501
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Qi H, Yu L, Zhou X, Wynn J, Zhao H, Guo Y, Zhu N, Kitaygorodsky A, Hernan R, Aspelund G, Lim FY, Crombleholme T, Cusick R, Azarow K, Danko ME, Chung D, Warner BW, Mychaliska GB, Potoka D, Wagner AJ, ElFiky M, Wilson JM, Nickerson D, Bamshad M, High FA, Longoni M, Donahoe PK, Chung WK, Shen Y. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. PLoS Genet 2018; 14:e1007822. [PMID: 30532227 PMCID: PMC6301721 DOI: 10.1371/journal.pgen.1007822] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 12/20/2018] [Accepted: 11/08/2018] [Indexed: 12/24/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe birth defect that is often accompanied by other congenital anomalies. Previous exome sequencing studies for CDH have supported a role of de novo damaging variants but did not identify any recurrently mutated genes. To investigate further the genetics of CDH, we analyzed de novo coding variants in 362 proband-parent trios including 271 new trios reported in this study. We identified four unrelated individuals with damaging de novo variants in MYRF (P = 5.3x10(-8)), including one likely gene-disrupting (LGD) and three deleterious missense (D-mis) variants. Eight additional individuals with de novo LGD or missense variants were identified from our other genetic studies or from the literature. Common phenotypes of MYRF de novo variant carriers include CDH, congenital heart disease and genitourinary abnormalities, suggesting that it represents a novel syndrome. MYRF is a membrane associated transcriptional factor highly expressed in developing diaphragm and is depleted of LGD variants in the general population. All de novo missense variants aggregated in two functional protein domains. Analyzing the transcriptome of patient-derived diaphragm fibroblast cells suggest that disease associated variants abolish the transcription factor activity. Furthermore, we showed that the remaining genes with damaging variants in CDH significantly overlap with genes implicated in other developmental disorders. Gene expression patterns and patient phenotypes support pleiotropic effects of damaging variants in these genes on CDH and other developmental disorders. Finally, functional enrichment analysis implicates the disruption of regulation of gene expression, kinase activities, intra-cellular signaling, and cytoskeleton organization as pathogenic mechanisms in CDH.
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Affiliation(s)
- Hongjian Qi
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Applied Mathematics and Applied Physics, Columbia University, New York, New York, United States of America
| | - Lan Yu
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Xueya Zhou
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Julia Wynn
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Haoquan Zhao
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
| | - Yicheng Guo
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
| | - Na Zhu
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Alexander Kitaygorodsky
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
| | - Rebecca Hernan
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Gudrun Aspelund
- Department of Surgery, Columbia University Medical Center, New York, New York, United States of America
| | - Foong-Yen Lim
- Cincinnati Children's Hospital, Cincinnati, Ohio, United States of America
| | | | - Robert Cusick
- Children's Hospital & Medical Center of Omaha, University of Nebraska College of Medicine, Omaha, Nebraska, United States of America
| | - Kenneth Azarow
- Department of Surgery, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Brad W Warner
- Washington University, St. Louis Children's Hospital, St. Louis, Missouri, United States of America
| | - George B Mychaliska
- University of Michigan, CS Mott Children's Hospital, Ann Arbor, Michigan, United States of America
| | - Douglas Potoka
- Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amy J Wagner
- Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Mahmoud ElFiky
- Department of Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Jay M Wilson
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Debbie Nickerson
- University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- University of Washington, Seattle, Washington, United States of America
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mauro Longoni
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Patricia K Donahoe
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Wendy K Chung
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
- Department of Medicine, Columbia University, New York, New York, United States of America
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
- JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, New York, United States of America
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502
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Abstract
PURPOSE OF REVIEW The aim of this study is to review genetics of congenital heart disease (CHD) with a focus on clinical applications, genetic testing and clinical challenges. RECENT FINDINGS With improved clinical care, there is a rapidly expanding population of adults, especially women, with CHD who have not undergone contemporary genetic assessment and do not understand their risk for having a child with CHD. Many patients have never undergone assessment or had genetic testing. A major barrier is medical geneticist availability, resulting in this burden of care shifting to providers outside of genetics. Even with current understanding, the cause for the majority of cases of CHD is still not known. There are significant gaps in knowledge in the realms of more complex causes such as noncoding variants, multigenic contribution and small structural chromosomal anomalies. SUMMARY Standard assessment of patients with CHD, including adult survivors, is indicated. The best first-line genetic assessment for most patients with CHD is a chromosomal microarray, and this will soon evolve to be genomic sequencing with copy number variant analysis. Due to lack of medical geneticists, creative solutions to maximize the number of patients with CHD who undergo assessment with standard protocols and plans for support with result interpretation need to be explored.
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503
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Impact of genetic studies on comprehension and treatment of congenital heart disease. PROGRESS IN PEDIATRIC CARDIOLOGY 2018. [DOI: 10.1016/j.ppedcard.2018.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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504
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Desgrange A, Le Garrec JF, Meilhac SM. Left-right asymmetry in heart development and disease: forming the right loop. Development 2018; 145:145/22/dev162776. [PMID: 30467108 DOI: 10.1242/dev.162776] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Extensive studies have shown how bilateral symmetry of the vertebrate embryo is broken during early development, resulting in a molecular left-right bias in the mesoderm. However, how this early asymmetry drives the asymmetric morphogenesis of visceral organs remains poorly understood. The heart provides a striking model of left-right asymmetric morphogenesis, undergoing rightward looping to shape an initially linear heart tube and align cardiac chambers. Importantly, abnormal left-right patterning is associated with severe congenital heart defects, as exemplified in heterotaxy syndrome. Here, we compare the mechanisms underlying the rightward looping of the heart tube in fish, chick and mouse embryos. We propose that heart looping is not only a question of direction, but also one of fine-tuning shape. This is discussed in the context of evolutionary and clinical perspectives.
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Affiliation(s)
- Audrey Desgrange
- Imagine-Institut Pasteur, Laboratory of Heart Morphogenesis, 75015 Paris, France.,INSERM UMR1163, Université Paris Descartes, 75015 Paris, France
| | - Jean-François Le Garrec
- Imagine-Institut Pasteur, Laboratory of Heart Morphogenesis, 75015 Paris, France.,INSERM UMR1163, Université Paris Descartes, 75015 Paris, France
| | - Sigolène M Meilhac
- Imagine-Institut Pasteur, Laboratory of Heart Morphogenesis, 75015 Paris, France .,INSERM UMR1163, Université Paris Descartes, 75015 Paris, France
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505
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Resilience to Pain: A Peripheral Component Identified Using Induced Pluripotent Stem Cells and Dynamic Clamp. J Neurosci 2018; 39:382-392. [PMID: 30459225 DOI: 10.1523/jneurosci.2433-18.2018] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 11/21/2022] Open
Abstract
Pain is a complex process that involves both detection in the peripheral nervous system and perception in the CNS. Individual-to-individual differences in pain are well documented, but not well understood. Here we capitalized on inherited erythromelalgia (IEM), a well characterized human genetic model of chronic pain, and studied a unique family containing related IEM subjects with the same disease-causing NaV1.7 mutation, which is known to make dorsal root ganglion (DRG) neurons hyperexcitable, but different pain profiles (affected son with severe pain, affected mother with moderate pain, and an unaffected father). We show, first, that, at least in some cases, relative sensitivity to pain can be modeled in subject-specific induced pluripotent stem cell (iPSC)-derived sensory neurons in vitro; second, that, in some cases, mechanisms operating in peripheral sensory neurons contribute to interindividual differences in pain; and third, using whole exome sequencing (WES) and dynamic clamp, we show that it is possible to pinpoint a specific variant of another gene, KCNQ in this particular kindred, that modulates the excitability of iPSC-derived sensory neurons in this family. While different gene variants may modulate DRG neuron excitability and thereby contribute to interindividual differences in pain in other families, this study shows that subject-specific iPSCs can be used to model interindividual differences in pain. We further provide proof-of-principle that iPSCs, WES, and dynamic clamp can be used to investigate peripheral mechanisms and pinpoint specific gene variants that modulate pain signaling and contribute to interindividual differences in pain.SIGNIFICANCE STATEMENT Individual-to-individual differences in pain are well documented, but not well understood. In this study, we show, first, that, at least in some cases, relative sensitivity to pain can be modeled in subject-specific induced pluripotent stem cell-derived sensory neurons in vitro; second, that, in some cases, mechanisms operating in peripheral sensory neurons contribute to interindividual differences in pain; and third, using whole exome sequencing and dynamic clamp, we show that it is possible to pinpoint a specific gene variant that modulates pain signaling and contributes to interindividual differences in pain.
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506
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Pierpont ME, Brueckner M, Chung WK, Garg V, Lacro RV, McGuire AL, Mital S, Priest JR, Pu WT, Roberts A, Ware SM, Gelb BD, Russell MW. Genetic Basis for Congenital Heart Disease: Revisited: A Scientific Statement From the American Heart Association. Circulation 2018; 138:e653-e711. [PMID: 30571578 PMCID: PMC6555769 DOI: 10.1161/cir.0000000000000606] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review provides an updated summary of the state of our knowledge of the genetic contributions to the pathogenesis of congenital heart disease. Since 2007, when the initial American Heart Association scientific statement on the genetic basis of congenital heart disease was published, new genomic techniques have become widely available that have dramatically changed our understanding of the causes of congenital heart disease and, clinically, have allowed more accurate definition of the pathogeneses of congenital heart disease in patients of all ages and even prenatally. Information is presented on new molecular testing techniques and their application to congenital heart disease, both isolated and associated with other congenital anomalies or syndromes. Recent advances in the understanding of copy number variants, syndromes, RASopathies, and heterotaxy/ciliopathies are provided. Insights into new research with congenital heart disease models, including genetically manipulated animals such as mice, chicks, and zebrafish, as well as human induced pluripotent stem cell-based approaches are provided to allow an understanding of how future research breakthroughs for congenital heart disease are likely to happen. It is anticipated that this review will provide a large range of health care-related personnel, including pediatric cardiologists, pediatricians, adult cardiologists, thoracic surgeons, obstetricians, geneticists, genetic counselors, and other related clinicians, timely information on the genetic aspects of congenital heart disease. The objective is to provide a comprehensive basis for interdisciplinary care for those with congenital heart disease.
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507
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Martin HC, Jones WD, McIntyre R, Sanchez-Andrade G, Sanderson M, Stephenson JD, Jones CP, Handsaker J, Gallone G, Bruntraeger M, McRae JF, Prigmore E, Short P, Niemi M, Kaplanis J, Radford EJ, Akawi N, Balasubramanian M, Dean J, Horton R, Hulbert A, Johnson DS, Johnson K, Kumar D, Lynch SA, Mehta SG, Morton J, Parker MJ, Splitt M, Turnpenny PD, Vasudevan PC, Wright M, Bassett A, Gerety SS, Wright CF, FitzPatrick DR, Firth HV, Hurles ME, Barrett JC. Quantifying the contribution of recessive coding variation to developmental disorders. Science 2018; 362:1161-1164. [PMID: 30409806 DOI: 10.1126/science.aar6731] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 08/10/2018] [Accepted: 10/29/2018] [Indexed: 12/13/2022]
Abstract
We estimated the genome-wide contribution of recessive coding variation in 6040 families from the Deciphering Developmental Disorders study. The proportion of cases attributable to recessive coding variants was 3.6% in patients of European ancestry, compared with 50% explained by de novo coding mutations. It was higher (31%) in patients with Pakistani ancestry, owing to elevated autozygosity. Half of this recessive burden is attributable to known genes. We identified two genes not previously associated with recessive developmental disorders, KDM5B and EIF3F, and functionally validated them with mouse and cellular models. Our results suggest that recessive coding variants account for a small fraction of currently undiagnosed nonconsanguineous individuals, and that the role of noncoding variants, incomplete penetrance, and polygenic mechanisms need further exploration.
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Affiliation(s)
- Hilary C Martin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
| | - Wendy D Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Great Ormond Street Hospital for Children, National Health Service (NHS) Foundation Trust, Great Ormond Street Hospital, Great Ormond Street, London WC1N 3JH, UK
| | - Rebecca McIntyre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Mark Sanderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - James D Stephenson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Carla P Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Juliet Handsaker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Giuseppe Gallone
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Jeremy F McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elena Prigmore
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Patrick Short
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mari Niemi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Joanna Kaplanis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elizabeth J Radford
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Paediatrics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nadia Akawi
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - John Dean
- Department of Genetics, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Rachel Horton
- Wessex Clinical Genetics Service, G Level, Princess Anne Hospital, Coxford Road, Southampton SO16 5YA, UK
| | - Alice Hulbert
- Cheshire and Merseyside Clinical Genetic Service, Liverpool Women's NHS Foundation Trust, Crown Street, Liverpool L8 7SS, UK
| | - Diana S Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - Katie Johnson
- Department of Clinical Genetics, City Hospital Campus, Hucknall Road, Nottingham NG5 1PB, UK
| | - Dhavendra Kumar
- Institute of Cancer and Genetics, University Hospital of Wales, Cardiff, UK
| | | | - Sarju G Mehta
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jenny Morton
- Clinical Genetics Unit, Birmingham Women's Hospital, Edgbaston, Birmingham B15 2TG, UK
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter D Turnpenny
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Pradeep C Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Michael Wright
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Andrew Bassett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sebastian S Gerety
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Caroline F Wright
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Research, Innovation, Learning and Development (RILD), Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - David R FitzPatrick
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
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508
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Ma L, Wang J, Li L, Qiao Q, Di RM, Li XM, Xu YJ, Zhang M, Li RG, Qiu XB, Li X, Yang YQ. ISL1 loss-of-function mutation contributes to congenital heart defects. Heart Vessels 2018; 34:658-668. [PMID: 30390123 DOI: 10.1007/s00380-018-1289-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/26/2018] [Indexed: 02/08/2023]
Abstract
Congenital heart defect (CHD) is the most common form of birth deformity and is responsible for substantial morbidity and mortality in humans. Increasing evidence has convincingly demonstrated that genetic defects play a pivotal role in the pathogenesis of CHD. However, CHD is a genetically heterogeneous disorder and the genetic basis underpinning CHD in the vast majority of cases remains elusive. This study was sought to identify the pathogenic mutation in the ISL1 gene contributing to CHD. A cohort of 210 unrelated patients with CHD and a total of 256 unrelated healthy individuals used as controls were registered. The coding exons and splicing boundaries of ISL1 were sequenced in all study subjects. The functional effect of an identified ISL1 mutation was evaluated using a dual-luciferase reporter assay system. A novel heterozygous ISL1 mutation, c.409G > T or p.E137X, was identified in an index patient with congenital patent ductus arteriosus and ventricular septal defect. Analysis of the proband's pedigree revealed that the mutation co-segregated with CHD, which was transmitted in the family in an autosomal dominant pattern with complete penetrance. The nonsense mutation was absent in 512 control chromosomes. Functional analysis unveiled that the mutant ISL1 protein failed to transactivate the promoter of MEF2C, alone or in synergy with TBX20. This study firstly implicates ISL1 loss-of-function mutation with CHD in humans, which provides novel insight into the molecular mechanism of CHD, implying potential implications for genetic counseling and individually tailored treatment of CHD patients.
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Affiliation(s)
- Lan Ma
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.,Department of Ultrasound, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Juan Wang
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Li Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Qi Qiao
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Ruo-Min Di
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Xiu-Mei Li
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Ying-Jia Xu
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Min Zhang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ruo-Gu Li
- 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
| | - Xun Li
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.
| | - Yi-Qing Yang
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China. .,Department of Cardiovascular Research Laboratory, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China. .,Department of Central Laboratory, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China.
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509
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Furey CG, Zeng X, Dong W, Jin SC, Choi J, Timberlake AT, Dunbar AM, Allocco AA, Günel M, Lifton RP, Kahle KT. Human Genetics and Molecular Mechanisms of Congenital Hydrocephalus. World Neurosurg 2018; 119:441-443. [PMID: 30205212 DOI: 10.1016/j.wneu.2018.09.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Xue Zeng
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Weilai Dong
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sheng Chih Jin
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Jungmin Choi
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Andrew T Timberlake
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Ashley M Dunbar
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
| | - August A Allocco
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA; Department of Neurosurgery, Pediatrics, and Cellular & Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA; Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA; Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, USA; Department of Neurosurgery, Pediatrics, and Cellular & Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, USA
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510
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Farr GH, Imani K, Pouv D, Maves L. Functional testing of a human PBX3 variant in zebrafish reveals a potential modifier role in congenital heart defects. Dis Model Mech 2018; 11:dmm035972. [PMID: 30355621 PMCID: PMC6215422 DOI: 10.1242/dmm.035972] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/03/2018] [Indexed: 12/21/2022] Open
Abstract
Whole-genome and exome sequencing efforts are increasingly identifying candidate genetic variants associated with human disease. However, predicting and testing the pathogenicity of a genetic variant remains challenging. Genome editing allows for the rigorous functional testing of human genetic variants in animal models. Congenital heart defects (CHDs) are a prominent example of a human disorder with complex genetics. An inherited sequence variant in the human PBX3 gene (PBX3 p.A136V) has previously been shown to be enriched in a CHD patient cohort, indicating that the PBX3 p.A136V variant could be a modifier allele for CHDs. Pbx genes encode three-amino-acid loop extension (TALE)-class homeodomain-containing DNA-binding proteins with diverse roles in development and disease, and are required for heart development in mouse and zebrafish. Here, we used CRISPR-Cas9 genome editing to directly test whether this Pbx gene variant acts as a genetic modifier in zebrafish heart development. We used a single-stranded oligodeoxynucleotide to precisely introduce the human PBX3 p.A136V variant in the homologous zebrafish pbx4 gene (pbx4 p.A131V). We observed that zebrafish that are homozygous for pbx4 p.A131V are viable as adults. However, the pbx4 p.A131V variant enhances the embryonic cardiac morphogenesis phenotype caused by loss of the known cardiac specification factor, Hand2. Our study is the first example of using precision genome editing in zebrafish to demonstrate a function for a human disease-associated single nucleotide variant of unknown significance. Our work underscores the importance of testing the roles of inherited variants, not just de novo variants, as genetic modifiers of CHDs. Our study provides a novel approach toward advancing our understanding of the complex genetics of CHDs.
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Affiliation(s)
- Gist H Farr
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Kimia Imani
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- University of Washington, Seattle, WA 98195, USA
| | - Darren Pouv
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- University of Washington, Seattle, WA 98195, USA
| | - Lisa Maves
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
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511
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Alankarage D, Ip E, Szot JO, Munro J, Blue GM, Harrison K, Cuny H, Enriquez A, Troup M, Humphreys DT, Wilson M, Harvey RP, Sholler GF, Graham RM, Ho JWK, Kirk EP, Pachter N, Chapman G, Winlaw DS, Giannoulatou E, Dunwoodie SL. Identification of clinically actionable variants from genome sequencing of families with congenital heart disease. Genet Med 2018; 21:1111-1120. [DOI: 10.1038/s41436-018-0296-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 08/28/2018] [Indexed: 12/20/2022] Open
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512
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Wang S, Mandell JD, Kumar Y, Sun N, Morris MT, Arbelaez J, Nasello C, Dong S, Duhn C, Zhao X, Yang Z, Padmanabhuni SS, Yu D, King RA, Dietrich A, Khalifa N, Dahl N, Huang AY, Neale BM, Coppola G, Mathews CA, Scharf JM, Fernandez TV, Buxbaum JD, De Rubeis S, Grice DE, Xing J, Heiman GA, Tischfield JA, Paschou P, Willsey AJ, State MW. De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis. Cell Rep 2018; 24:3441-3454.e12. [PMID: 30257206 PMCID: PMC6475626 DOI: 10.1016/j.celrep.2018.08.082] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/13/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022] Open
Abstract
We previously established the contribution of de novo damaging sequence variants to Tourette disorder (TD) through whole-exome sequencing of 511 trios. Here, we sequence an additional 291 TD trios and analyze the combined set of 802 trios. We observe an overrepresentation of de novo damaging variants in simplex, but not multiplex, families; we identify a high-confidence TD risk gene, CELSR3 (cadherin EGF LAG seven-pass G-type receptor 3); we find that the genes mutated in TD patients are enriched for those related to cell polarity, suggesting a common pathway underlying pathobiology; and we confirm a statistically significant excess of de novo copy number variants in TD. Finally, we identify significant overlap of de novo sequence variants between TD and obsessive-compulsive disorder and de novo copy number variants between TD and autism spectrum disorder, consistent with shared genetic risk.
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Affiliation(s)
- Sheng Wang
- College of Biological Sciences, China Agricultural University, Beijing, China; National Institute of Biological Sciences, Beijing, China; Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey D Mandell
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Yogesh Kumar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Nawei Sun
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Montana T Morris
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Juan Arbelaez
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Cara Nasello
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Clif Duhn
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Xin Zhao
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiatong University School of Medicine, Shanghai, China
| | - Zhiyu Yang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Dongmei Yu
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert A King
- Yale Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Najah Khalifa
- Department of Neuroscience, Child and Adolescent Psychiatry Uppsala University, Uppsala, Sweden; Centre for Research and Development, Region Gävleborg, Gävle, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Alden Y Huang
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin M Neale
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Giovanni Coppola
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jeremiah M Scharf
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thomas V Fernandez
- Yale Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silvia De Rubeis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
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513
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Assoum M, Lines MA, Elpeleg O, Darmency V, Whiting S, Edvardson S, Devinsky O, Heinzen E, Hernan RR, Antignac C, Deleuze JF, Des Portes V, Bertholet-Thomas A, Belot A, Geller E, Lemesle M, Duffourd Y, Thauvin-Robinet C, Thevenon J, Chung W, Lowenstein DH, Faivre L. Further delineation of the clinical spectrum of de novo TRIM8 truncating mutations. Am J Med Genet A 2018; 176:2470-2478. [PMID: 30244534 DOI: 10.1002/ajmg.a.40357] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 04/22/2018] [Accepted: 05/17/2018] [Indexed: 12/21/2022]
Abstract
De novo mutations of the TRIM8 gene, which codes for a tripartite motif protein, have been identified using whole exome sequencing (WES) in two patients with epileptic encephalopathy (EE), but these reports were not sufficient to conclude that TRIM8 was a novel gene responsible for EE. Here we report four additional patients presenting with EE and de novo truncating mutations of TRIM8 detected by WES, and give further details of the patient previously reported by the Epi4K consortium. Epilepsy of variable severity was diagnosed in children aged 2 months to 3.5 years of age. All patients had developmental delay of variable severity with no or very limited language, often associated with behavioral anomalies and unspecific facial features or MRI brain abnormalities. The phenotypic variability observed in these patients appeared related to the severity of the epilepsy. One patient presented pharmacoresistant EE with regression, recurrent infections and nephrotic syndrome, compatible with the brain and kidney expression of TRIM8. Interestingly, all mutations were located at the highly conserved C-terminus section of TRIM8. This collaborative study confirms that TRIM8 is a novel gene responsible for EE, possibly associated with nephrotic syndrome. This report brings new evidence on the pathogenicity of TRIM8 mutations and highlights the value of data-sharing to delineate the phenotypic characteristics and biological basis of extremely rare disorders.
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Affiliation(s)
- Mirna Assoum
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France
| | - Matthew A Lines
- Division of Metabolics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Véronique Darmency
- Service de Neurophysiologie Clinique Pole Neurosciences Hôpital d'Enfants, Dijon, France
| | - Sharon Whiting
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Simon Edvardson
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Orrin Devinsky
- NYU and Saint Barnabas Epilepsy Centers NYU School of Medicine, New York, New York
| | - Erin Heinzen
- Institute for Genomic Medicine Columbia University Medical Center, New York, New York
| | - Rebecca Rose Hernan
- Department of Pediatrics and Molecular Genetics, Columbia University, New York, New York
| | - Corinne Antignac
- Laboratoire de Génétique Moléculaire, Institut de Recherche Necker Enfants Malades, CHU Paris - Hôpital Necker-Enfants Malades, Paris, France.,Equipe Néphropathies héréditaires et rein en développement, Inserm U983, Institut Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | | | - Vincent Des Portes
- Centre de référence « Déficiences Intellectuelles de causes rares », HFME, HCL F-69675, Bron, France.,ISC CNRS UMR 5304, Université de Lyon, Lyon, France
| | - Aurélie Bertholet-Thomas
- Centre de référence des rhumatismes inflammatoires et des maladies auto-immunes systémiques rares de l'enfant (RAISE), HFME HCL INSERM U1111, Lyon, France.,Service de Néphrologie, Rhumatologie et Dermatologie pédiatriques, Hôpital Femme Mère Enfant Hospices Civils de Lyon GH Est, Bron, France
| | - Alexandre Belot
- Centre de référence des rhumatismes inflammatoires et des maladies auto-immunes systémiques rares de l'enfant (RAISE), HFME HCL INSERM U1111, Lyon, France.,Service de Néphrologie, Rhumatologie et Dermatologie pédiatriques, Hôpital Femme Mère Enfant Hospices Civils de Lyon GH Est, Bron, France
| | - Eric Geller
- NYU and Saint Barnabas Epilepsy Centers NYU School of Medicine, New York, New York
| | - Martine Lemesle
- Service de Neurophysiologie Clinique Pole Neurosciences Hôpital d'Enfants, Dijon, France
| | - Yannis Duffourd
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire TRANSLAD CHU Dijon et Université de Bourgogne-Franche Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est CHU, Dijon, France
| | - Christel Thauvin-Robinet
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire TRANSLAD CHU Dijon et Université de Bourgogne-Franche Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est CHU, Dijon, France.,Centre de Référence Déficience Intellectuelle de causes rares (Defi-Bourgogne), CHU, Dijon, France
| | - Julien Thevenon
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire TRANSLAD CHU Dijon et Université de Bourgogne-Franche Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est CHU, Dijon, France
| | - Wendy Chung
- Kennedy Family Professor of Pediatrics and Medicine, Columbia University, New York, New York
| | - Daniel H Lowenstein
- Department of Neurology, University of California, San Francisco, San Francisco, California
| | - Laurence Faivre
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire TRANSLAD CHU Dijon et Université de Bourgogne-Franche Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est CHU, Dijon, France.,Centre de Référence Déficience Intellectuelle de causes rares (Defi-Bourgogne), CHU, Dijon, France
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514
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Haploinsufficiency of vascular endothelial growth factor related signaling genes is associated with tetralogy of Fallot. Genet Med 2018; 21:1001-1007. [PMID: 30232381 PMCID: PMC6752294 DOI: 10.1038/s41436-018-0260-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/26/2018] [Indexed: 12/18/2022] Open
Abstract
Purpose To determine disease-associated single-gene variants in conotruncal defects, particularly tetralogy of Fallot (TOF). Methods We analyzed for rare loss-of-function and deleterious variants in FLT4 (VEGFR3) and other genes in the vascular endothelial growth factor (VEGF) pathway, as part of a genome sequencing study involving 175 adults with TOF from a single site. Results We identified nine (5.1%) probands with novel FLT4 variants: seven loss-of-function, including an 8-kb deletion, and two predicted damaging. In ten other probands we found likely disruptive variants in VEGF-related genes: KDR (VEGFR2; two stopgain and two nonsynonymous variants), VEGFA, FGD5, BCAR1, IQGAP1, FOXO1, and PRDM1. Detection of VEGF-related variants (19/175, 10.9%) was associated with an increased prevalence of absent pulmonary valve (26.3% vs. 3.4%, p < 0.0001) and right aortic arch (52.6% vs. 29.1%, p = 0.029). Extracardiac anomalies were rare. In an attempt to replicate findings, we identified three loss-of-function or damaging variants in FLT4, KDR, and IQGAP1 in ten independent families with TOF. Conclusion Loss-of-function variants in FLT4 and KDR contribute substantially to the genetic basis of TOF. The findings support dysregulated VEGF signaling as a novel mechanism contributing to the pathogenesis of TOF.
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515
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Mullis MN, Matsui T, Schell R, Foree R, Ehrenreich IM. The complex underpinnings of genetic background effects. Nat Commun 2018; 9:3548. [PMID: 30224702 PMCID: PMC6141565 DOI: 10.1038/s41467-018-06023-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 08/09/2018] [Indexed: 12/01/2022] Open
Abstract
Genetic interactions between mutations and standing polymorphisms can cause mutations to show distinct phenotypic effects in different individuals. To characterize the genetic architecture of these so-called background effects, we genotype 1411 wild-type and mutant yeast cross progeny and measure their growth in 10 environments. Using these data, we map 1086 interactions between segregating loci and 7 different gene knockouts. Each knockout exhibits between 73 and 543 interactions, with 89% of all interactions involving higher-order epistasis between a knockout and multiple loci. Identified loci interact with as few as one knockout and as many as all seven knockouts. In mutants, loci interacting with fewer and more knockouts tend to show enhanced and reduced phenotypic effects, respectively. Cross–environment analysis reveals that most interactions between the knockouts and segregating loci also involve the environment. These results illustrate the complicated interactions between mutations, standing polymorphisms, and the environment that cause background effects. Mutations often show distinct phenotypic effects across different genetic backgrounds. Here the authors describe the genetic basis of these so-called background effects using data on genotype and growth in 10 environments from 1411 segregants from a cross of two strains of budding yeast.
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Affiliation(s)
- Martin N Mullis
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
| | - Takeshi Matsui
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
| | - Rachel Schell
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Ryan Foree
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
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516
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Genetic Imbalances in Argentinean Patients with Congenital Conotruncal Heart Defects. Genes (Basel) 2018; 9:genes9090454. [PMID: 30208644 PMCID: PMC6162499 DOI: 10.3390/genes9090454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/23/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023] Open
Abstract
Congenital conotruncal heart defects (CCHD) are a subset of serious congenital heart defects (CHD) of the cardiac outflow tracts or great arteries. Its frequency is estimated in 1/1000 live births, accounting for approximately 10–30% of all CHD cases. Chromosomal abnormalities and copy number variants (CNVs) contribute to the disease risk in patients with syndromic and/or non-syndromic forms. Although largely studied in several populations, their frequencies are barely reported for Latin American countries. The aim of this study was to analyze chromosomal abnormalities, 22q11 deletions, and other genomic imbalances in a group of Argentinean patients with CCHD of unknown etiology. A cohort of 219 patients with isolated CCHD or associated with other major anomalies were referred from different provinces of Argentina. Cytogenetic studies, Multiplex-Ligation-Probe-Amplification (MLPA) and fluorescent in situ hybridization (FISH) analysis were performed. No cytogenetic abnormalities were found. 22q11 deletion was found in 23.5% of the patients from our cohort, 66% only had CHD with no other major anomalies. None of the patients with transposition of the great vessels (TGV) carried the 22q11 deletion. Other 4 clinically relevant CNVs were also observed: a distal low copy repeat (LCR)D-E 22q11 duplication, and 17p13.3, 4q35 and TBX1 deletions. In summary, 25.8% of CCHD patients presented imbalances associated with the disease.
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517
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Stiller B, Schunkert H. Fifty generations of Icelanders help to explain a cause of aortic coarctation. Eur Heart J 2018; 39:3250-3252. [PMID: 29697798 DOI: 10.1093/eurheartj/ehy230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Barbara Stiller
- Deutsches Herzzentrum München, Lazarettstrasse 36, Munich, Germany.,Technische Universität München, Munich, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Lazarettstrasse 36, Munich, Germany.,Technische Universität München, Munich, Germany.,Deutsches Zentrum für Herz- und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
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518
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From vascular biology to vascular medicine. THE EUROBIOTECH JOURNAL 2018. [DOI: 10.2478/ebtj-2018-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Cardiovascular disorders include various conditions characterized by morphological and functional defects of the heart and vascular system. Molecular biology techniques (in particular DNA sequencing) have recently offered new insights into the etiology of cardiovascular defects, revealing their association with germline as well as somatic mutations.
Genetic tests are evaluated on the basis of their analytical and clinical validity, clinical utility, and ethical, legal and social implications. Next generation sequencing is so far the best approach for molecular diagnosis of congenital heart defects and vascular anomalies, the genetic and phenotypic heterogeneity of which makes them difficult to diagnose. Understanding the molecular causes of congenital heart defects and vascular anomalies has permitted clinical trials of drugs targeting affected genes and pathways.
The articles in this Special Issue aim to provide guidance for those concerned with diagnosis and research in the field of cardiovascular defects. The approach to genetic testing is discussed.
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519
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Choi JO, Fan C, Kim D, Sharif M, An H, Park Y. Elucidating the transactivation domain of the pleiotropic transcription factor Myrf. Sci Rep 2018; 8:13075. [PMID: 30166609 PMCID: PMC6117317 DOI: 10.1038/s41598-018-31477-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/20/2018] [Indexed: 12/31/2022] Open
Abstract
Myrf is a newly discovered membrane-bound transcription factor that plays an essential role in as diverse organisms as human, worm, and slime mold. Myrf is generated as a type-II membrane protein in the endoplasmic reticulum (ER). It forms homo-oligomers to undergo auto-cleavage that releases Myrf N-terminal fragment from the ER membrane as a homo-trimer. The homo-trimer of Myrf N-terminal fragments enters the nucleus and binds the Myrf motif to activate transcription. Despite its prominent role as a transcriptional activator, little is known about the transactivation domain of Myrf. Here, we report that the N-terminal-most (NTM) domain of Myrf is required for transcriptional activity and, when fused to a Gal4 fragment, enables it to activate transcription. The transactivation function of the NTM domain did not require homo-trimerization. We also discovered that the NTM domain can be sumoylated at three lysine residues (K123, K208, and K276), with K276 serving as the main acceptor. K276 sumoylation repressed the transactivation function of the NTM domain without affecting the stability or nuclear localization of Myrf N-terminal fragment. In sum, this study identifies the NTM domain as the transactivation domain of Myrf and the potential regulatory impact of its K276 sumoylation.
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Affiliation(s)
- Jin-Ok Choi
- Hunter James Kelly Research Institute, Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, NY, 14203, USA
| | - Chuandong Fan
- Hunter James Kelly Research Institute, Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, NY, 14203, USA
| | - Dongkyeong Kim
- Hunter James Kelly Research Institute, Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, NY, 14203, USA
| | - Mohamed Sharif
- Hunter James Kelly Research Institute, Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, NY, 14203, USA
| | - Hongjoo An
- Hunter James Kelly Research Institute, Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, NY, 14203, USA
| | - Yungki Park
- Hunter James Kelly Research Institute, Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, NY, 14203, USA.
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520
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Xiao D, Wang H, Hao L, Guo X, Ma X, Qian Y, Chen H, Ma J, Zhang J, Sheng W, Shou W, Huang G, Ma D. The roles of SMYD4 in epigenetic regulation of cardiac development in zebrafish. PLoS Genet 2018; 14:e1007578. [PMID: 30110327 PMCID: PMC6110521 DOI: 10.1371/journal.pgen.1007578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 08/27/2018] [Accepted: 07/20/2018] [Indexed: 12/15/2022] Open
Abstract
SMYD4 belongs to a family of lysine methyltransferases. We analyzed the role of smyd4 in zebrafish development by generating a smyd4 mutant zebrafish line (smyd4L544Efs*1) using the CRISPR/Cas9 technology. The maternal and zygotic smyd4L544Efs*1 mutants demonstrated severe cardiac malformations, including defects in left-right patterning and looping and hypoplastic ventricles, suggesting that smyd4 was critical for heart development. Importantly, we identified two rare SMYD4 genetic variants in a 208-patient cohort with congenital heart defects. Both biochemical and functional analyses indicated that SMYD4(G345D) was pathogenic. Our data suggested that smyd4 functions as a histone methyltransferase and, by interacting with HDAC1, also serves as a potential modulator for histone acetylation. Transcriptome and bioinformatics analyses of smyd4L544Efs*1 and wild-type developing hearts suggested that smyd4 is a key epigenetic regulator involved in regulating endoplasmic reticulum-mediated protein processing and several important metabolic pathways in developing zebrafish hearts. SMYD4 belongs to a SET and MYND domain-containing lysine methyltransferase. In zebrafish, smyd4 is ubiquitously expressed in early embryos and becomes enriched in the developing heart at 48 hours post-fertilization (hpf). We generated a smyd4 mutant zebrafish line (smyd4L544Efs*1) using the CRISPR/Cas9 technology. The maternal and zygotic smyd4L544Efs*1 mutants demonstrated a strong defect in cardiomyocyte proliferation, which led to a severe cardiac malformation, including left-right looping defects and hypoplastic ventricles. More importantly, two rare genetic variants of SMYD4 were enriched in a 208-patient cohort with congenital heart defects. Both biochemical and functional analyses indicated that SMYD4(G345D) was highly pathogenic. Using mass spectrometric analysis, SMYD4 was shown to specifically interact with histone deacetylase 1 (HDAC1) via its MYND domain. Altered di- and tri-methylation of histone 3 lysine 4 (H3K4me2 and H3K4me3) and acetylation of histone 3 in smyd4L544Efs*1 mutants suggested that smyd4 plays an important role in epigenetic regulation. Transcriptome and pathway analyses demonstrated that the expression levels of 3,856 genes were significantly altered, which included cardiac contractile genes, key signaling pathways in cardiac development, the endoplasmic reticulum-mediated protein processing pathway, and several important metabolic pathways. Taken together, our data suggests that smyd4 is a key epigenetic regulator of cardiac development.
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Affiliation(s)
- Deyong Xiao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Huijun Wang
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
| | - Lili Hao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiao Guo
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiaojing Ma
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- Pediatric Heart Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Yanyan Qian
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
| | - Hongbo Chen
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
| | - Jing Ma
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- Pediatric Heart Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei Sheng
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- Pediatric Heart Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Weinian Shou
- Cardiovascular Developmental Biology Group, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States of America
- * E-mail: (WS); (GH); (DM)
| | - Guoying Huang
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- Pediatric Heart Center, Children’s Hospital of Fudan University, Shanghai, China
- * E-mail: (WS); (GH); (DM)
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- * E-mail: (WS); (GH); (DM)
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521
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Biobank-driven genomic discovery yields new insight into atrial fibrillation biology. Nat Genet 2018; 50:1234-1239. [PMID: 30061737 DOI: 10.1038/s41588-018-0171-3] [Citation(s) in RCA: 489] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/01/2018] [Indexed: 02/07/2023]
Abstract
To identify genetic variation underlying atrial fibrillation, the most common cardiac arrhythmia, we performed a genome-wide association study of >1,000,000 people, including 60,620 atrial fibrillation cases and 970,216 controls. We identified 142 independent risk variants at 111 loci and prioritized 151 functional candidate genes likely to be involved in atrial fibrillation. Many of the identified risk variants fall near genes where more deleterious mutations have been reported to cause serious heart defects in humans (GATA4, MYH6, NKX2-5, PITX2, TBX5)1, or near genes important for striated muscle function and integrity (for example, CFL2, MYH7, PKP2, RBM20, SGCG, SSPN). Pathway and functional enrichment analyses also suggested that many of the putative atrial fibrillation genes act via cardiac structural remodeling, potentially in the form of an 'atrial cardiomyopathy'2, either during fetal heart development or as a response to stress in the adult heart.
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522
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Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell 2018; 174:505-520. [PMID: 30053424 PMCID: PMC6247911 DOI: 10.1016/j.cell.2018.06.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/11/2022]
Abstract
Although gene discovery in neuropsychiatric disorders, including autism spectrum disorder, intellectual disability, epilepsy, schizophrenia, and Tourette disorder, has accelerated, resulting in a large number of molecular clues, it has proven difficult to generate specific hypotheses without the corresponding datasets at the protein complex and functional pathway level. Here, we describe one path forward-an initiative aimed at mapping the physical and genetic interaction networks of these conditions and then using these maps to connect the genomic data to neurobiology and, ultimately, the clinic. These efforts will include a team of geneticists, structural biologists, neurobiologists, systems biologists, and clinicians, leveraging a wide array of experimental approaches and creating a collaborative infrastructure necessary for long-term investigation. This initiative will ultimately intersect with parallel studies that focus on other diseases, as there is a significant overlap with genes implicated in cancer, infectious disease, and congenital heart defects.
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Affiliation(s)
- A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Montana T Morris
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sheng Wang
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Helen R Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nia Teerikorpi
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tierney B Baum
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kevin J Bender
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tejal A Desai
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Graeme W Davis
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward Chang
- Department of Neurological Surgery, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vikaas Sohal
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel H Lowenstein
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hao Li
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Agard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael J Keiser
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian Shoichet
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark von Zastrow
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lennart Mucke
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Steven Finkbeiner
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Li Gan
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Ruth Huttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hugo J Bellen
- Departments of Molecular and Human Genetics and Neuroscience, Neurological Research Institute at TCH, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Loren M Frank
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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523
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Furey CG, Choi J, Jin SC, Zeng X, Timberlake AT, Nelson-Williams C, Mansuri MS, Lu Q, Duran D, Panchagnula S, Allocco A, Karimy JK, Khanna A, Gaillard JR, DeSpenza T, Antwi P, Loring E, Butler WE, Smith ER, Warf BC, Strahle JM, Limbrick DD, Storm PB, Heuer G, Jackson EM, Iskandar BJ, Johnston JM, Tikhonova I, Castaldi C, López-Giráldez F, Bjornson RD, Knight JR, Bilguvar K, Mane S, Alper SL, Haider S, Guclu B, Bayri Y, Sahin Y, Apuzzo MLJ, Duncan CC, DiLuna ML, Günel M, Lifton RP, Kahle KT. De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus. Neuron 2018; 99:302-314.e4. [PMID: 29983323 PMCID: PMC7839075 DOI: 10.1016/j.neuron.2018.06.019] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/03/2018] [Accepted: 06/12/2018] [Indexed: 12/30/2022]
Abstract
Congenital hydrocephalus (CH), featuring markedly enlarged brain ventricles, is thought to arise from failed cerebrospinal fluid (CSF) homeostasis and is treated with lifelong surgical CSF shunting with substantial morbidity. CH pathogenesis is poorly understood. Exome sequencing of 125 CH trios and 52 additional probands identified three genes with significant burden of rare damaging de novo or transmitted mutations: TRIM71 (p = 2.15 × 10-7), SMARCC1 (p = 8.15 × 10-10), and PTCH1 (p = 1.06 × 10-6). Additionally, two de novo duplications were identified at the SHH locus, encoding the PTCH1 ligand (p = 1.2 × 10-4). Together, these probands account for ∼10% of studied cases. Strikingly, all four genes are required for neural tube development and regulate ventricular zone neural stem cell fate. These results implicate impaired neurogenesis (rather than active CSF accumulation) in the pathogenesis of a subset of CH patients, with potential diagnostic, prognostic, and therapeutic ramifications.
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Affiliation(s)
- Charuta Gavankar Furey
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jungmin Choi
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xue Zeng
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Andrew T Timberlake
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carol Nelson-Williams
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - M Shahid Mansuri
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Qiongshi Lu
- Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, WI 53706, USA
| | - Daniel Duran
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shreyas Panchagnula
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - August Allocco
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jason K Karimy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Arjun Khanna
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jonathan R Gaillard
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Prince Antwi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Erin Loring
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - William E Butler
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Edward R Smith
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin C Warf
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer M Strahle
- Department of Neurological Surgery and Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - David D Limbrick
- Department of Neurological Surgery and Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Phillip B Storm
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Gregory Heuer
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Eric M Jackson
- Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Bermans J Iskandar
- Department of Neurological Surgery, University of Wisconsin Medical School, Madison, WI 53726, USA
| | - James M Johnston
- Department of Neurosurgery, University of Alabama School of Medicine, Birmingham, AL 35233, USA
| | - Irina Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | | | | | - Robert D Bjornson
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - James R Knight
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, UK
| | - Bulent Guclu
- Kartal Dr. Lutfi Kirdar Research and Training Hospital, Istanbul 34860, Turkey
| | - Yasar Bayri
- Acibadem Mehmet Ali Aydinlar University, School of Medicine, Department of Neurosurgery, Division of Pediatric Neurosurgery, Istanbul 34752, Turkey
| | - Yener Sahin
- Acibadem Mehmet Ali Aydinlar University, School of Medicine, Department of Neurosurgery, Division of Pediatric Neurosurgery, Istanbul 34752, Turkey
| | - Michael L J Apuzzo
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Charles C Duncan
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Michael L DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Murat Günel
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Kristopher T Kahle
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, USA.
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524
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HIRA directly targets the enhancers of selected cardiac transcription factors during in vitro differentiation of mouse embryonic stem cells. Mol Biol Rep 2018; 45:1001-1011. [PMID: 30030774 PMCID: PMC6156767 DOI: 10.1007/s11033-018-4247-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/08/2018] [Indexed: 01/06/2023]
Abstract
HIRA is a histone chaperone known to modulate gene expression through the deposition of H3.3. Conditional knockout of Hira in embryonic mouse hearts leads to cardiac septal defects. Loss of function mutation in HIRA, together with other chromatin modifiers, was found in patients with congenital heart diseases. However, the effects of HIRA on gene expression at earlier stages of cardiogenic mesoderm differentiation have not yet been studied. Differentiation of mouse embryonic stem cells (mESCs) towards cardiomyocytes mimics some of these early events and is an accepted model of these early stages. We performed RNA-Seq and H3.3-HA ChIP-seq on both WT and Hira-null mESCs and early cardiomyocyte progenitors of both genotypes. Analysis of RNA-seq data showed differential down regulation of cardiovascular development-related genes in Hira-null cardiomyocytes compared to WT cardiomyocytes. We found HIRA-dependent H3.3 deposition at these genes. In particular, we observed that HIRA influenced directly the expression of the transcription factors Gata6, Meis1 and Tbx2, essential for cardiac septation, through H3.3 deposition. We therefore identified new direct targets of HIRA during cardiac differentiation.
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525
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Zhu N, Welch CL, Wang J, Allen PM, Gonzaga-Jauregui C, Ma L, King AK, Krishnan U, Rosenzweig EB, Ivy DD, Austin ED, Hamid R, Pauciulo MW, Lutz KA, Nichols WC, Reid JG, Overton JD, Baras A, Dewey FE, Shen Y, Chung WK. Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease. Genome Med 2018; 10:56. [PMID: 30029678 PMCID: PMC6054746 DOI: 10.1186/s13073-018-0566-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/09/2018] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a rare disease characterized by distinctive changes in pulmonary arterioles that lead to progressive pulmonary arterial pressures, right-sided heart failure, and a high mortality rate. Up to 30% of adult and 75% of pediatric PAH cases are associated with congenital heart disease (PAH-CHD), and the underlying etiology is largely unknown. There are no known major risk genes for PAH-CHD. METHODS To identify novel genetic causes of PAH-CHD, we performed whole exome sequencing in 256 PAH-CHD patients. We performed a case-control gene-based association test of rare deleterious variants using 7509 gnomAD whole genome sequencing population controls. We then screened a separate cohort of 413 idiopathic and familial PAH patients without CHD for rare deleterious variants in the top association gene. RESULTS We identified SOX17 as a novel candidate risk gene (p = 5.5e-7). SOX17 is highly constrained and encodes a transcription factor involved in Wnt/β-catenin and Notch signaling during development. We estimate that rare deleterious variants contribute to approximately 3.2% of PAH-CHD cases. The coding variants identified include likely gene-disrupting (LGD) and deleterious missense, with most of the missense variants occurring in a highly conserved HMG-box protein domain. We further observed an enrichment of rare deleterious variants in putative targets of SOX17, many of which are highly expressed in developing heart and pulmonary vasculature. In the cohort of PAH without CHD, rare deleterious variants of SOX17 were observed in 0.7% of cases. CONCLUSIONS These data strongly implicate SOX17 as a new risk gene contributing to PAH-CHD as well as idiopathic/familial PAH. Replication in other PAH cohorts and further characterization of the clinical phenotype will be important to confirm the precise role of SOX17 and better estimate the contribution of genes regulated by SOX17.
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Affiliation(s)
- Na Zhu
- Department of Pediatrics, Columbia University Medical Center, New York, NY USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY USA
| | - Carrie L. Welch
- Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | - Jiayao Wang
- Department of Pediatrics, Columbia University Medical Center, New York, NY USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY USA
| | - Philip M. Allen
- Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | | | - Lijiang Ma
- Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | - Alejandra K. King
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Usha Krishnan
- Department of Pediatrics, Columbia University Medical Center, New York, NY USA
| | - Erika B. Rosenzweig
- Department of Pediatrics, Columbia University Medical Center, New York, NY USA
- Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - D. Dunbar Ivy
- Department of Pediatric Cardiology, Children’s Hospital Colorado, Denver, CO USA
| | - Eric D. Austin
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Michael W. Pauciulo
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of CincinnatiCollege of Medicine, Cincinnati, OH USA
| | - Katie A. Lutz
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - William C. Nichols
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of CincinnatiCollege of Medicine, Cincinnati, OH USA
| | - Jeffrey G. Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - John D. Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Frederick E. Dewey
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY USA
- Department of Biomedical Informatics, Columbia University, New York, NY USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY USA
- Department of Medicine, Columbia University Medical Center, New York, NY USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY USA
- New York, USA
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526
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Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes. Am J Hum Genet 2018; 103:58-73. [PMID: 29961570 DOI: 10.1016/j.ajhg.2018.05.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/24/2018] [Indexed: 01/17/2023] Open
Abstract
Integration of detailed phenotype information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. Here, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. We assessed EHR-Phenolyzer on 28 pediatric individuals with confirmed diagnoses of monogenic diseases and found that the genes with causal variants were ranked among the top 100 genes selected by EHR-Phenolyzer for 16/28 individuals (p < 2.2 × 10-16), supporting the value of phenotype-driven gene prioritization in diagnostic sequence interpretation. To assess the generalizability, we replicated this finding on an independent EHR dataset of ten individuals with a positive diagnosis from a different institution. We then assessed the broader utility by examining two additional EHR datasets, including 31 individuals who were suspected of having a Mendelian disease and underwent different types of genetic testing and 20 individuals with positive diagnoses of specific Mendelian etiologies of chronic kidney disease from exome sequencing. Finally, through several retrospective case studies, we demonstrated how combined analyses of genotype data and deep phenotype data from EHRs can expedite genetic diagnoses. In summary, EHR-Phenolyzer leverages EHR narratives to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the broader implementation of genomic medicine.
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527
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Pawlak M, Niescierowicz K, Winata CL. Decoding the Heart through Next Generation Sequencing Approaches. Genes (Basel) 2018; 9:E289. [PMID: 29880785 PMCID: PMC6027153 DOI: 10.3390/genes9060289] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/28/2018] [Accepted: 06/04/2018] [Indexed: 12/23/2022] Open
Abstract
: Vertebrate organs develop through a complex process which involves interaction between multiple signaling pathways at the molecular, cell, and tissue levels. Heart development is an example of such complex process which, when disrupted, results in congenital heart disease (CHD). This complexity necessitates a holistic approach which allows the visualization of genome-wide interaction networks, as opposed to assessment of limited subsets of factors. Genomics offers a powerful solution to address the problem of biological complexity by enabling the observation of molecular processes at a genome-wide scale. The emergence of next generation sequencing (NGS) technology has facilitated the expansion of genomics, increasing its output capacity and applicability in various biological disciplines. The application of NGS in various aspects of heart biology has resulted in new discoveries, generating novel insights into this field of study. Here we review the contributions of NGS technology into the understanding of heart development and its disruption reflected in CHD and discuss how emerging NGS based methodologies can contribute to the further understanding of heart repair.
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Affiliation(s)
- Michal Pawlak
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
| | | | - Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
- Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany.
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528
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Antwi P, Hong CS, Duran D, Jin SC, Dong W, DiLuna M, Kahle KT. A novel association of campomelic dysplasia and hydrocephalus with an unbalanced chromosomal translocation upstream of SOX9. Cold Spring Harb Mol Case Stud 2018; 4:a002766. [PMID: 29695406 PMCID: PMC5983176 DOI: 10.1101/mcs.a002766] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/26/2018] [Indexed: 11/29/2022] Open
Abstract
Campomelic dysplasia is a rare skeletal dysplasia characterized by Pierre Robin sequence, craniofacial dysmorphism, shortening and angulation of long bones, tracheobronchomalacia, and occasionally sex reversal. The disease is due to mutations in SOX9 or chromosomal rearrangements involving the long arm of Chromosome 17 harboring the SOX9 locus. SOX9, a transcription factor, is indispensible in establishing and maintaining neural stem cells in the central nervous system. We present a patient with angulation of long bones and external female genitalia on prenatal ultrasound who was subsequently found to harbor the chromosomal abnormality 46, XY, t(6;17) (p21.1;q24.3) on prenatal genetic testing. Comparative genomic hybridization revealed deletions at 6p21.1 and 17q24.3, the latter being 2.3 Mb upstream of SOX9 Whole-exome sequencing did not identify pathogenic variants in SOX9, suggesting that the 17q24.3 deletion represents a translocation breakpoint farther upstream of SOX9 than previously identified. At 2 mo of age the patient developed progressive communicating ventriculomegaly and thinning of the cortical mantle without clinical signs of increased intracranial pressure. This case suggests ventriculomegaly in some cases represents not a primary impairment of cerebrospinal fluid dynamics, but an epiphenomenon driven by a genetic dysregulation of neural progenitor cell fate.
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Affiliation(s)
- Prince Antwi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Christopher S Hong
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Daniel Duran
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Weilai Dong
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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529
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Pasipoularides A. The new era of whole-exome sequencing in congenital heart disease: brand-new insights into rare pathogenic variants. J Thorac Dis 2018; 10:S1923-S1929. [PMID: 30023082 PMCID: PMC6036033 DOI: 10.21037/jtd.2018.05.56] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/03/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Ares Pasipoularides
- Department of Surgery, Emeritus Faculty of Surgery and of Biomedical Engineering, Duke University School of Medicine and Graduate School, Durham, NC, USA
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530
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Han X, Chen S, Flynn E, Wu S, Wintner D, Shen Y. Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders. Nat Commun 2018; 9:2138. [PMID: 29849042 PMCID: PMC5976622 DOI: 10.1038/s41467-018-04552-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 05/08/2018] [Indexed: 12/21/2022] Open
Abstract
Haploinsufficiency is a major mechanism of genetic risk in developmental disorders. Accurate prediction of haploinsufficient genes is essential for prioritizing and interpreting deleterious variants in genetic studies. Current methods based on mutation intolerance in population data suffer from inadequate power for genes with short transcripts. Here we show haploinsufficiency is strongly associated with epigenomic patterns, and develop a computational method (Episcore) to predict haploinsufficiency leveraging epigenomic data from a broad range of tissue and cell types by machine learning methods. Based on data from recent exome sequencing studies on developmental disorders, Episcore achieves better performance in prioritizing likely-gene-disrupting (LGD) de novo variants than current methods. We further show that Episcore is less-biased by gene size, and complementary to mutation intolerance metrics for prioritizing LGD variants. Our approach enables new applications of epigenomic data and facilitates discovery and interpretation of novel risk variants implicated in developmental disorders. Predicting haploinsufficient genes helps to understand the genetic risk underlying developmental disorders. Here, the authors develop a Random Forest-based method that uses epigenomic data to predict haploinsufficiency, Episcore, which is complementary to methods based on mutation intolerance scores.
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Affiliation(s)
- Xinwei Han
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.,Department of Pediatrics, Columbia University, New York, NY, 10032, USA.,Constellation Pharmaceuticals, 215 First Street, Cambridge, MA, 02142, USA
| | - Siying Chen
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.,The Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY, 10032, USA
| | - Elise Flynn
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.,The Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY, 10032, USA
| | - Shuang Wu
- Department of Biostatistics, Columbia University, New York, NY, 10032, USA
| | - Dana Wintner
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA. .,Department of Biomedical Informatics, Columbia University, New York, NY, 10032, USA. .,JP Sulzberger Columbia Genome Center, Columbia University, New York, NY, 10032, USA.
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531
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Abstract
The precise location of variants in the human genome is of utmost importance. We present a unique approach, coverage-based single nucleotide variant (SNV) identification (COBASI), which uses only perfect matches between the reads of a sequence project and a reference genome to detect and accurately identify de novo SNVs. From the perfect matches, a representation of the read coverage per nucleotide along the genome, the variation landscape, is generated. SNVs are then pinpointed as significant changes in coverage and de novo SNVs can be identified with high precision. The performance of COBASI was analyzed using simulations and experimentally validated by sequencing de novo SNVs identified from a parent–offspring trio. We propose this pipeline as a useful tool for different genomic applications. The precise determination of de novo genetic variants has enormous implications across different fields of biology and medicine, particularly personalized medicine. Currently, de novo variations are identified by mapping sample reads from a parent–offspring trio to a reference genome, allowing for a certain degree of differences. While widely used, this approach often introduces false-positive (FP) results due to misaligned reads and mischaracterized sequencing errors. In a previous study, we developed an alternative approach to accurately identify single nucleotide variants (SNVs) using only perfect matches. However, this approach could be applied only to haploid regions of the genome and was computationally intensive. In this study, we present a unique approach, coverage-based single nucleotide variant identification (COBASI), which allows the exploration of the entire genome using second-generation short sequence reads without extensive computing requirements. COBASI identifies SNVs using changes in coverage of exactly matching unique substrings, and is particularly suited for pinpointing de novo SNVs. Unlike other approaches that require population frequencies across hundreds of samples to filter out any methodological biases, COBASI can be applied to detect de novo SNVs within isolated families. We demonstrate this capability through extensive simulation studies and by studying a parent–offspring trio we sequenced using short reads. Experimental validation of all 58 candidate de novo SNVs and a selection of non-de novo SNVs found in the trio confirmed zero FP calls. COBASI is available as open source at https://github.com/Laura-Gomez/COBASI for any researcher to use.
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532
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Cheng H, Dharmadhikari AV, Varland S, Ma N, Domingo D, Kleyner R, Rope AF, Yoon M, Stray-Pedersen A, Posey JE, Crews SR, Eldomery MK, Akdemir ZC, Lewis AM, Sutton VR, Rosenfeld JA, Conboy E, Agre K, Xia F, Walkiewicz M, Longoni M, High FA, van Slegtenhorst MA, Mancini GMS, Finnila CR, van Haeringen A, den Hollander N, Ruivenkamp C, Naidu S, Mahida S, Palmer EE, Murray L, Lim D, Jayakar P, Parker MJ, Giusto S, Stracuzzi E, Romano C, Beighley JS, Bernier RA, Küry S, Nizon M, Corbett MA, Shaw M, Gardner A, Barnett C, Armstrong R, Kassahn KS, Van Dijck A, Vandeweyer G, Kleefstra T, Schieving J, Jongmans MJ, de Vries BBA, Pfundt R, Kerr B, Rojas SK, Boycott KM, Person R, Willaert R, Eichler EE, Kooy RF, Yang Y, Wu JC, Lupski JR, Arnesen T, Cooper GM, Chung WK, Gecz J, Stessman HAF, Meng L, Lyon GJ. Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies. Am J Hum Genet 2018; 102:985-994. [PMID: 29656860 DOI: 10.1016/j.ajhg.2018.03.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/27/2018] [Indexed: 11/30/2022] Open
Abstract
N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.
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Affiliation(s)
| | | | - Sylvia Varland
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Ning Ma
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Deepti Domingo
- School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Robert Kleyner
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Alan F Rope
- Department of Medical Genetics, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Asbjørg Stray-Pedersen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, and Institute of Clinical Medicine, University of Oslo, N-0318 Oslo, Norway
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah R Crews
- Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA
| | - Vernon R Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erin Conboy
- Department of Clinical Genomics, Mayo Clinic, MN 55905, USA
| | - Katherine Agre
- Department of Clinical Genomics, Mayo Clinic, MN 55905, USA
| | - Fan Xia
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Magdalena Walkiewicz
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; The National Institute of Allergy and Infectious Disease, The National Institutes of Health, Bethesda, MD 20892, USA
| | - Mauro Longoni
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Frances A High
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Marjon A van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | | | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Nicolette den Hollander
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Sakkubai Naidu
- Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA
| | - Sonal Mahida
- Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA
| | - Elizabeth E Palmer
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW 2031, Australia
| | - Lucinda Murray
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Derek Lim
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL 33155, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Stefania Giusto
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | - Emanuela Stracuzzi
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | - Corrado Romano
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | | | - Raphael A Bernier
- Department of Psychiatry, University of Washington, Seattle WA, 98195, USA
| | - Sébastien Küry
- Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France
| | - Mathilde Nizon
- Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Alison Gardner
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Christopher Barnett
- Paediatric and Reproductive Genetics, South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), Adelaide, SA 5006, Australia
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Clinical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Jolanda Schieving
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Marjolijn J Jongmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9PL, UK; Division of Evolution and Genomic Sciences School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Samantha K Rojas
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | | | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Yaping Yang
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center of Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway; Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Jozef Gecz
- School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia; Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Holly A F Stessman
- Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA
| | - Linyan Meng
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA.
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533
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An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nat Genet 2018; 50:727-736. [PMID: 29700473 DOI: 10.1038/s41588-018-0107-y] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 03/06/2018] [Indexed: 11/08/2022]
Abstract
Genomic association studies of common or rare protein-coding variation have established robust statistical approaches to account for multiple testing. Here we present a comparable framework to evaluate rare and de novo noncoding single-nucleotide variants, insertion/deletions, and all classes of structural variation from whole-genome sequencing (WGS). Integrating genomic annotations at the level of nucleotides, genes, and regulatory regions, we define 51,801 annotation categories. Analyses of 519 autism spectrum disorder families did not identify association with any categories after correction for 4,123 effective tests. Without appropriate correction, biologically plausible associations are observed in both cases and controls. Despite excluding previously identified gene-disrupting mutations, coding regions still exhibited the strongest associations. Thus, in autism, the contribution of de novo noncoding variation is probably modest in comparison to that of de novo coding variants. Robust results from future WGS studies will require large cohorts and comprehensive analytical strategies that consider the substantial multiple-testing burden.
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534
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535
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Russell MW, Chung WK, Kaltman JR, Miller TA. Advances in the Understanding of the Genetic Determinants of Congenital Heart Disease and Their Impact on Clinical Outcomes. J Am Heart Assoc 2018; 7:e006906. [PMID: 29523523 PMCID: PMC5907537 DOI: 10.1161/jaha.117.006906] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mark W Russell
- Division of Pediatric Cardiology, University of Michigan, Ann Arbor, MI
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY
| | - Jonathan R Kaltman
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD
| | - Thomas A Miller
- Department of Pediatrics, University of Utah, Salt Lake City, UT
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536
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Hauser NS, Solomon BD, Vilboux T, Khromykh A, Baveja R, Bodian DL. Experience with genomic sequencing in pediatric patients with congenital cardiac defects in a large community hospital. Mol Genet Genomic Med 2018; 6:200-212. [PMID: 29368431 PMCID: PMC5902396 DOI: 10.1002/mgg3.357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Congenital cardiac defects, whether isolated or as part of a larger syndrome, are the most common type of human birth defect occurring on average in about 1% of live births depending on the malformation. As there is an expanding understanding of the underlying molecular mechanisms by which a cardiac defect may occur, there is a need to assess the current rates of diagnosis of cardiac defects by molecular sequencing in a clinical setting. METHODS AND RESULTS In this report, we evaluated 34 neonatal and pediatric patients born with a cardiac defect and their parents using exomized preexisting whole genome sequencing (WGS) data to model clinically available exon-based tests. Overall, we identified candidate variants in previously reported cardiac-related genes in 35% (12/34) of the probands. These include clearly pathogenic variants in two of 34 patients (6%) and variants of uncertain significance in relevant genes in 10 patients (26%), of these latter 10, 2 segregated with clinically apparent findings in the family trios. CONCLUSIONS These findings suggest that with current knowledge of the proteins underlying CHD, genomic sequencing can identify the underlying genetic etiology in certain patients; however, this technology currently does not have a high enough yield to be of routine clinical use in the screening of pediatric congenital cardiac defects.
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Affiliation(s)
- Natalie S. Hauser
- Inova Translational Medicine InstituteFalls ChurchVAUSA
- Inova Children's HospitalInova Health SystemFalls ChurchVAUSA
| | - Benjamin D. Solomon
- Inova Translational Medicine InstituteFalls ChurchVAUSA
- Present address:
GeneDxGaithersburgMDUSA
| | | | | | - Rajiv Baveja
- Inova Children's HospitalInova Health SystemFalls ChurchVAUSA
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Szot JO, Cuny H, Blue GM, Humphreys DT, Ip E, Harrison K, Sholler GF, Giannoulatou E, Leo P, Duncan EL, Sparrow DB, Ho JWK, Graham RM, Pachter N, Chapman G, Winlaw DS, Dunwoodie SL. A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2018; 11:e001978. [PMID: 29555671 DOI: 10.1161/circgen.117.001978] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/18/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Congenital heart disease (CHD)-structural abnormalities of the heart that arise during embryonic development-is the most common inborn malformation, affecting ≤1% of the population. However, currently, only a minority of cases can be explained by genetic abnormalities. The goal of this study was to identify disease-causal genetic variants in 30 families affected by CHD. METHODS Whole-exome sequencing was performed with the DNA of multiple family members. We utilized a 2-tiered whole-exome variant screening and interpretation procedure. First, we manually curated a high-confidence list of 90 genes known to cause CHD in humans, identified predicted damaging variants in genes on this list, and rated their pathogenicity using American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. RESULTS In 3 families (10%), we found pathogenic variants in known CHD genes TBX5, TFAP2B, and PTPN11, explaining the cardiac lesions. Second, exomes were comprehensively analyzed to identify additional predicted damaging variants that segregate with disease in CHD candidate genes. In 10 additional families (33%), likely disease-causal variants were uncovered in PBX1, CNOT1, ZFP36L2, TEK, USP34, UPF2, KDM5A, KMT2C, TIE1, TEAD2, and FLT4. CONCLUSIONS The pathogenesis of CHD could be explained using our high-confidence CHD gene list for variant filtering in a subset of cases. Furthermore, our unbiased screening procedure of family exomes implicates additional genes and variants in the pathogenesis of CHD, which suggest themselves for functional validation. This 2-tiered approach provides a means of (1) identifying clinically actionable variants and (2) identifying additional disease-causal genes, both of which are essential for improving the molecular diagnosis of CHD.
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Affiliation(s)
- Justin O Szot
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Hartmut Cuny
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Gillian M Blue
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - David T Humphreys
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Eddie Ip
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Katrina Harrison
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Gary F Sholler
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Eleni Giannoulatou
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Paul Leo
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Emma L Duncan
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Duncan B Sparrow
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Joshua W K Ho
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Robert M Graham
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Nicholas Pachter
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Gavin Chapman
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - David S Winlaw
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.)
| | - Sally L Dunwoodie
- From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.).
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Deniz E, Mis EK, Lane M, Khokha MK. CRISPR/Cas9 F0 Screening of Congenital Heart Disease Genes in Xenopus tropicalis. Methods Mol Biol 2018; 1865:163-174. [PMID: 30151766 DOI: 10.1007/978-1-4939-8784-9_12] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In the US and Europe, birth defects are the leading cause of infant mortality. Among birth defects, Congenital Heart Disease (CHD) occurs in approximately 8 out of 1000 live births, affects 1.3 million newborns per year worldwide, and has the highest mortality rate. While there is evidence to indicate that CHD does have a genetic basis, most of the CHD burden remains unexplained genetically. Fortunately, new genomics technologies are enabling genetic analyses of CHD patients. Whole exome sequencing of trios as well as copy number variations assayed by high-density SNP arrays can now be obtained at high efficiency and relatively low cost. These efforts are identifying a number of sequence variations in patients with CHD, but only a small percentage have second unrelated alleles to validate them as disease causing. Importantly, most of these candidate genes do not have an identified molecular mechanism implicating them in cardiac development. Therefore, there is a pressing need to develop rapid functional assays to evaluate candidate genes for a role in cardiac development, and then to investigate the underlying developmental mechanisms. Most recently, the advent of CRISPR/Cas9 genome editing technology has greatly enhanced the ability to manipulate and observe the function of the genome in model systems and cell culture. Incorporating the power of a developmental system such as Xenopus tropicalis with the CRISPR/Cas9 system and the microscale imaging modality optical coherence tomography (OCT), the analysis of thousands of different genes in cardiac development becomes possible.
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Affiliation(s)
- Engin Deniz
- Pediatric Genomics Discovery Program, Section of Pediatric Critical Care, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA.
| | - Emily K Mis
- Pediatric Genomics Discovery Program, Section of Pediatric Critical Care, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Section of Pediatric Critical Care, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Section of Pediatric Critical Care, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
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