combination with 3 other published studies (n=1451) and identified 3 genes (FLT4, NOTCH1, TBX1) to be significant, whereas a subgroup analysis involving 391 Chinese subjects identified only GATA6 as significant. Conclusions We suggest that these significant genes in our rare and ultrarare burden analyses warrant prioritization for clinical testing implied for rare inherited and de novo variants. Additionally, associations on ClinVar for these genes were predominantly variants of uncertain significance. Therefore, a more stringent assessment of gene-disease associations in a larger and ethnically diverse cohort is required to be prudent for future curation of conotruncal cardiac defect genes.
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Affiliation(s)
- Martin M C Chui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Mullin H C Yu
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Sandra Y Y Wong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Kin-Shing Lun
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine The Hong Kong Children's Hospital Hong Kong SAR China
| | - Tak-Cheung Yung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine The Hong Kong Children's Hospital Hong Kong SAR China
| | - Anna K Y Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China
| | - Pak-Cheong Chow
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine The Hong Kong Children's Hospital Hong Kong SAR China
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine The University of Hong Kong Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine The Hong Kong Children's Hospital Hong Kong SAR China.,Department of Paediatrics and Adolescent Medicine Queen Mary Hospital Hong Kong SAR China
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15
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Gudkov M, Thibaut L, Khushi M, Blue GM, Winlaw DS, Dunwoodie SL, Giannoulatou E. ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole-genome sequencing data. BMC Bioinformatics 2023; 24:49. [PMID: 36792982 PMCID: PMC9930243 DOI: 10.1186/s12859-023-05154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 01/19/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND A wide range of tools are available for the detection of copy number variants (CNVs) from whole-genome sequencing (WGS) data. However, none of them focus on clinically-relevant CNVs, such as those that are associated with known genetic syndromes. Such variants are often large in size, typically 1-5 Mb, but currently available CNV callers have been developed and benchmarked for the discovery of smaller variants. Thus, the ability of these programs to detect tens of real syndromic CNVs remains largely unknown. RESULTS Here we present ConanVarvar, a tool which implements a complete workflow for the targeted analysis of large germline CNVs from WGS data. ConanVarvar comes with an intuitive R Shiny graphical user interface and annotates identified variants with information about 56 associated syndromic conditions. We benchmarked ConanVarvar and four other programs on a dataset containing real and simulated syndromic CNVs larger than 1 Mb. In comparison to other tools, ConanVarvar reports 10-30 times less false-positive variants without compromising sensitivity and is quicker to run, especially on large batches of samples. CONCLUSIONS ConanVarvar is a useful instrument for primary analysis in disease sequencing studies, where large CNVs could be the cause of disease.
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Affiliation(s)
- Mikhail Gudkov
- grid.1057.30000 0000 9472 3971Victor Chang Cardiac Research Institute, Sydney, NSW 2010 Australia ,grid.1013.30000 0004 1936 834XSchool of Biomedical Engineering, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1005.40000 0004 4902 0432St Vincent’s Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW 2010 Australia
| | - Loïc Thibaut
- grid.1057.30000 0000 9472 3971Victor Chang Cardiac Research Institute, Sydney, NSW 2010 Australia ,grid.1005.40000 0004 4902 0432School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW 2052 Australia
| | - Matloob Khushi
- grid.1013.30000 0004 1936 834XSchool of Computer Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Gillian M. Blue
- grid.1013.30000 0004 1936 834XSydney Medical School, The University of Sydney, Sydney, NSW 2006 Australia ,grid.413973.b0000 0000 9690 854XHeart Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145 Australia
| | - David S. Winlaw
- grid.1013.30000 0004 1936 834XSydney Medical School, The University of Sydney, Sydney, NSW 2006 Australia ,grid.413973.b0000 0000 9690 854XHeart Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145 Australia
| | - Sally L. Dunwoodie
- grid.1057.30000 0000 9472 3971Victor Chang Cardiac Research Institute, Sydney, NSW 2010 Australia ,grid.1005.40000 0004 4902 0432St Vincent’s Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW 2010 Australia ,grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052 Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia. .,St Vincent's Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, 2010, Australia.
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16
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Muñoz H, Enríquez G, Ortega X, Pinto M, Hosiasson S, Germain A, Díaz C, Cortés F. Diagnóstico de cardiopatías congénitas: ecografía de cribado, ecocardiografía fetal y medicina de precisión. REVISTA MÉDICA CLÍNICA LAS CONDES 2023. [DOI: 10.1016/j.rmclc.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
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17
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Blue GM, Ip EKK, Troup M, Dale RC, Sholler GF, Harvey RP, Dunwoodie SL, Giannoulatou E, Winlaw DS. Insights into the genetic architecture underlying complex, critical congenital heart disease. Am Heart J 2022; 254:166-171. [PMID: 36115390 DOI: 10.1016/j.ahj.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/06/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
Congenital heart disease (CHD) has a multifactorial aetiology, raising the possibility of an underlying genetic burden, predisposing to disease but also variable expression, including variation in disease severity, and incomplete penetrance. Using whole genome sequencing (WGS), the findings of this study, indicate that complex, critical CHD is distinct from other types of disease due to increased genetic burden in common variation, specifically among established CHD genes. Additionally, these findings highlight associations with regulatory genes and environmental "stressors" in the final presentation of disease.
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Affiliation(s)
- Gillian M Blue
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Eddie K K Ip
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia
| | - Michael Troup
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia
| | - Russell C Dale
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Gary F Sholler
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia; School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - David S Winlaw
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, The University of Sydney, Sydney, Australia; Cincinnati Children's Hospital Medical Center, Heart Institute, Cardiothoracic Surgery, Cincinnati, OH.
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18
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BCOR variants are associated with X-linked recessive partial epilepsy. Epilepsy Res 2022; 187:107036. [DOI: 10.1016/j.eplepsyres.2022.107036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/12/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022]
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19
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Wilde AAM, Semsarian C, Márquez MF, Shamloo AS, Ackerman MJ, Ashley EA, Sternick EB, Barajas-Martinez H, Behr ER, Bezzina CR, Breckpot J, Charron P, Chockalingam P, Crotti L, Gollob MH, Lubitz S, Makita N, Ohno S, Ortiz-Genga M, Sacilotto L, Schulze-Bahr E, Shimizu W, Sotoodehnia N, Tadros R, Ware JS, Winlaw DS, Kaufman ES. European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the state of genetic testing for cardiac diseases. Europace 2022; 24:1307-1367. [PMID: 35373836 PMCID: PMC9435643 DOI: 10.1093/europace/euac030] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Arthur A M Wilde
- Heart Centre, Department of Cardiology, Amsterdam Universitair Medische
Centra, Amsterdam, location AMC, The Netherlands
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute,
University of Sydney, Sydney, Australia
| | - Manlio F Márquez
- Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de
México, Mexico
- Member of the Latin American Heart Rhythm Society (LAHRS)
| | | | - Michael J Ackerman
- Departments of Cardiovascular Medicine, Pediatric and Adolescent Medicine,
and Molecular Pharmacology & Experimental Therapeutics; Divisions of Heart Rhythm
Services and Pediatric Cardiology; Windland Smith Rice Genetic Heart Rhythm Clinic and
Windland Smith Rice Sudden Death Genomics Laboratory, Mayo
Clinic, Rochester, MN, USA
| | - Euan A Ashley
- Department of Cardiovascular Medicine, Stanford University,
Stanford, California, USA
| | - Eduardo Back Sternick
- Arrhythmia and Electrophysiology Unit, Biocor Institute,
Minas Gerais, Brazil; and
Member of the Latin American Heart Rhythm Society (LAHRS)
| | - Héctor Barajas-Martinez
- Cardiovascular Research, Lankenau Institute of Medical
Research, Wynnewood, PA, USA; and Member of the Latin American Heart Rhythm Society (LAHRS)
| | - Elijah R Behr
- Cardiovascular Clinical Academic Group, Institute of Molecular and Clinical
Sciences, St. George’s, University of London; St. George’s University Hospitals NHS
Foundation Trust, London, UK; Mayo Clinic Healthcare, London
| | - Connie R Bezzina
- Amsterdam UMC Heart Center, Department of Experimental
Cardiology, Amsterdam, The
Netherlands
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven,
Leuven, Belgium
| | - Philippe Charron
- Sorbonne Université, APHP, Centre de Référence des Maladies Cardiaques
Héréditaires, ICAN, Inserm UMR1166, Hôpital
Pitié-Salpêtrière, Paris, France
| | | | - Lia Crotti
- Center for Cardiac Arrhythmias of Genetic Origin,
Istituto Auxologico Italiano, IRCCS, Milan, Italy
- Cardiomyopathy Unit and Cardiac Rehabilitation Unit, San Luca Hospital,
Istituto Auxologico Italiano, IRCCS, Milan,
Italy
- Department of Medicine and Surgery, University of
Milano-Bicocca, Milan, Italy
| | - Michael H Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology,
University of Toronto, Toronto, ON, Canada
| | - Steven Lubitz
- Cardiac Arrhythmia Service, Massachusetts General Hospital and Harvard
Medical School, Boston, MA, USA
| | - Naomasa Makita
- National Cerebral and Cardiovascular Center, Research
Institute, Suita, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular
Center, Suita, Japan
| | - Martín Ortiz-Genga
- Clinical Department, Health in Code, A
Coruña, Spain; and Member of the Latin
American Heart Rhythm Society (LAHRS)
| | - Luciana Sacilotto
- Arrhythmia Unit, Instituto do Coracao, Hospital das Clinicas HCFMUSP,
Faculdade de Medicina, Universidade de Sao Paulo, Sao
Paulo, Brazil; and Member of the Latin
American Heart Rhythm Society (LAHRS)
| | - Eric Schulze-Bahr
- Institute for Genetics of Heart Diseases, University Hospital
Münster, Münster, Germany
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, Graduate School of Medicine, Nippon
Medical School, Bunkyo-ku, Tokyo, Japan
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of
Medicine, University of Washington, Seattle, WA,
USA
| | - Rafik Tadros
- Cardiovascular Genetics Center, Department of Medicine, Montreal Heart
Institute, Université de Montréal, Montreal,
Canada
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical
Sciences, Imperial College London, London,
UK
- Royal Brompton & Harefield Hospitals, Guy’s
and St. Thomas’ NHS Foundation Trust, London, UK
| | - David S Winlaw
- Cincinnati Children's Hospital Medical Centre, University of
Cincinnati, Cincinnati, OH, USA
| | - Elizabeth S Kaufman
- Metrohealth Medical Center, Case Western Reserve University,
Cleveland, OH, USA
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20
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Wilde AAM, Semsarian C, Márquez MF, Sepehri Shamloo A, Ackerman MJ, Ashley EA, Sternick Eduardo B, Barajas‐Martinez H, Behr ER, Bezzina CR, Breckpot J, Charron P, Chockalingam P, Crotti L, Gollob MH, Lubitz S, Makita N, Ohno S, Ortiz‐Genga M, Sacilotto L, Schulze‐Bahr E, Shimizu W, Sotoodehnia N, Tadros R, Ware JS, Winlaw DS, Kaufman ES, Aiba T, Bollmann A, Choi J, Dalal A, Darrieux F, Giudicessi J, Guerchicoff M, Hong K, Krahn AD, Mac Intyre C, Mackall JA, Mont L, Napolitano C, Ochoa Juan P, Peichl P, Pereira AC, Schwartz PJ, Skinner J, Stellbrink C, Tfelt‐Hansen J, Deneke T. European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the state of genetic testing for cardiac diseases. J Arrhythm 2022; 38:491-553. [PMID: 35936045 PMCID: PMC9347209 DOI: 10.1002/joa3.12717] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Arthur A. M. Wilde
- Heart Centre, Department of Cardiology, Amsterdam Universitair Medische CentraAmsterdamThe Netherlands
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary InstituteUniversity of SydneySydneyAustralia
| | - Manlio F. Márquez
- Instituto Nacional de Cardiología Ignacio ChávezCiudad de MéxicoMexico
| | | | - Michael J. Ackerman
- Departments of Cardiovascular Medicine, Pediatric and Adolescent Medicine, and Molecular Pharmacology & Experimental Therapeutics; Divisions of Heart Rhythm Services and Pediatric Cardiology; Windland Smith Rice Genetic Heart Rhythm Clinic and Windland Smith Rice Sudden Death Genomics Laboratory, Mayo ClinicRochesterMNUSA
| | - Euan A. Ashley
- Department of Cardiovascular MedicineStanford UniversityStanfordCAUSA
| | | | | | - Elijah R. Behr
- Cardiovascular Clinical Academic Group, Institute of Molecular and Clinical Sciences, St. George’sUniversity of London; St. George’s University Hospitals NHS Foundation TrustLondonUKMayo Clinic HealthcareLondon
| | - Connie R. Bezzina
- Amsterdam UMC Heart Center, Department of Experimental CardiologyAmsterdamThe Netherlands
| | - Jeroen Breckpot
- Center for Human GeneticsUniversity Hospitals LeuvenLeuvenBelgium
| | | | | | - Lia Crotti
- Center for Cardiac Arrhythmias of Genetic Origin, Istituto Auxologico Italiano, IRCCSMilanItaly
- Cardiomyopathy Unit and Cardiac Rehabilitation Unit, San Luca Hospital, Istituto Auxologico Italiano, IRCCSMilanItaly
- Department of Medicine and SurgeryUniversity of Milano‐BicoccaMilanItaly
| | - Michael H. Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of CardiologyUniversity of TorontoTorontoONCanada
| | - Steven Lubitz
- Cardiac Arrhythmia ServiceMassachusetts General Hospital and Harvard Medical SchoolBostonMAUSA
| | - Naomasa Makita
- National Cerebral and Cardiovascular CenterResearch InstituteSuitaJapan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular CenterSuitaJapan
| | | | - Luciana Sacilotto
- Arrhythmia Unit, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao PauloBrazil
| | - Eric Schulze‐Bahr
- Institute for Genetics of Heart DiseasesUniversity Hospital MünsterMünsterGermany
| | - Wataru Shimizu
- Department of Cardiovascular MedicineGraduate School of MedicineTokyoJapan
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of MedicineUniversity of WashingtonSeattleWAUSA
| | - Rafik Tadros
- Cardiovascular Genetics Center, Department of Medicine, Montreal Heart InstituteUniversité de MontréalMontrealCanada
| | - James S. Ware
- National Heart and Lung Institute and MRC London Institute of Medical SciencesImperial College LondonLondonUK
- Royal Brompton & Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation TrustLondonUK
| | - David S. Winlaw
- Cincinnati Children's Hospital Medical CentreUniversity of CincinnatiCincinnatiOHUSA
| | | | - Takeshi Aiba
- Department of Clinical Laboratory Medicine and Genetics, National Cerebral and Cardiovascular Center, SuitaOsakaJapan
| | - Andreas Bollmann
- Department of ElectrophysiologyHeart Center Leipzig at University of LeipzigLeipzigGermany
- Leipzig Heart InstituteLeipzigGermany
| | - Jong‐Il Choi
- Division of Cardiology, Department of Internal Medicine, Korea University Anam HospitalKorea University College of MedicineSeoulRepublic of Korea
| | - Aarti Dalal
- Department of Pediatrics, Division of CardiologyVanderbilt University School of MedicineNashvilleTNUSA
| | - Francisco Darrieux
- Arrhythmia Unit, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São PauloSão PauloBrazil
| | - John Giudicessi
- Department of Cardiovascular Medicine (Divisions of Heart Rhythm Services and Circulatory Failure and the Windland Smith Rice Genetic Heart Rhythm Clinic), Mayo ClinicRochesterMNUSA
| | - Mariana Guerchicoff
- Division of Pediatric Arrhythmia and Electrophysiology, Italian Hospital of Buenos AiresBuenos AiresArgentina
| | - Kui Hong
- Department of Cardiovascular MedicineThe Second Affiliated Hospital of Nanchang UniversityNanchangChina
| | - Andrew D. Krahn
- Division of CardiologyUniversity of British ColumbiaVancouverCanada
| | - Ciorsti Mac Intyre
- Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo ClinicRochesterMNUSA
| | - Judith A. Mackall
- Center for Cardiac Electrophysiology and Pacing, University Hospitals Cleveland Medical CenterCase Western Reserve University School of MedicineClevelandOHUSA
| | - Lluís Mont
- Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS). Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Cardiovasculares (CIBERCV), MadridSpain
| | - Carlo Napolitano
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri, IRCCSPaviaItaly
- Department of Molecular MedicineUniversity of PaviaPaviaItaly
| | - Pablo Ochoa Juan
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), MadridSpain
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de HierroMadridSpain
- Centro de Investigacion Biomedica en Red en Enfermedades Cariovasculares (CIBERCV), MadridSpain
| | - Petr Peichl
- Department of CardiologyInstitute for Clinical and Experimental MedicinePragueCzech Republic
| | - Alexandre C. Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart InstituteUniversity of São Paulo Medical SchoolSão PauloBrazil
- Hipercol Brasil ProgramSão PauloBrazil
| | - Peter J. Schwartz
- Center for Cardiac Arrhythmias of Genetic Origin, Istituto Auxologico Italiano, IRCCSMilanItaly
| | - Jon Skinner
- Sydney Childrens Hospital NetworkUniversity of SydneySydneyAustralia
| | - Christoph Stellbrink
- Department of Cardiology and Intensive Care MedicineUniversity Hospital Campus Klinikum BielefeldBielefeldGermany
| | - Jacob Tfelt‐Hansen
- The Department of Cardiology, the Heart Centre, Copenhagen University Hospital, Rigshopitalet, Copenhagen, Denmark; Section of genetics, Department of Forensic Medicine, Faculty of Medical SciencesUniversity of CopenhagenDenmark
| | - Thomas Deneke
- Heart Center Bad NeustadtBad Neustadt a.d. SaaleGermany
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21
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Chen J, Zhang M, Zou H, Aniagu S, Jiang Y, Chen T. Synergistic protective effects of folic acid and resveratrol against fine particulate matter-induced heart malformations in zebrafish embryos. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113825. [PMID: 36068752 DOI: 10.1016/j.ecoenv.2022.113825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/19/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Ambient fine particulate matter (PM2.5) is a major environmental health problem worldwide, and recent studies indicate that maternal PM2.5 exposure is closely associated with congenital heart diseases (CHDs) in offspring. We previously found that supplementation with folic acid (FA) or Resveratrol (RSV) could protect against heart defects in zebrafish embryos exposed to extractable organic matter (EOM) from PM2.5 by targeting aryl hydrocarbon receptor (AHR) signaling and reactive oxygen species (ROS) production respectively. Thus, we hypothesized that FA combined with RSV may have a synergistic protective effect against PM2.5-induced heart defects. To test our hypothesis, we treated zebrafish embryos with EOM in the presence or absence of FA, RSV or a combination of both. We found that RSV and FA showed a clear synergistic protection against EOM-induced heart defects in zebrafish embryos. Further studies showed that FA and RSV suppressed EOM-induced AHR activity and ROS generation respectively. Although only RSV inhibited EOM-induced apoptosis, FA enhanced the inhibitory effect of RSV. Moreover, vitamin C (VC), a typical antioxidant, also exhibits a synergistic inhibitory effect with FA on EOM-induced apoptosis and heart defects. In conclusion, supplementation with FA and RSV have a synergistic protective effect against PM2.5-induced heart defects in zebrafish embryos by targeting AHR activity and ROS production respectively. Our results indicate that, in the presence of antioxidants, FA even at a low concentration level could protect against the high risk of CHDs caused by air pollution.
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Affiliation(s)
- Jin Chen
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Mingxuan Zhang
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Hongmei Zou
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Stanley Aniagu
- Toxicology, Risk Assessment, and Research Division, Texas Commission on Environmental Quality, 12015 Park 35 Cir, Austin, TX, USA
| | - Yan Jiang
- Medical College of Soochow University, Suzhou, China.
| | - Tao Chen
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China.
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22
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Choudhury TZ, Garg V. Molecular genetic mechanisms of congenital heart disease. Curr Opin Genet Dev 2022; 75:101949. [PMID: 35816939 PMCID: PMC9673038 DOI: 10.1016/j.gde.2022.101949] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/28/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Abstract
Congenital heart disease (CHD) affects ~1% of all live births, but a definitive etiology is identified in only ~50%. The causes include chromosomal aneuploidies and copy-number variations, pathogenic variation in single genes, and exposure to environmental factors. High-throughput sequencing of large CHD patient cohorts and continued expansion of the complex molecular regulation of cardiac morphogenesis has uncovered numerous disease-causing genes, but the previously held monogenic model for CHD etiology does not sufficiently explain the heterogeneity and incomplete penetrance of CHD phenotypes. Here, we provide a summary of well-known genetic contributors to CHD and discuss emerging concepts supporting complex genetic mechanisms that may provide explanations for cases that currently lack a molecular diagnosis.
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Affiliation(s)
- Talita Z Choudhury
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Heart Center, Nationwide Children's Hospital, Columbus, OH, USA.
| | - Vidu Garg
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Heart Center, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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23
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Wilde AAM, Semsarian C, Márquez MF, Sepehri Shamloo A, Ackerman MJ, Ashley EA, Sternick EB, Barajas-Martinez H, Behr ER, Bezzina CR, Breckpot J, Charron P, Chockalingam P, Crotti L, Gollob MH, Lubitz S, Makita N, Ohno S, Ortiz-Genga M, Sacilotto L, Schulze-Bahr E, Shimizu W, Sotoodehnia N, Tadros R, Ware JS, Winlaw DS, Kaufman ES, Aiba T, Bollmann A, Choi JI, Dalal A, Darrieux F, Giudicessi J, Guerchicoff M, Hong K, Krahn AD, MacIntyre C, Mackall JA, Mont L, Napolitano C, Ochoa JP, Peichl P, Pereira AC, Schwartz PJ, Skinner J, Stellbrink C, Tfelt-Hansen J, Deneke T. European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the State of Genetic Testing for Cardiac Diseases. Heart Rhythm 2022; 19:e1-e60. [PMID: 35390533 DOI: 10.1016/j.hrthm.2022.03.1225] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Arthur A M Wilde
- Heart Centre, Department of Cardiology, Amsterdam Universitair Medische Centra, Amsterdam, location AMC, The Netherlands.
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia.
| | - Manlio F Márquez
- Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico; and Member of the Latin American Heart Rhythm Society (LAHRS).
| | | | - Michael J Ackerman
- Departments of Cardiovascular Medicine, Pediatric and Adolescent Medicine, and Molecular Pharmacology & Experimental Therapeutics; Divisions of Heart Rhythm Services and Pediatric Cardiology; Windland Smith Rice Genetic Heart Rhythm Clinic and Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Euan A Ashley
- Department of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| | - Eduardo Back Sternick
- Arrhythmia and Electrophysiology Unit, Biocor Institute, Minas Gerais, Brazil; and Member of the Latin American Heart Rhythm Society (LAHRS)
| | | | - Elijah R Behr
- Cardiovascular Clinical Academic Group, Institute of Molecular and Clinical Sciences, St. George's, University of London; St. George's University Hospitals NHS Foundation Trust, London, UK; Mayo Clinic Healthcare, London
| | - Connie R Bezzina
- Amsterdam UMC Heart Center, Department of Experimental Cardiology, Amsterdam, The Netherlands
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Charron
- Sorbonne Université, APHP, Centre de Référence des Maladies Cardiaques Héréditaires, ICAN, Inserm UMR1166, Hôpital Pitié-Salpêtrière, Paris, France
| | | | - Lia Crotti
- Center for Cardiac Arrhythmias of Genetic Origin, Istituto Auxologico Italiano, IRCCS, Milan, Italy; Cardiomyopathy Unit and Cardiac Rehabilitation Unit, San Luca Hospital, Istituto Auxologico Italiano, IRCCS, Milan, Italy; Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Michael H Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology, University of Toronto, Toronto, ON, Canada
| | - Steven Lubitz
- Cardiac Arrhythmia Service, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Naomasa Makita
- National Cerebral and Cardiovascular Center, Research Institute, Suita, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Martín Ortiz-Genga
- Clinical Department, Health in Code, A Coruña, Spain; and Member of the Latin American Heart Rhythm Society (LAHRS)
| | - Luciana Sacilotto
- Arrhythmia Unit, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil; and Member of the Latin American Heart Rhythm Society (LAHRS)
| | - Eric Schulze-Bahr
- Institute for Genetics of Heart Diseases, University Hospital Münster, Münster, Germany
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, Graduate School of Medicine, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Rafik Tadros
- Cardiovascular Genetics Center, Department of Medicine, Montreal Heart Institute, Université de Montréal, Montreal, Canada
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - David S Winlaw
- Cincinnati Children's Hospital Medical Centre, University of Cincinnati, Cincinnati, OH, USA
| | - Elizabeth S Kaufman
- Metrohealth Medical Center, Case Western Reserve University, Cleveland, OH, USA.
| | - Takeshi Aiba
- Department of Clinical Laboratory Medicine and Genetics, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Andreas Bollmann
- Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, Leipzig, Germany; Leipzig Heart Institute, Leipzig Heart Digital, Leipzig, Germany
| | - Jong-Il Choi
- Division of Cardiology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Aarti Dalal
- Department of Pediatrics, Division of Cardiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Francisco Darrieux
- Arrhythmia Unit, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - John Giudicessi
- Department of Cardiovascular Medicine (Divisions of Heart Rhythm Services and Circulatory Failure and the Windland Smith Rice Genetic Heart Rhythm Clinic), Mayo Clinic, Rochester, MN, USA
| | - Mariana Guerchicoff
- Division of Pediatric Arrhythmia and Electrophysiology, Italian Hospital of Buenos Aires, Buenos Aires, Argentina
| | - Kui Hong
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Andrew D Krahn
- Division of Cardiology, University of British Columbia, Vancouver, Canada
| | - Ciorsti MacIntyre
- Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, MN, USA
| | - Judith A Mackall
- Center for Cardiac Electrophysiology and Pacing, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Lluís Mont
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Carlo Napolitano
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri, IRCCS, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Juan Pablo Ochoa
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, Madrid, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Cariovasculares (CIBERCV), Madrid, Spain
| | - Petr Peichl
- Department of Cardiology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, São Paulo 05403-000, Brazil; Hipercol Brasil Program, São Paulo, Brazil
| | - Peter J Schwartz
- Center for Cardiac Arrhythmias of Genetic Origin, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Jon Skinner
- Sydney Childrens Hospital Network, University of Sydney, Sydney, Australia
| | - Christoph Stellbrink
- Department of Cardiology and Intensive Care Medicine, University Hospital Campus Klinikum Bielefeld, Bielefeld, Germany
| | - Jacob Tfelt-Hansen
- The Department of Cardiology, the Heart Centre, Copenhagen University Hospital, Rigshopitalet, Copenhagen, Denmark; Section of Genetics, Department of Forensic Medicine, Faculty of Medical Sciences, University of Copenhagen, Denmark
| | - Thomas Deneke
- Heart Center Bad Neustadt, Bad Neustadt a.d. Saale, Germany
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24
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Yang A, Alankarage D, Cuny H, Ip EK, Almog M, Lu J, Das D, Enriquez A, Szot JO, Humphreys DT, Blue GM, Ho JW, Winlaw DS, Dunwoodie SL, Giannoulatou E. CHDgene: A Curated Database for Congenital Heart Disease Genes. Circ Genom Precis Med 2022; 15:e003539. [DOI: 10.1161/circgen.121.003539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Andrian Yang
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
| | - Dimuthu Alankarage
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
| | - Hartmut Cuny
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
| | - Eddie K.K. Ip
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
| | - Moran Almog
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
| | - Jessica Lu
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
- UNSW Sydney, Kensington, Australia (E.K.K.I., J.L., A.E., D.T.H., S.L.D., E.G.)
| | - Debjani Das
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
| | - Annabelle Enriquez
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
- UNSW Sydney, Kensington, Australia (E.K.K.I., J.L., A.E., D.T.H., S.L.D., E.G.)
| | - Justin O. Szot
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
| | - David T. Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
- UNSW Sydney, Kensington, Australia (E.K.K.I., J.L., A.E., D.T.H., S.L.D., E.G.)
| | - Gillian M. Blue
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
- Heart Centre for Children, The Children’s Hospital at Westmead, Australia (G.M.B.)
- Sydney Medical School, The University of Sydney, Australia (G.M.B.)
| | - Joshua W.K. Ho
- School of Biomedical Sciences, University of Hong Kong (J.W.K.H.)
- Laboratory for Data Discovery for Health (D24H), Hong Kong Science Park (J.W.K.H.)
| | - David S. Winlaw
- Heart Institute, Cincinnati Children’s Hospital Medical Center, OH (D.S.W.)
| | - Sally L. Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
- UNSW Sydney, Kensington, Australia (E.K.K.I., J.L., A.E., D.T.H., S.L.D., E.G.)
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia (A.Y., D.A., H.C., E.K.K.I., M.A., J.L., D.D., A.E., J.O.S., D.T.H., G.M.B., S.L.D., E.G.)
- UNSW Sydney, Kensington, Australia (E.K.K.I., J.L., A.E., D.T.H., S.L.D., E.G.)
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25
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Jegathisawaran J, Tsiplova K, Hayeems RZ, Marshall CR, Stavropoulos DJ, Pereira SL, Thiruvahindrapuram B, Liston E, Reuter MS, Manshaei R, Cohn I, Jobling R, Kim RH, Mital S, Ungar WJ. Trio genome sequencing for developmental delay and pediatric heart conditions: A comparative microcost analysis. Genet Med 2022; 24:1027-1036. [PMID: 35219592 DOI: 10.1016/j.gim.2022.01.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Genome sequencing (GS) can aid clinical management of multiple pediatric conditions. Insurers require accurate cost information to inform funding and implementation decisions. The objective was to compare the laboratory workflows and microcosts of trio GS testing in children with developmental delay (DD) and in children with cardiac conditions. METHODS Cost items related to each step in trio GS (child and 2 parents) for both populations were identified and measured. Program costs over 5 years were estimated. Probabilistic and deterministic analyses were conducted. RESULTS The mean cost per trio GS was CAD$6634.11 (95% CI = 6352.29-6913.40) for DD and CAD$8053.10 (95% CI = 7699.30-8558.10) for cardiac conditions. The 5-year program cost was CAD$28.11 million (95% CI = 26.91-29.29) for DD and CAD$5.63 million (95% CI = 5.38-5.98) for cardiac conditions. Supplies constituted the largest cost component for both populations. The higher cost per sample for the population with cardiac conditions was due to the inclusion of pharmacogenomics, higher bioinformatics labor costs, and a more labor intensive case review. CONCLUSION This analysis indicated important variation in trio GS workflow and costs between pediatric populations in a single institution. Enhanced understanding of the clinical utility and costs of GS can inform harmonization and implementation decision-making.
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Affiliation(s)
- Jathishinie Jegathisawaran
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Kate Tsiplova
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Robin Z Hayeems
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christian R Marshall
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Eriskay Liston
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
| | - Miriam S Reuter
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Iris Cohn
- Clinical Pharmacology and Toxicology & Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rebekah Jobling
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Raymond H Kim
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health System, Toronto, Ontario, Canada; Department of Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Seema Mital
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health System, Toronto, Ontario, Canada; Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.
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26
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Shi JW, Cao H, Hong L, Ma J, Cui L, Zhang Y, Song X, Liu J, Yang Y, Lv Q, Zhang L, Wang J, Xie M. Diagnostic yield of whole exome data in fetuses aborted for conotruncal malformations. Prenat Diagn 2022; 42:852-861. [PMID: 35420166 DOI: 10.1002/pd.6147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 11/05/2022]
Abstract
OBJECTIVE We investigated a custom congenital heart disease (CHD) geneset to assess the diagnostic value of whole-exome sequencing (WES) in karyotype- and copy number variation (CNV)-negative aborted fetuses with conotruncal defects (CTD), and to explore the impact of postnatal phenotyping on genetic diagnosis. METHODS We sequentially analyzed CNV-seq and WES data from 47 CTD fetuses detected by prenatal ultrasonography. Fetuses with either a confirmed aneuploidy or pathogenic CNV were excluded from the WES analyses, which were performed following the American College of Medical Genetics and Genomics recommendations and a custom CHD-geneset. Imaging and autopsy were applied to obtain postnatal phenotypic information about aborted fetuses. RESULTS CNV-seq identified aneuploidy in 7/47 cases while 13/47 fetuses were CNV-positive. Eighty-five rare deleterious variants in 61 genes (from custom geneset) were identified by WES in the remaining fetuses. Of these, five (likely) pathogenic variants (LPV/PV) were identified in five fetuses, revealing a 10.6% incremental diagnostic yield. Furthermore, RERE:c.2461_2472delGGGATGTGGCGA was reclassified as LPV based on postnatal phenotypic data. CONCLUSION We have developed and defined a CHD gene panel that can be utilized in a subset of fetuses with CTDs. We demonstrate the utility of incorporating both prenatal and postnatal phenotypic information may facilitate WES diagnostics. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jia-Wei Shi
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Haiyan Cao
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Liu Hong
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Jing Ma
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Li Cui
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Yi Zhang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Xiaoyan Song
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Juanjuan Liu
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Yali Yang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Qing Lv
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Li Zhang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Jing Wang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Mingxing Xie
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Clinical Research Center for Medical Imaging in Hubei Province, Wuhan, 430022, China.,Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
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Ip EKK, Troup M, Xu C, Winlaw DS, Dunwoodie SL, Giannoulatou E. Benchmarking the Effectiveness and Accuracy of Multiple Mitochondrial DNA Variant Callers: Practical Implications for Clinical Application. Front Genet 2022; 13:692257. [PMID: 35350246 PMCID: PMC8957813 DOI: 10.3389/fgene.2022.692257] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/27/2022] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations contribute to human disease across a range of severity, from rare, highly penetrant mutations causal for monogenic disorders to mutations with milder contributions to phenotypes. mtDNA variation can exist in all copies of mtDNA or in a percentage of mtDNA copies and can be detected with levels as low as 1%. The large number of copies of mtDNA and the possibility of multiple alternative alleles at the same DNA nucleotide position make the task of identifying allelic variation in mtDNA very challenging. In recent years, specialized variant calling algorithms have been developed that are tailored to identify mtDNA variation from whole-genome sequencing (WGS) data. However, very few studies have systematically evaluated and compared these methods for the detection of both homoplasmy and heteroplasmy. A publicly available synthetic gold standard dataset was used to assess four mtDNA variant callers (Mutserve, mitoCaller, MitoSeek, and MToolBox), and the commonly used Genome Analysis Toolkit “best practices” pipeline, which is included in most current WGS pipelines. We also used WGS data from 126 trios and calculated the percentage of maternally inherited variants as a metric of calling accuracy, especially for homoplasmic variants. We additionally compared multiple pathogenicity prediction resources for mtDNA variants. Although the accuracy of homoplasmic variant detection was high for the majority of the callers with high concordance across callers, we found a very low concordance rate between mtDNA variant callers for heteroplasmic variants ranging from 2.8% to 3.6%, for heteroplasmy thresholds of 5% and 1%. Overall, Mutserve showed the best performance using the synthetic benchmark dataset. The analysis of mtDNA pathogenicity resources also showed low concordance in prediction results. We have shown that while homoplasmic variant calling is consistent between callers, there remains a significant discrepancy in heteroplasmic variant calling. We found that resources like population frequency databases and pathogenicity predictors are now available for variant annotation but still need refinement and improvement. With its peculiarities, the mitochondria require special considerations, and we advocate that caution needs to be taken when analyzing mtDNA data from WGS data.
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Affiliation(s)
- Eddie K K Ip
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, Sydney, NSW, Australia
| | - Michael Troup
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Colin Xu
- School of Computer Science and Engineering, Sydney, NSW, Australia
| | - David S Winlaw
- Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Centre, Heart Institute, Cincinnati, OH, United States
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, Sydney, NSW, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, Sydney, NSW, Australia
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28
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Whole genome sequencing in transposition of the great arteries and associations with clinically relevant heart, brain and laterality genes. Am Heart J 2022; 244:1-13. [PMID: 34670123 DOI: 10.1016/j.ahj.2021.10.185] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND The most common cyanotic congenital heart disease (CHD) requiring management as a neonate is transposition of great arteries (TGA). Clinically, up to 50% of TGA patients develop some form of neurodevelopmental disability (NDD), thought to have a significant genetic component. A "ciliopathy" and links with laterality disorders have been proposed. This first report of whole genome sequencing in TGA, sought to identify clinically relevant variants contributing to heart, brain and laterality defects. METHODS Initial whole genome sequencing analyses on 100 TGA patients focussed on established disease genes related to CHD (n = 107), NDD (n = 659) and heterotaxy (n = 74). Single variant as well as copy number variant analyses were conducted. Variant pathogenicity was assessed using the American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. RESULTS Fifty-five putatively damaging variants were identified in established disease genes associated with CHD, NDD and heterotaxy; however, no clinically relevant variants could be attributed to disease. Notably, case-control analyses identified significantly more predicted-damaging, silent and total variants in TGA cases than healthy controls in established CHD genes (P < .001), NDD genes (P < .001) as well as across the three gene panels (P < .001). CONCLUSION We present compelling evidence that the majority of TGA is not caused by monogenic rare variants and is most likely oligogenic and/or polygenic in nature, highlighting the complex genetic architecture and multifactorial influences on this CHD sub-type and its long-term sequelae. Assessment of variant burden in key heart, brain and/or laterality genes may be required to unravel the genetic contributions to TGA and related disabilities.
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29
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Kalisch-Smith JI, Morris EC, Strevens MAA, Redpath AN, Klaourakis K, Szumska D, Outhwaite JE, Sun X, Vieira JM, Smart N, De Val S, Riley PR, Sparrow DB. Analysis of Placental Arteriovenous Formation Reveals New Insights Into Embryos With Congenital Heart Defects. Front Genet 2022; 12:806136. [PMID: 35126469 PMCID: PMC8809359 DOI: 10.3389/fgene.2021.806136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
The placental vasculature provides the developing embryo with a circulation to deliver nutrients and dispose of waste products. However, in the mouse, the vascular components of the chorio-allantoic placenta have been largely unexplored due to a lack of well-validated molecular markers. This is required to study how these blood vessels form in development and how they are impacted by embryonic or maternal defects. Here, we employed marker analysis to characterize the arterial/arteriole and venous/venule endothelial cells (ECs) during normal mouse placental development. We reveal that placental ECs are potentially unique compared with their embryonic counterparts. We assessed embryonic markers of arterial ECs, venous ECs, and their capillary counterparts-arteriole and venule ECs. Major findings were that the arterial tree exclusively expressed Dll4, and venous vascular tree could be distinguished from the arterial tree by Endomucin (EMCN) expression levels. The relationship between the placenta and developing heart is particularly interesting. These two organs form at the same stages of embryogenesis and are well known to affect each other's growth trajectories. However, although there are many mouse models of heart defects, these are not routinely assessed for placental defects. Using these new placental vascular markers, we reveal that mouse embryos from one model of heart defects, caused by maternal iron deficiency, also have defects in the formation of the placental arterial, but not the venous, vascular tree. Defects to the embryonic cardiovascular system can therefore have a significant impact on blood flow delivery and expansion of the placental arterial tree.
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Affiliation(s)
- Jacinta I. Kalisch-Smith
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Emily C. Morris
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Mary A. A. Strevens
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Andia N. Redpath
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Kostantinos Klaourakis
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Dorota Szumska
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Ludvig Institute for Cancer Research Ltd., University of Oxford, Oxford, United Kingdom
| | | | - Xin Sun
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Joaquim Miguel Vieira
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicola Smart
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Sarah De Val
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Ludvig Institute for Cancer Research Ltd., University of Oxford, Oxford, United Kingdom
| | - Paul R. Riley
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Duncan B. Sparrow
- BHF Centre for Research Excellence, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
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30
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Akiel M. The genetic architecture behind congenital heart disease: A review of genetic and epigenetic factors. JOURNAL OF NATURE AND SCIENCE OF MEDICINE 2022. [DOI: 10.4103/jnsm.jnsm_126_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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31
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Tang CSM, Mononen M, Lam WY, Jin SC, Zhuang X, Garcia-Barcelo MM, Lin Q, Yang Y, Sahara M, Eroglu E, Chien KR, Hong H, Tam PK, Gruber PJ. Sequencing of a Chinese tetralogy of fallot cohort reveals clustering mutations in myogenic heart progenitors. JCI Insight 2021; 7:152198. [PMID: 34905512 PMCID: PMC8855809 DOI: 10.1172/jci.insight.152198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic heart defect, yet the underlying genetic mechanisms remain poorly understood. Here, we performed whole-genome sequencing analysis on 146 nonsyndromic TOF parent-offspring trios of Chinese ethnicity. Comparison of de novo variants and recessive genotypes of this data set with data from a European cohort identified both overlapping and potentially novel gene loci and revealed differential functional enrichment between cohorts. To assess the impact of these mutations on early cardiac development, we integrated single-cell and spatial transcriptomics of early human heart development with our genetic findings. We discovered that the candidate gene expression was enriched in the myogenic progenitors of the cardiac outflow tract. Moreover, subsets of the candidate genes were found in specific gene coexpression modules along the cardiomyocyte differentiation trajectory. These integrative functional analyses help dissect the pathogenesis of TOF, revealing cellular hotspots in early heart development resulting in cardiac malformations.
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Affiliation(s)
- Clara Sze Man Tang
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Mimmi Mononen
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Wai-Yee Lam
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, United States of America
| | - Xuehan Zhuang
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Qiongfen Lin
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yujia Yang
- Department of Surgery, Yale University School of Medicine, New Haven, United States of America
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Elif Eroglu
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Kenneth R Chien
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Haifa Hong
- Department of Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai, China
| | - Paul Kh Tam
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Peter J Gruber
- Yale University School of Medicine, New Haven, United States of America
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32
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Yang X, Breuss MW, Xu X, Antaki D, James KN, Stanley V, Ball LL, George RD, Wirth SA, Cao B, Nguyen A, McEvoy-Venneri J, Chai G, Nahas S, Van Der Kraan L, Ding Y, Sebat J, Gleeson JG. Developmental and temporal characteristics of clonal sperm mosaicism. Cell 2021; 184:4772-4783.e15. [PMID: 34388390 PMCID: PMC8496133 DOI: 10.1016/j.cell.2021.07.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 07/14/2021] [Indexed: 01/07/2023]
Abstract
Throughout development and aging, human cells accumulate mutations resulting in genomic mosaicism and genetic diversity at the cellular level. Mosaic mutations present in the gonads can affect both the individual and the offspring and subsequent generations. Here, we explore patterns and temporal stability of clonal mosaic mutations in male gonads by sequencing ejaculated sperm. Through 300× whole-genome sequencing of blood and sperm from healthy men, we find each ejaculate carries on average 33.3 ± 12.1 (mean ± SD) clonal mosaic variants, nearly all of which are detected in serial sampling, with the majority absent from sampled somal tissues. Their temporal stability and mutational signature suggest origins during embryonic development from a largely immutable stem cell niche. Clonal mosaicism likely contributes a transmissible, predicted pathogenic exonic variant for 1 in 15 men, representing a life-long threat of transmission for these individuals and a significant burden on human population health.
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Affiliation(s)
- Xiaoxu Yang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Martin W Breuss
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Xin Xu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Danny Antaki
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kiely N James
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Renee D George
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sara A Wirth
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Beibei Cao
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - An Nguyen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Guoliang Chai
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 92093, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.
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Helm BM, Landis BJ, Ware SM. Genetic Evaluation of Inpatient Neonatal and Infantile Congenital Heart Defects: New Findings and Review of the Literature. Genes (Basel) 2021; 12:genes12081244. [PMID: 34440418 PMCID: PMC8391303 DOI: 10.3390/genes12081244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 02/05/2023] Open
Abstract
The use of clinical genetics evaluations and testing for infants with congenital heart defects (CHDs) is subject to practice variation. This single-institution cross-sectional study of all inpatient infants with severe CHDs evaluated 440 patients using a cardiovascular genetics service (2014–2019). In total, 376 (85.5%) had chromosome microarray (CMA), of which 55 (14.6%) were diagnostic in syndromic (N = 35) or isolated (N = 20) presentations. Genetic diagnoses were made in all CHD classes. Diagnostic yield was higher in syndromic appearing infants, but geneticists’ dysmorphology exams lacked complete sensitivity and 6.5% of isolated CHD cases had diagnostic CMA. Interestingly, diagnostic results (15.8%) in left ventricular outflow tract obstruction (LVOTO) defects occurred most often in patients with isolated CHD. Geneticists’ evaluations were particularly important for second-tier molecular testing (10.5% test-specific yield), bringing the overall genetic testing yield to 17%. We assess these results in the context of previous studies. Cumulative evidence provides a rationale for comprehensive, standardized genetic evaluation in infants with severe CHDs regardless of lesion or extracardiac anomalies because genetic diagnoses that impact care are easily missed. These findings support routine CMA testing in infants with severe CHDs and underscore the importance of copy-number analysis with newer testing strategies such as exome and genome sequencing.
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Affiliation(s)
- Benjamin M. Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202, USA
- Correspondence: ; Tel.: +1-317-944-3966
| | - Benjamin J. Landis
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Stephanie M. Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
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Shickh S, Mighton C, Uleryk E, Pechlivanoglou P, Bombard Y. The clinical utility of exome and genome sequencing across clinical indications: a systematic review. Hum Genet 2021; 140:1403-1416. [PMID: 34368901 DOI: 10.1007/s00439-021-02331-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Exome sequencing and genome sequencing have the potential to improve clinical utility for patients undergoing genetic investigations. However, evidence of clinical utility is limited to pediatric populations; we aimed to fill this gap by conducting a systematic review of the literature on the clinical utility of exome/genome sequencing across disease indications in pediatric and adult populations. MEDLINE, EMBASE and Cochrane Library were searched between 2016 and 2020. Quantitative studies evaluating diagnostic yield were included; other measures of clinical utility such as changes to clinical management were documented if reported. Two reviewers screened, extracted data, and appraised risk of bias. Fifty studies met our inclusion criteria. All studies reported diagnostic yield, which ranged from 3 to 70%, with higher range of yields reported for neurological indications and acute illness ranging from 22 to 68% and 37-70%, respectively. Diagnoses triggered a range of clinical management changes including surveillance, reproductive-risk counseling, and identifying at-risk relatives in 4-100% of patients, with higher frequencies reported for acute illness ranging from 67 to 95%. The frequency of variants of uncertain significance ranged from 5 to 85% across studies with a potential trend of decreasing frequency over time and higher rates identified in patients of non-European ancestry. This review provides evidence for a higher range of diagnostic yield of exome/genome sequencing compared to standard genetic tests, particularly in neurological and acute indications. However, we identified significant heterogeneity in study procedures and outcomes, precluding a meaningful meta-analysis and certainty in the evidence available for decision-making. Future research that incorporates a comprehensive and consistent approach in capturing clinical utility of exome/genome sequencing across broader ancestral groups is necessary to improve diagnostic accuracy and yield and allow for analysis of trends over time.Prospero registration CRD42019094101.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | | | - Petros Pechlivanoglou
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
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Alankarage D, Szot JO, Pachter N, Slavotinek A, Selleri L, Shieh JT, Winlaw D, Giannoulatou E, Chapman G, Dunwoodie SL. Functional characterization of a novel PBX1 de novo missense variant identified in a patient with syndromic congenital heart disease. Hum Mol Genet 2021; 29:1068-1082. [PMID: 31625560 DOI: 10.1093/hmg/ddz231] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/13/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
Pre-B cell leukemia factor 1 (PBX1) is an essential developmental transcription factor, mutations in which have recently been associated with CAKUTHED syndrome, characterized by multiple congenital defects including congenital heart disease (CHD). During analysis of a whole-exome-sequenced cohort of heterogeneous CHD patients, we identified a de novo missense variant, PBX1:c.551G>C p.R184P, in a patient with tetralogy of Fallot with absent pulmonary valve and extra-cardiac phenotypes. Functional analysis of this variant by creating a CRISPR-Cas9 gene-edited mouse model revealed multiple congenital anomalies. Congenital heart defects (persistent truncus arteriosus and ventricular septal defect), hypoplastic lungs, hypoplastic/ectopic kidneys, aplastic adrenal glands and spleen, as well as atretic trachea and palate defects were observed in the homozygous mutant embryos at multiple stages of development. We also observed developmental anomalies in a proportion of heterozygous embryos, suggestive of a dominant mode of inheritance. Analysis of gene expression and protein levels revealed that although Pbx1 transcripts are higher in homozygotes, amounts of PBX1 protein are significantly decreased. Here, we have presented the first functional model of a missense PBX1 variant and provided strong evidence that p.R184P is disease-causal. Our findings also expand the phenotypic spectrum associated with pathogenic PBX1 variants in both humans and mice.
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Affiliation(s)
- Dimuthu Alankarage
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia
| | - Justin O Szot
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia
| | - Nick Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Western Australia, 6008 Perth, Australia.,University of Western Australia, School of Paediatrics and Child Health, Western Australia, 6009 Perth, Australia
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, 94158 CA, USA.,Institute of Human Genetics, University of California San Francisco, San Francisco, 94143 CA, USA
| | - Licia Selleri
- Institute of Human Genetics, University of California San Francisco, San Francisco, 94143 CA, USA.,Program in Craniofacial Biology, Department of Orofacial Sciences, University of California San Francisco, San Francisco, 94143 CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, 94143 CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, 94158 CA, USA.,Institute of Human Genetics, University of California San Francisco, San Francisco, 94143 CA, USA
| | - David Winlaw
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Heart Centre for Children, The Children's Hospital at Westmead, New South Wales, 2145 Sydney, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, University of Sydney, New South Wales, 2006 Sydney, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Faculty of Medicine, University of New South Wales, St Vincent's Clinical School, New South Wales, 2010 Sydney, Australia
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Faculty of Medicine, University of New South Wales, St Vincent's Clinical School, New South Wales, 2010 Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Department of Embryology, New South Wales, 2010 Sydney, Australia.,Faculty of Medicine, University of New South Wales, St Vincent's Clinical School, New South Wales, 2010 Sydney, Australia
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Diab NS, Barish S, Dong W, Zhao S, Allington G, Yu X, Kahle KT, Brueckner M, Jin SC. Molecular Genetics and Complex Inheritance of Congenital Heart Disease. Genes (Basel) 2021; 12:1020. [PMID: 34209044 PMCID: PMC8307500 DOI: 10.3390/genes12071020] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 01/09/2023] Open
Abstract
Congenital heart disease (CHD) is the most common congenital malformation and the leading cause of mortality therein. Genetic etiologies contribute to an estimated 90% of CHD cases, but so far, a molecular diagnosis remains unsolved in up to 55% of patients. Copy number variations and aneuploidy account for ~23% of cases overall, and high-throughput genomic technologies have revealed additional types of genetic variation in CHD. The first CHD risk genotypes identified through high-throughput sequencing were de novo mutations, many of which occur in chromatin modifying genes. Murine models of cardiogenesis further support the damaging nature of chromatin modifying CHD mutations. Transmitted mutations have also been identified through sequencing of population scale CHD cohorts, and many transmitted mutations are enriched in cilia genes and Notch or VEGF pathway genes. While we have come a long way in identifying the causes of CHD, more work is required to end the diagnostic odyssey for all CHD families. Complex genetic explanations of CHD are emerging but will require increasingly sophisticated analysis strategies applied to very large CHD cohorts before they can come to fruition in providing molecular diagnoses to genetically unsolved patients. In this review, we discuss the genetic architecture of CHD and biological pathways involved in its pathogenesis.
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Affiliation(s)
- Nicholas S. Diab
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Syndi Barish
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Shujuan Zhao
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
| | - Garrett Allington
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Xiaobing Yu
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Computer Science & Engineering, Washington University, St. Louis, MO 63130, USA
| | - Kristopher T. Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA;
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sheng Chih Jin
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Pediatrics, School of Medicine, Washington University, St. Louis, MO 63110, USA
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Kalisch-Smith JI, Ved N, Szumska D, Munro J, Troup M, Harris SE, Rodriguez-Caro H, Jacquemot A, Miller JJ, Stuart EM, Wolna M, Hardman E, Prin F, Lana-Elola E, Aoidi R, Fisher EMC, Tybulewicz VLJ, Mohun TJ, Lakhal-Littleton S, De Val S, Giannoulatou E, Sparrow DB. Maternal iron deficiency perturbs embryonic cardiovascular development in mice. Nat Commun 2021; 12:3447. [PMID: 34103494 PMCID: PMC8187484 DOI: 10.1038/s41467-021-23660-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 05/07/2021] [Indexed: 02/05/2023] Open
Abstract
Congenital heart disease (CHD) is the most common class of human birth defects, with a prevalence of 0.9% of births. However, two-thirds of cases have an unknown cause, and many of these are thought to be caused by in utero exposure to environmental teratogens. Here we identify a potential teratogen causing CHD in mice: maternal iron deficiency (ID). We show that maternal ID in mice causes severe cardiovascular defects in the offspring. These defects likely arise from increased retinoic acid signalling in ID embryos. The defects can be prevented by iron administration in early pregnancy. It has also been proposed that teratogen exposure may potentiate the effects of genetic predisposition to CHD through gene-environment interaction. Here we show that maternal ID increases the severity of heart and craniofacial defects in a mouse model of Down syndrome. It will be important to understand if the effects of maternal ID seen here in mice may have clinical implications for women.
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Affiliation(s)
- Jacinta I Kalisch-Smith
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Nikita Ved
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Dorota Szumska
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Jacob Munro
- Victor Chang Cardiac Research Institute, Molecular, Structural and Computational Biology Division, Sydney, NSW, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Michael Troup
- Victor Chang Cardiac Research Institute, Molecular, Structural and Computational Biology Division, Sydney, NSW, Australia
| | - Shelley E Harris
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
- Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Helena Rodriguez-Caro
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Aimée Jacquemot
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
- Ealing Hospital, London, UK
| | - Jack J Miller
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK
- Oxford Centre for Clinical Magnetic Resonance Research, John Radcliffe Hospital, Oxford, UK
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Eleanor M Stuart
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Magda Wolna
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Emily Hardman
- Heart Development Laboratory, The Francis Crick Institute, London, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Fabrice Prin
- Heart Development Laboratory, The Francis Crick Institute, London, UK
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Eva Lana-Elola
- Immune Cell Biology and Down Syndrome Laboratory, The Francis Crick Institute, London, UK
| | - Rifdat Aoidi
- Immune Cell Biology and Down Syndrome Laboratory, The Francis Crick Institute, London, UK
| | | | - Victor L J Tybulewicz
- Immune Cell Biology and Down Syndrome Laboratory, The Francis Crick Institute, London, UK
- Imperial College London, London, UK
| | - Timothy J Mohun
- Heart Development Laboratory, The Francis Crick Institute, London, UK
| | - Samira Lakhal-Littleton
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Sarah De Val
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK
- Ludwig Institute for Cancer Research Limited, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Molecular, Structural and Computational Biology Division, Sydney, NSW, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Duncan B Sparrow
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, UK.
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38
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Genetic testing for congenital heart disease: The future is now. Trends Cardiovasc Med 2021; 32:320-321. [PMID: 34062259 DOI: 10.1016/j.tcm.2021.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 11/22/2022]
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A new era of genetic testing in congenital heart disease: A review. Trends Cardiovasc Med 2021; 32:311-319. [PMID: 33964404 DOI: 10.1016/j.tcm.2021.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/07/2021] [Accepted: 04/29/2021] [Indexed: 11/24/2022]
Abstract
Genetic and genomic testing in pediatric CHD is becoming increasingly routine, and can have important psychosocial, clinical and reproductive implications. In this paper we highlight important challenges and considerations when providing genetics consults and testing in pediatric CHD and illustrate the role of a dedicated CHD genetics clinic. Key lessons include that a) a genetic diagnosis can have clinical utility that justifies testing early in life, b) adequate genetic counselling is crucial to ensure families are supported, understand the range of possible results, and are prepared for new or unexpected health information, and c) further integration of the clinical genetics and cardiology workflows will be required to effectively manage the burgeoning information arising from genetic testing. Our experience demonstrates that a dedicated CHD genetics clinic is a valuable addition to a multidisciplinary team providing care to children with CHD.
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Precision Medicine in Cardiovascular Disease: Genetics and Impact on Phenotypes: JACC Focus Seminar 1/5. J Am Coll Cardiol 2021; 77:2517-2530. [PMID: 34016265 DOI: 10.1016/j.jacc.2020.12.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/23/2022]
Abstract
Our understanding of the genetic basis of cardiovascular diseases (CVDs) has evolved rapidly. This has resulted from a combination of dedicated research in well phenotyped CVD patients, the sequencing of the human genome, and the ready accessibility and decreasing cost of next-generation sequencing technologies. This increased knowledge of the genetic basis of CVDs has heralded the era of precision medicine. This encompasses many elements including improved diagnosis, family screening, assistance with reproductive decisions, targeted therapeutics guided by both phenotype and genotype, and providing important insights into risk stratification and prognosis. Furthermore, novel insights into genetic mechanisms, clinical rollout of polygenic risk scores for common CVDs, and the promise of genome editing approaches to effectively cure disease represent some of the exciting future endeavors that will change established clinical approaches. This Part 1 of a 5-part series focuses on the underpinnings and fundamental aspects of precision medicine.
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Zhao L, Jiang WF, Yang CX, Qiao Q, Xu YJ, Shi HY, Qiu XB, Wu SH, Yang YQ. SOX17 loss-of-function variation underlying familial congenital heart disease. Eur J Med Genet 2021; 64:104211. [PMID: 33794346 DOI: 10.1016/j.ejmg.2021.104211] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/11/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
As the most prevalent form of human birth defect, congenital heart disease (CHD) contributes to substantial morbidity, mortality and socioeconomic burden worldwide. Aggregating evidence has convincingly demonstrated that genetic defects exert a pivotal role in the pathogenesis of CHD, and causative mutations in multiple genes have been causally linked to CHD. Nevertheless, CHD is of pronounced genetic heterogeneity, and the genetic components underpinning CHD in the overwhelming majority of patients remain obscure. In this research, a four-generation consanguineous family suffering from CHD transmitted in an autosomal dominant mode was recruited. By whole-exome sequencing and bioinformatics analyses as well as Sanger sequencing analyses of the family members, a new heterozygous SOX17 variation, NM_022454.4: c.553G > T; p.(Glu185*), was identified to co-segregate with CHD in the family, with complete penetrance. The nonsense variation was neither detected in 310 unrelated healthy volunteers used as controls nor retrieved in such population genetics databases as the Exome Aggregation Consortium database, Genome Aggregation Database, and the Single Nucleotide Polymorphism database. Functional assays by utilizing a dual-luciferase reporter assay system unveiled that the Glu185*-mutant SOX17 protein had no transcriptional activity on its two target genes NOTCH1 and GATA4, which have been reported to cause CHD. Furthermore, the mutation abrogated the synergistic transactivation between SOX17 and NKX2.5, another established CHD-causing transcription factor. These findings firstly indicate SOX17 loss-of-function mutation predisposes to familial CHD, which adds novel insight to the molecular mechanism of CHD, implying potential implications for genetic risk appraisal and individualized prophylaxis of the family members affected with CHD.
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Affiliation(s)
- Lan Zhao
- Department of Cardiology, Yantaishan Hospital, Yantai, 264003, Shandong Province, China
| | - Wei-Feng Jiang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Chen-Xi Yang
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Qi Qiao
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Ying-Jia Xu
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Hong-Yu Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shao-Hui Wu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China; Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China; Central Laboratory, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China.
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42
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Ekure EN, Adeyemo A, Liu H, Sokunbi O, Kalu N, Martinez AF, Owosela B, Tekendo-Ngongang C, Addissie YA, Olusegun-Joseph A, Ikebudu D, Berger SI, Muenke M, Han Z, Kruszka P. Exome Sequencing and Congenital Heart Disease in Sub-Saharan Africa. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2021; 14:e003108. [PMID: 33448881 DOI: 10.1161/circgen.120.003108] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common birth defect and affects roughly 1% of the global population. There have been many large CHD sequencing projects in developing countries but none in sub-Saharan Africa. In this exome sequencing study, we recruited families from Lagos, Nigeria, affected by structural heart disease. METHODS Ninety-eight participants with CHD and an average age of 3.6 years were recruited from Lagos, Nigeria. Exome sequencing was performed on probands and parents when available. For genes of high interest, we conducted functional studies in Drosophila using a cardiac-specific RNA interference-based gene silencing system. RESULTS The 3 most common CHDs were tetralogy of Fallot (20%), isolated ventricular septal defect (14%), and transposition of the great arteries (8%). Ten percent of the cohort had pathogenic or likely pathogenic variants in genes known to cause CHD. In 64 complete trios, we found 34 de novo variants that were not present in the African population in the Genome Aggregation Database (v3). Nineteen loss of function variants were identified using the genome-wide distribution of selection effects for heterozygous protein-truncating variants (shet). Nine genes caused a significant mortality when silenced in the Drosophila heart, including 4 novel disease genes not previously associated with CHD (UBB, EIF4G3, SREBF1, and METTL23). CONCLUSIONS This study identifies novel candidate genes and variants for CHD and facilitates comparisons with previous CHD sequencing studies in predominantly European cohorts. The study represents an important first step in genomic studies of CHD in understudied populations. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT01952171.
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Affiliation(s)
- Ekanem N Ekure
- Department of Pediatrics (E.N.E., O.S., N.K.), College of Medicine, University of Lagos/Lagos University Teaching Hospital, Nigeria
| | | | - Hanhan Liu
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore (H.L., Z.H.)
| | - Ogochukwu Sokunbi
- Department of Pediatrics (E.N.E., O.S., N.K.), College of Medicine, University of Lagos/Lagos University Teaching Hospital, Nigeria
| | - Nnenna Kalu
- Department of Pediatrics (E.N.E., O.S., N.K.), College of Medicine, University of Lagos/Lagos University Teaching Hospital, Nigeria
| | - Ariel F Martinez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda (A.F.M., B.O., C.T.-N., Y.A.A., M.M., P.K.)
| | - Babajide Owosela
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda (A.F.M., B.O., C.T.-N., Y.A.A., M.M., P.K.)
| | - Cedrik Tekendo-Ngongang
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda (A.F.M., B.O., C.T.-N., Y.A.A., M.M., P.K.)
| | - Yonit A Addissie
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda (A.F.M., B.O., C.T.-N., Y.A.A., M.M., P.K.)
| | - Akinsanya Olusegun-Joseph
- Department of Medicine (A.O.-J.), College of Medicine, University of Lagos/Lagos University Teaching Hospital, Nigeria
| | - Desmond Ikebudu
- Central Research Laboratory, College of Medicine, University of Lagos, Idi-Araba, Nigeria (D.I.)
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC (S.I.B.)
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda (A.F.M., B.O., C.T.-N., Y.A.A., M.M., P.K.)
| | - Zhe Han
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore (H.L., Z.H.)
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda (A.F.M., B.O., C.T.-N., Y.A.A., M.M., P.K.)
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43
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Jiang WF, Xu YJ, Zhao CM, Wang XH, Qiu XB, Liu X, Wu SH, Yang YQ. A novel TBX5 mutation predisposes to familial cardiac septal defects and atrial fibrillation as well as bicuspid aortic valve. Genet Mol Biol 2020; 43:e20200142. [PMID: 33306779 PMCID: PMC7783509 DOI: 10.1590/1678-4685-gmb-2020-0142] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/19/2020] [Indexed: 02/06/2023] Open
Abstract
TBX5 has been linked to Holt-Oram syndrome, with congenital heart defect (CHD) and atrial fibrillation (AF) being two major cardiac phenotypes. However, the prevalence of a TBX5 variation in patients with CHD and AF remains obscure. In this research, by sequencing analysis of TBX5 in 178 index patients with both CHD and AF, a novel heterozygous variation, NM_000192.3: c.577G>T; p.(Gly193*), was identified in one index patient with CHD and AF as well as bicuspid aortic valve (BAV), with an allele frequency of approximately 0.28%. Genetic analysis of the proband's pedigree showed that the variation co-segregated with the diseases. The pathogenic variation was not detected in 292 unrelated healthy subjects. Functional analysis by using a dual-luciferase reporter assay system showed that the Gly193*-mutant TBX5 protein failed to transcriptionally activate its target genes MYH6 and NPPA. Moreover, the mutation nullified the synergistic transactivation between TBX5 and GATA4 as well as NKX2-5. Additionally, whole-exome sequencing analysis showed no other genes contributing to the diseases. This investigation firstly links a pathogenic variant in the TBX5 gene to familial CHD and AF as well as BAV, suggesting that CHD and AF as well as BAV share a common developmental basis in a subset of patients.
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Affiliation(s)
- Wei-Feng Jiang
- Shanghai Jiao Tong University, Department of Cardiology, Shanghai Chest Hospital, Shanghai, China
| | - Ying-Jia Xu
- Fudan University, Department of Cardiology, Shanghai Fifth People's Hospital, Shanghai, China
| | - Cui-Mei Zhao
- Tongji University School of Medicine, Department of Cardiology, Tongji Hospital, Shanghai, China
| | - Xin-Hua Wang
- Shanghai Jiao Tong University School of Medicine, Department of Cardiology, Renji Hospital, Shanghai, China
| | - Xing-Biao Qiu
- Shanghai Jiao Tong University, Department of Cardiology, Shanghai Chest Hospital, Shanghai, China
| | - Xu Liu
- Shanghai Jiao Tong University, Department of Cardiology, Shanghai Chest Hospital, Shanghai, China
| | - Shao-Hui Wu
- Shanghai Jiao Tong University, Department of Cardiology, Shanghai Chest Hospital, Shanghai, China
| | - Yi-Qing Yang
- Fudan University, Department of Cardiology, Shanghai Fifth People's Hospital, Shanghai, China.,Fudan University, Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Shanghai, China.,Fudan University, Central Laboratory, Shanghai Fifth People's Hospital, Shanghai, China
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44
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Blue GM, Smith J, Sholler GF, Semsarian C, Winlaw DS. Current Practice of Genetic Testing and Counselling in Congenital Heart Disease: An Australian Perspective. Heart Lung Circ 2020; 29:1733-1736. [PMID: 32868177 DOI: 10.1016/j.hlc.2020.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/17/2020] [Accepted: 07/31/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Gillian M Blue
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Janine Smith
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Gary F Sholler
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Christopher Semsarian
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia; Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - David S Winlaw
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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45
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Molecular diagnostics for congenital heart disease: a narrative review of the current technologies and applications. JOURNAL OF BIO-X RESEARCH 2020. [DOI: 10.1097/jbr.0000000000000068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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46
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Chapman G, Moreau JLM, I P E, Szot JO, Iyer KR, Shi H, Yam MX, O’Reilly VC, Enriquez A, Greasby JA, Alankarage D, Martin EMMA, Hanna BC, Edwards M, Monger S, Blue GM, Winlaw DS, Ritchie HE, Grieve SM, Giannoulatou E, Sparrow DB, Dunwoodie SL. Functional genomics and gene-environment interaction highlight the complexity of congenital heart disease caused by Notch pathway variants. Hum Mol Genet 2020; 29:566-579. [PMID: 31813956 PMCID: PMC7068028 DOI: 10.1093/hmg/ddz270] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/05/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common birth defect and brings with it significant mortality and morbidity. The application of exome and genome sequencing has greatly improved the rate of genetic diagnosis for CHD but the cause in the majority of cases remains uncertain. It is clear that genetics, as well as environmental influences, play roles in the aetiology of CHD. Here we address both these aspects of causation with respect to the Notch signalling pathway. In our CHD cohort, variants in core Notch pathway genes account for 20% of those that cause disease, a rate that did not increase with the inclusion of genes of the broader Notch pathway and its regulators. This is reinforced by case-control burden analysis where variants in Notch pathway genes are enriched in CHD patients. This enrichment is due to variation in NOTCH1. Functional analysis of some novel missense NOTCH1 and DLL4 variants in cultured cells demonstrate reduced signalling activity, allowing variant reclassification. Although loss-of-function variants in DLL4 are known to cause Adams-Oliver syndrome, this is the first report of a hypomorphic DLL4 allele as a cause of isolated CHD. Finally, we demonstrate a gene-environment interaction in mouse embryos between Notch1 heterozygosity and low oxygen- or anti-arrhythmic drug-induced gestational hypoxia, resulting in an increased incidence of heart defects. This implies that exposure to environmental insults such as hypoxia could explain variable expressivity and penetrance of observed CHD in families carrying Notch pathway variants.
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Affiliation(s)
- Gavin Chapman
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Julie L M Moreau
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Eddie I P
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Justin O Szot
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Kavitha R Iyer
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Hongjun Shi
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- Institute for Basic Medical Sciences, Westlake University, Hangzhou, China
| | - Michelle X Yam
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | | | - Annabelle Enriquez
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, NSW, 2145, Australia
- Discipline of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Joelene A Greasby
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | | | - Ella M M A Martin
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | | | - Matthew Edwards
- Hunter Genetics, John Hunter Hospital, Newcastle, NSW, 2298, Australia
- Department of Paediatrics, School of Medicine, Western Sydney University, Sydney, NSW, 2560, Australia
| | - Steven Monger
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Gillian M Blue
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- Kids Heart Research, Heart Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW, 2145, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - David S Winlaw
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- Kids Heart Research, Heart Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW, 2145, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Helen E Ritchie
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Stuart M Grieve
- Sydney Translational Imaging Laboratory, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- Department of Radiology, Royal Prince Alfred Hospital, Sydney, NSW, 2050, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Duncan B Sparrow
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
- Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia
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47
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Murphy NM, Samarasekera TS, Macaskill L, Mullen J, Rombauts LJF. Genome sequencing of human in vitro fertilisation embryos for pathogenic variation screening. Sci Rep 2020; 10:3795. [PMID: 32123222 PMCID: PMC7052235 DOI: 10.1038/s41598-020-60704-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 02/13/2020] [Indexed: 12/22/2022] Open
Abstract
Whole-genome sequencing of preimplantation human embryos to detect and screen for genetic diseases is a technically challenging extension to preconception screening. Combining preconception genetic screening with preimplantation testing of human embryos facilitates the detection of de novo mutations and self-validates transmitted variant detection in both the reproductive couple and the embryo’s samples. Here we describe a trio testing workflow that involves whole-genome sequencing of amplified DNA from biopsied embryo trophectoderm cells and genomic DNA from both parents. Variant prediction software and annotation databases were used to assess variants of unknown significance and previously not described de novo variants in five single-gene preimplantation genetic testing couples and eleven of their embryos. Pathogenic variation, tandem repeat, copy number and structural variations were examined against variant calls for compound heterozygosity and predicted disease status was ascertained. Multiple trio testing showed complete concordance with known variants ascertained by single-nucleotide polymorphism array and uncovered de novo and transmitted pathogenic variants. This pilot study describes a method of whole-genome sequencing and analysis for embryo selection in high-risk couples to prevent early life fatal genetic conditions that adversely affect the quality of life of the individual and families.
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Affiliation(s)
- Nicholas M Murphy
- Genetic Technologies Ltd., Victoria, Australia. .,Monash IVF, Clayton, Victoria, Australia. .,GenEmbryomics Pty. Ltd., Victoria, Australia. .,Drug Delivery Disposition and Dynamics, Faculty of Pharmacy and Pharmaceutical Sciences, Parkville, Melbourne, Victoria, Australia.
| | | | | | | | - Luk J F Rombauts
- Monash IVF, Clayton, Victoria, Australia.,Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's & Newborn Program, Monash Health, Victoria, Australia
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48
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"Why and how did this happen?": development and evaluation of an information resource for parents of children with CHD. Cardiol Young 2020; 30:346-352. [PMID: 31920192 DOI: 10.1017/s1047951119003226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND The causes of CHD are complex and often unknown, leading parents to ask how and why this has happened. Genetic counselling has been shown to benefit these parents by providing information and support; however, most parents currently do not receive this service. This study aimed to develop a brochure to determine whether an information resource could improve parents' knowledge about CHD causation and inheritance and increase psychosocial functioning. METHODS In development, the resource was assessed against several readability scales and piloted. Parents of children attending preadmission clinic for surgery were included. Assessments occurred pre- and post-receiving the information resource using a purpose-designed knowledge measure and validated psychological measures. RESULTS Participant's (n = 52) knowledge scores increased significantly from the pre-questionnaire ( ${\overline x}\, = \,5/10$ , sd = 2.086) to post-questionnaire ( $\overline x\, = \,7.88/10$ , sd = 2.094, p < 0.001), with all aware that CHD can be caused by genetic factors after reading the brochure. Perceived personal control also increased from pre- ( $\overline x\, = \,11.856/18$ , sd = 4.339) to post-brochure ( $\overline x\, = \,14.644/18$ , sd = 3.733, p < 0.001), and many reported reduced feelings of guilt. No negative emotional response to the brochure was reported. The information provided was considered relevant (88%), reassuring (86%), and 88% would recommend the brochure to other parents. However, some wanted more emotional support and assistance in what to tell their child. CONCLUSIONS Use of the information resource significantly enhanced parents' knowledge of CHD causation and increased their psychosocial functioning. It is a valuable resource in the absence of genetic counselling; however, it should not replace formal genetic counselling when required.
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49
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Ip E, Chapman G, Winlaw D, Dunwoodie SL, Giannoulatou E. VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:540-545. [PMID: 31765830 PMCID: PMC7056850 DOI: 10.1016/j.gpb.2019.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 08/26/2019] [Accepted: 11/08/2019] [Indexed: 11/29/2022]
Abstract
Next-generation sequencing (NGS) technologies generate thousands to millions of genetic variants per sample. Identification of potential disease-causal variants is labor intensive as it relies on filtering using various annotation metrics and consideration of multiple pathogenicity prediction scores. We have developed VPOT (variant prioritization ordering tool), a python-based command line tool that allows researchers to create a single fully customizable pathogenicity ranking score from any number of annotation values, each with a user-defined weighting. The use of VPOT can be informative when analyzing entire cohorts, as variants in a cohort can be prioritized. VPOT also provides additional functions to allow variant filtering based on a candidate gene list or by affected status in a family pedigree. VPOT outperforms similar tools in terms of efficacy, flexibility, scalability, and computational performance. VPOT is freely available for public use at GitHub (https://github.com/VCCRI/VPOT/). Documentation for installation along with a user tutorial, a default parameter file, and test data are provided.
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Affiliation(s)
- Eddie Ip
- Victor Chang Cardiac Research Institute, Sydney 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Sydney 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia
| | - David Winlaw
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney 2145, Australia; Sydney Medical School, University of Sydney, Sydney 2050, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2033, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Sydney 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia.
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50
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Verrall CE, Blue GM, Loughran-Fowlds A, Kasparian N, Gecz J, Walker K, Dunwoodie SL, Cordina R, Sholler G, Badawi N, Winlaw D. 'Big issues' in neurodevelopment for children and adults with congenital heart disease. Open Heart 2019; 6:e000998. [PMID: 31354955 PMCID: PMC6615801 DOI: 10.1136/openhrt-2018-000998] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 04/26/2019] [Indexed: 12/12/2022] Open
Abstract
It is established that neurodevelopmental disability (NDD) is common in neonates undergoing complex surgery for congenital heart disease (CHD); however, the trajectory of disability over the lifetime of individuals with CHD is unknown. Several ‘big issues’ remain undetermined and further research is needed in order to optimise patient care and service delivery, to assess the efficacy of intervention strategies and to promote best outcomes in individuals of all ages with CHD. This review article discusses ‘gaps’ in our knowledge of NDD in CHD and proposes future directions.
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Affiliation(s)
- Charlotte E Verrall
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia
| | - Gillian M Blue
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia
| | - Alison Loughran-Fowlds
- Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia.,Grace Centre for Newborn Care, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Nadine Kasparian
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Paediatrics, School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Jozef Gecz
- Faculty of Health and Medical Sciences, University of Adelaide School of Medicine, Adelaide, South Australia, Australia
| | - Karen Walker
- Grace Centre for Newborn Care, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Sally L Dunwoodie
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,Faculties of Medicine and Science, University of New South Wales, Sydney, NSW, Australia
| | - Rachael Cordina
- Cardiology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,Discipline of Medicine, Sydney Medical School, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia
| | - Gary Sholler
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia
| | - Nadia Badawi
- Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia.,Grace Centre for Newborn Care, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - David Winlaw
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia
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