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Cacheiro P, Lawson S, Van den Veyver IB, Marengo G, Zocche D, Murray SA, Duyzend M, Robinson PN, Smedley D. Lethal phenotypes in Mendelian disorders. Genet Med 2024; 26:101141. [PMID: 38629401 PMCID: PMC11232373 DOI: 10.1016/j.gim.2024.101141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
PURPOSE Existing resources that characterize the essentiality status of genes are based on either proliferation assessment in human cell lines, viability evaluation in mouse knockouts, or constraint metrics derived from human population sequencing studies. Several repositories document phenotypic annotations for rare disorders; however, there is a lack of comprehensive reporting on lethal phenotypes. METHODS We queried Online Mendelian Inheritance in Man for terms related to lethality and classified all Mendelian genes according to the earliest age of death recorded for the associated disorders, from prenatal death to no reports of premature death. We characterized the genes across these lethality categories, examined the evidence on viability from mouse models and explored how this information could be used for novel gene discovery. RESULTS We developed the Lethal Phenotypes Portal to showcase this curated catalog of human essential genes. Differences in the mode of inheritance, physiological systems affected, and disease class were found for genes in different lethality categories, as well as discrepancies between the lethal phenotypes observed in mouse and human. CONCLUSION We anticipate that this resource will aid clinicians in the diagnosis of early lethal conditions and assist researchers in investigating the properties that make these genes essential for human development.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Samantha Lawson
- ITS Research, Queen Mary University of London, London, United Kingdom
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | - Gabriel Marengo
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park and St Mark's Hospitals, London, United Kingdom
| | | | - Michael Duyzend
- Massachusetts General Hospital, Boston, MA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Peter N Robinson
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom.
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Cacheiro P, Pava D, Parkinson H, VanZanten M, Wilson R, Gunes O, The International Mouse Phenotyping Consortium, Smedley D. Computational identification of disease models through cross-species phenotype comparison. Dis Model Mech 2024; 17:dmm050604. [PMID: 38881316 PMCID: PMC11247498 DOI: 10.1242/dmm.050604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/11/2024] [Indexed: 06/18/2024] Open
Abstract
The use of standardised phenotyping screens to identify abnormal phenotypes in mouse knockouts, together with the use of ontologies to describe such phenotypic features, allows the implementation of an automated and unbiased pipeline to identify new models of disease by performing phenotype comparisons across species. Using data from the International Mouse Phenotyping Consortium (IMPC), approximately half of mouse mutants are able to mimic, at least partially, the human ortholog disease phenotypes as computed by the PhenoDigm algorithm. We found the number of phenotypic abnormalities in the mouse and the corresponding Mendelian disorder, the pleiotropy and severity of the disease, and the viability and zygosity status of the mouse knockout to be associated with the ability of mouse models to recapitulate the human disorder. An analysis of the IMPC impact on disease gene discovery through a publication-tracking system revealed that the resource has been implicated in at least 109 validated rare disease-gene associations over the last decade.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Diego Pava
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maya VanZanten
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert Wilson
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Osman Gunes
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
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Duyzend MH, Cacheiro P, Jacobsen JO, Giordano J, Brand H, Wapner RJ, Talkowski ME, Robinson PN, Smedley D. Improving prenatal diagnosis through standards and aggregation. Prenat Diagn 2024; 44:454-464. [PMID: 38242839 PMCID: PMC11006584 DOI: 10.1002/pd.6522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 01/21/2024]
Abstract
Advances in sequencing and imaging technologies enable enhanced assessment in the prenatal space, with a goal to diagnose and predict the natural history of disease, to direct targeted therapies, and to implement clinical management, including transfer of care, election of supportive care, and selection of surgical interventions. The current lack of standardization and aggregation stymies variant interpretation and gene discovery, which hinders the provision of prenatal precision medicine, leaving clinicians and patients without an accurate diagnosis. With large amounts of data generated, it is imperative to establish standards for data collection, processing, and aggregation. Aggregated and homogeneously processed genetic and phenotypic data permits dissection of the genomic architecture of prenatal presentations of disease and provides a dataset on which data analysis algorithms can be tuned to the prenatal space. Here we discuss the importance of generating aggregate data sets and how the prenatal space is driving the development of interoperable standards and phenotype-driven tools.
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Affiliation(s)
- Michael H. Duyzend
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Pilar Cacheiro
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Julius O.B. Jacobsen
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jessica Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J. Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E. Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
| | - Damian Smedley
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
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Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB, Sirota M, Snyder MP, Yatsenko SA, Rajkovic A. Miscarriage risk assessment: a bioinformatic approach to identifying candidate lethal genes and variants. Hum Genet 2024; 143:185-195. [PMID: 38302665 PMCID: PMC10881709 DOI: 10.1007/s00439-023-02637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/25/2023] [Indexed: 02/03/2024]
Abstract
PURPOSE Miscarriage, often resulting from a variety of genetic factors, is a common pregnancy outcome. Preconception genetic carrier screening (PGCS) identifies at-risk partners for newborn genetic disorders; however, PGCS panels currently lack miscarriage-related genes. In this study, we evaluated the potential impact of both known and candidate genes on prenatal lethality and the effectiveness of PGCS in diverse populations. METHODS We analyzed 125,748 human exome sequences and mouse and human gene function databases. Our goals were to identify genes crucial for human fetal survival (lethal genes), to find variants not present in a homozygous state in healthy humans, and to estimate carrier rates of known and candidate lethal genes in various populations and ethnic groups. RESULTS This study identified 138 genes in which heterozygous lethal variants are present in the general population with a frequency of 0.5% or greater. Screening for these 138 genes could identify 4.6% (in the Finnish population) to 39.8% (in the East Asian population) of couples at risk of miscarriage. This explains the cause of pregnancy loss in approximately 1.1-10% of cases affected by biallelic lethal variants. CONCLUSION This study has identified a set of genes and variants potentially associated with lethality across different ethnic backgrounds. The variation of these genes across ethnic groups underscores the need for a comprehensive, pan-ethnic PGCS panel that includes genes related to miscarriage.
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Affiliation(s)
- Mona Aminbeidokhti
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jia-Hua Qu
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Shweta Belur
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Hakan Cakmak
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Eleni Jaswa
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Ruth B Lathi
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, 94305, USA
| | - Marina Sirota
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, 94143, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Svetlana A Yatsenko
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Magee-Women Research Institute, Pittsburgh, PA, 15213, USA
| | - Aleksandar Rajkovic
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA.
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA.
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Cacheiro P, Lawson S, Van den Veyver IB, Marengo G, Zocche D, Murray SA, Duyzend M, Robinson PN, Smedley D. Lethal phenotypes in Mendelian disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.12.24301168. [PMID: 38260283 PMCID: PMC10802756 DOI: 10.1101/2024.01.12.24301168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Essential genes are those whose function is required for cell proliferation and/or organism survival. A gene's intolerance to loss-of-function can be allocated within a spectrum, as opposed to being considered a binary feature, since this function might be essential at different stages of development, genetic backgrounds or other contexts. Existing resources that collect and characterise the essentiality status of genes are based on either proliferation assessment in human cell lines, embryonic and postnatal viability evaluation in different model organisms, and gene metrics such as intolerance to variation scores derived from human population sequencing studies. There are also several repositories available that document phenotypic annotations for rare disorders in humans such as the Online Mendelian Inheritance in Man (OMIM) and the Human Phenotype Ontology (HPO) knowledgebases. This raises the prospect of being able to use clinical data, including lethality as the most severe phenotypic manifestation, to further our characterisation of gene essentiality. Here we queried OMIM for terms related to lethality and classified all Mendelian genes into categories, according to the earliest age of death recorded for the associated disorders, from prenatal death to no reports of premature death. To showcase this curated catalogue of human essential genes, we developed the Lethal Phenotypes Portal (https://lethalphenotypes.research.its.qmul.ac.uk), where we also explore the relationships between these lethality categories, constraint metrics and viability in cell lines and mouse. Further analysis of the genes in these categories reveals differences in the mode of inheritance of the associated disorders, physiological systems affected and disease class. We highlight how the phenotypic similarity between genes in the same lethality category combined with gene family/group information can be used for novel disease gene discovery. Finally, we explore the overlaps and discrepancies between the lethal phenotypes observed in mouse and human and discuss potential explanations that include differences in transcriptional regulation, functional compensation and molecular disease mechanisms. We anticipate that this resource will aid clinicians in the diagnosis of early lethal conditions and assist researchers in investigating the properties that make these genes essential for human development.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Ignatia B. Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Gabriel Marengo
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park & St Mark’s Hospitals, London, UK
| | | | | | - Peter N. Robinson
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK
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Yap P, Riley LG, Kakadia PM, Bohlander SK, Curran B, Rahimi MJ, Alburaiky S, Hayes I, Oppermann H, Print C, Cooper ST, Le Quesne Stabej P. Biallelic ATP2B1 variants as a likely cause of a novel neurodevelopmental malformation syndrome with primary hypoparathyroidism. Eur J Hum Genet 2024; 32:125-129. [PMID: 37926713 PMCID: PMC10772071 DOI: 10.1038/s41431-023-01484-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/22/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
ATP2B1 encodes plasma membrane calcium-transporting-ATPase1 and plays an essential role in maintaining intracellular calcium homeostasis that regulates diverse signaling pathways. Heterozygous de novo missense and truncating ATP2B1 variants are associated with a neurodevelopmental phenotype of variable expressivity. We describe a proband with distinctive craniofacial gestalt, Pierre-Robin sequence, neurodevelopmental and growth deficit, periventricular heterotopia, brachymesophalangy, cutaneous syndactyly, and persistent hypocalcemia from primary hypoparathyroidism. Proband-parent trio exome sequencing identified compound heterozygous ATP2B1 variants: a maternally inherited splice-site (c.3060+2 T > G) and paternally inherited missense c.2938 G > T; p.(Val980Leu). Reverse-transcription-PCR on the proband's fibroblast-derived mRNA showed aberrantly spliced ATP2B1 transcripts targeted for nonsense-mediated decay. All correctly-spliced ATP2B1 mRNA encoding p.(Val980Leu) functionally causes decreased cellular Ca2+ extrusion. Immunoblotting showed reduced fibroblast ATP2B1. We conclude that biallelic ATP2B1 variants are the likely cause of the proband's phenotype, strengthening the association of ATP2B1 as a neurodevelopmental gene and expanding the phenotypic characterization of a biallelic loss-of-function genotype.
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Affiliation(s)
- Patrick Yap
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.
- Genetic Health Service New Zealand - Northern hub, Auckland, New Zealand.
| | - Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and The Children's Medical Research Institute, Sydney, NSW, 2145, Australia
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Purvi M Kakadia
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Ben Curran
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Meer Jacob Rahimi
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, 04103, Germany
| | - Salam Alburaiky
- Genetic Health Service New Zealand - Northern hub, Auckland, New Zealand
| | - Ian Hayes
- Genetic Health Service New Zealand - Northern hub, Auckland, New Zealand
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, 04103, Germany
| | - Cristin Print
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Sandra T Cooper
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, NSW, 2145, Australia
- The Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Polona Le Quesne Stabej
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
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7
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Cacheiro P, Smedley D. Essential genes: a cross-species perspective. Mamm Genome 2023; 34:357-363. [PMID: 36897351 PMCID: PMC10382395 DOI: 10.1007/s00335-023-09984-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/17/2023] [Indexed: 03/11/2023]
Abstract
Protein coding genes exhibit different degrees of intolerance to loss-of-function variation. The most intolerant genes, whose function is essential for cell or/and organism survival, inform on fundamental biological processes related to cell proliferation and organism development and provide a window on the molecular mechanisms of human disease. Here we present a brief overview of the resources and knowledge gathered around gene essentiality, from cancer cell lines to model organisms to human development. We outline the implications of using different sources of evidence and definitions to determine which genes are essential and highlight how information on the essentiality status of a gene can inform novel disease gene discovery and therapeutic target identification.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK.
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8
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Kaur S, Roberts DD. Why do humans need thrombospondin-1? J Cell Commun Signal 2023; 17:485-493. [PMID: 36689135 PMCID: PMC10409698 DOI: 10.1007/s12079-023-00722-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/07/2023] [Indexed: 01/24/2023] Open
Abstract
Matricellular proteins comprise several families of secreted proteins that function in higher animals at the interface between cells and their surrounding extracellular matrix. Targeted gene disruptions that result in loss of viability in mice have revealed critical roles for several matricellular proteins in murine embryonic development, including two members of the cellular communication network (CCN) gene family. In contrast, mice lacking single or multiple members of the thrombospondin (THBS) gene family remain viable and fertile. The frequency of loss of function mutants, identified using human deep exome sequencing data, provided evidence that some of the essential genes in mice, including Ccn1, are also essential genes in humans. However, a deficit in loss of function mutants in humans indicated that THBS1 is also highly loss-intolerant. In addition to roles in embryonic development or adult reproduction, genes may be loss-intolerant in humans because their function is needed to survive environmental stresses that are encountered between birth and reproduction. Laboratory mice live in a protected environment that lacks the exposures to pathogens and injury that humans routinely face. However, subjecting Thbs1-/- mice to defined stresses has provided valuable insights into functions of thrombospondin-1 that could account for the loss-intolerance of THBS1 in humans. Stress response models using transgenic mice have identified protective functions of thrombospondin-1 in the cardiovascular system (red) and immune defenses (blue) that could account for its intolerance to loss of function mutants in humans.
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Affiliation(s)
- Sukhbir Kaur
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10 Room 2S235, 10 Center Dr, Bethesda, MD, 20892-1500, USA
| | - David D Roberts
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10 Room 2S235, 10 Center Dr, Bethesda, MD, 20892-1500, USA.
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9
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Oddsson A, Sulem P, Sveinbjornsson G, Arnadottir GA, Steinthorsdottir V, Halldorsson GH, Atlason BA, Oskarsson GR, Helgason H, Nielsen HS, Westergaard D, Karjalainen JM, Katrinardottir H, Fridriksdottir R, Jensson BO, Tragante V, Ferkingstad E, Jonsson H, Gudjonsson SA, Beyter D, Moore KHS, Thordardottir HB, Kristmundsdottir S, Stefansson OA, Rantapää-Dahlqvist S, Sonderby IE, Didriksen M, Stridh P, Haavik J, Tryggvadottir L, Frei O, Walters GB, Kockum I, Hjalgrim H, Olafsdottir TA, Selbaek G, Nyegaard M, Erikstrup C, Brodersen T, Saevarsdottir S, Olsson T, Nielsen KR, Haraldsson A, Bruun MT, Hansen TF, Steingrimsdottir T, Jacobsen RL, Lie RT, Djurovic S, Alfredsson L, Lopez de Lapuente Portilla A, Brunak S, Melsted P, Halldorsson BV, Saemundsdottir J, Magnusson OT, Padyukov L, Banasik K, Rafnar T, Askling J, Klareskog L, Pedersen OB, Masson G, Havdahl A, Nilsson B, Andreassen OA, Daly M, Ostrowski SR, Jonsdottir I, Stefansson H, Holm H, Helgason A, Thorsteinsdottir U, Stefansson K, Gudbjartsson DF. Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality. Nat Commun 2023; 14:3453. [PMID: 37301908 PMCID: PMC10257723 DOI: 10.1038/s41467-023-38951-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.
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Affiliation(s)
| | | | | | - Gudny A Arnadottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Henriette Svarre Nielsen
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - David Westergaard
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Juha M Karjalainen
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Kristjan H S Moore
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Helga B Thordardottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ida Elken Sonderby
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Pernilla Stridh
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Bergen Center of Brain Plasticity, Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Laufey Tryggvadottir
- Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland
- Faculty of Medicine, BMC, Laeknagardur, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Oleksandr Frei
- NORMENT Centre, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | | | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Geir Selbaek
- Norwegian National Centre of Ageing and Health, Vestfold Hospital Trust, Tonsberg, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mette Nyegaard
- Deptartment of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thorsten Brodersen
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | - Saedis Saevarsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Asgeir Haraldsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Thora Steingrimsdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Soren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pall Melsted
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | | | - Leonid Padyukov
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Johan Askling
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ole Birger Pedersen
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | | | - Alexandra Havdahl
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Bjorn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund, Sweden
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Mark Daly
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Deptartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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10
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Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB, Sirota M, Snyder MP, Yatsenko SA, Rajkovic A. Preconception Genetic Carrier Screening for Miscarriage Risk Assessment: A Bioinformatic Approach to Identifying Candidate Lethal Genes and Variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.25.23290518. [PMID: 37398382 PMCID: PMC10312874 DOI: 10.1101/2023.05.25.23290518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Purpose Miscarriage, due to genetically heterogeneous etiology, is a common outcome of pregnancy. Preconception genetic carrier screening (PGCS) identifies at-risk partners for newborn genetic disorders; however, PGCS panels currently lack miscarriage-related genes. Here we assessed the theoretical impact of known and candidate genes on prenatal lethality and the PGCS among diverse populations. Methods Human exome sequencing and mouse gene function databases were analyzed to define genes essential for human fetal survival (lethal genes), identify variants that are absent in a homozygous state in healthy human population, and to estimate carrier rates for known and candidate lethal genes. Results Among 138 genes, potential lethal variants are present in the general population with a frequency of 0.5% or greater. Preconception screening for these 138 genes would identify from 4.6% (Finnish population) to 39.8% (East Asian population) of couples that are at-risk for miscarriage, explaining a cause for pregnancy loss for ∼1.1-10% of conceptions affected by biallelic lethal variants. Conclusion This study identified a set of genes and variants potentially associated with lethality across different ethnic backgrounds. The diversity of these genes amongst the various ethnic groups highlights the importance of designing a pan-ethnic PGCS panel comprising miscarriage-related genes.
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11
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Cacheiro P, Westerberg CH, Mager J, Dickinson ME, Nutter LMJ, Muñoz-Fuentes V, Hsu CW, Van den Veyver IB, Flenniken AM, McKerlie C, Murray SA, Teboul L, Heaney JD, Lloyd KCK, Lanoue L, Braun RE, White JK, Creighton AK, Laurin V, Guo R, Qu D, Wells S, Cleak J, Bunton-Stasyshyn R, Stewart M, Harrisson J, Mason J, Haseli Mashhadi H, Parkinson H, Mallon AM, Smedley D. Mendelian gene identification through mouse embryo viability screening. Genome Med 2022; 14:119. [PMID: 36229886 PMCID: PMC9563108 DOI: 10.1186/s13073-022-01118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 09/26/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The diagnostic rate of Mendelian disorders in sequencing studies continues to increase, along with the pace of novel disease gene discovery. However, variant interpretation in novel genes not currently associated with disease is particularly challenging and strategies combining gene functional evidence with approaches that evaluate the phenotypic similarities between patients and model organisms have proven successful. A full spectrum of intolerance to loss-of-function variation has been previously described, providing evidence that gene essentiality should not be considered as a simple and fixed binary property. METHODS Here we further dissected this spectrum by assessing the embryonic stage at which homozygous loss-of-function results in lethality in mice from the International Mouse Phenotyping Consortium, classifying the set of lethal genes into one of three windows of lethality: early, mid, or late gestation lethal. We studied the correlation between these windows of lethality and various gene features including expression across development, paralogy and constraint metrics together with human disease phenotypes. We explored a gene similarity approach for novel gene discovery and investigated unsolved cases from the 100,000 Genomes Project. RESULTS We found that genes in the early gestation lethal category have distinct characteristics and are enriched for genes linked with recessive forms of inherited metabolic disease. We identified several genes sharing multiple features with known biallelic forms of inborn errors of the metabolism and found signs of enrichment of biallelic predicted pathogenic variants among early gestation lethal genes in patients recruited under this disease category. We highlight two novel gene candidates with phenotypic overlap between the patients and the mouse knockouts. CONCLUSIONS Information on the developmental period at which embryonic lethality occurs in the knockout mouse may be used for novel disease gene discovery that helps to prioritise variants in unsolved rare disease cases.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lauryl M J Nutter
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.,Department of Education, Innovation and Technology, Baylor College of Medicine, Houston, TX, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Ann M Flenniken
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Colin McKerlie
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | | | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | | | | | - Amie K Creighton
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Valerie Laurin
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Ruolin Guo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Dawei Qu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - James Cleak
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | | | - Michelle Stewart
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jackie Harrisson
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | | | | | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK.
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12
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Bryen SJ, Yuen M, Joshi H, Dawes R, Zhang K, Lu JK, Jones KJ, Liang C, Wong WK, Peduto AJ, Waddell LB, Evesson FJ, Cooper ST. Prevalence, parameters, and pathogenic mechanisms for splice-altering acceptor variants that disrupt the AG exclusion zone. HGG ADVANCES 2022; 3:100125. [PMID: 35847480 PMCID: PMC9284458 DOI: 10.1016/j.xhgg.2022.100125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/19/2022] [Indexed: 10/26/2022] Open
Abstract
Predicting the pathogenicity of acceptor splice-site variants outside the essential AG is challenging, due to high sequence diversity of the extended splice-site region. Critical analysis of 24,445 intronic extended acceptor splice-site variants reported in ClinVar and the Leiden Open Variation Database (LOVD) demonstrates 41.9% of pathogenic variants create an AG dinucleotide between the predicted branchpoint and acceptor (AG-creating variants in the AG exclusion zone), 28.4% result in loss of a pyrimidine at the -3 position, and 15.1% result in loss of one or more pyrimidines in the polypyrimidine tract. Pathogenicity of AG-creating variants was highly influenced by their position. We define a high-risk zone for pathogenicity: > 6 nucleotides downstream of the predicted branchpoint and >5 nucleotides upstream from the acceptor, where 93.1% of pathogenic AG-creating variants arise and where naturally occurring AG dinucleotides are concordantly depleted (5.8% of natural AGs). SpliceAI effectively predicts pathogenicity of AG-creating variants, achieving 95% sensitivity and 69% specificity. We highlight clinical examples showing contrasting mechanisms for mis-splicing arising from AG variants: (1) cryptic acceptor created; (2) splicing silencer created: an introduced AG silences the acceptor, resulting in exon skipping, intron retention, and/or use of an alternative existing cryptic acceptor; and (3) splicing silencer disrupted: loss of a deep intronic AG activates inclusion of a pseudo-exon. In conclusion, we establish AG-creating variants as a common class of pathogenic extended acceptor variant and outline factors conferring critical risk for mis-splicing for AG-creating variants in the AG exclusion zone, between the branchpoint and acceptor.
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Affiliation(s)
- Samantha J. Bryen
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Michaela Yuen
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Himanshu Joshi
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Ruebena Dawes
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Katharine Zhang
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Jessica K. Lu
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Kristi J. Jones
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
- Department of Clinical Genetics, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Christina Liang
- Department of Neurology, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
- Department of Neurogenetics, Northern Clinical School, Kolling Institute, University of Sydney, NSW 2065, Australia
| | - Wui-Kwan Wong
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Anthony J. Peduto
- Department of Radiology, Westmead Hospital, Western Clinical School, University of Sydney, Westmead, NSW 2145, Australia
| | - Leigh B. Waddell
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Frances J. Evesson
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Sandra T. Cooper
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
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13
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Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO, Kristmundsdottir S, Sigurpalsdottir BD, Stefansson OA, Beyter D, Holley G, Tragante V, Gylfason A, Olason PI, Zink F, Asgeirsdottir M, Sverrisson ST, Sigurdsson B, Gudjonsson SA, Sigurdsson GT, Halldorsson GH, Sveinbjornsson G, Norland K, Styrkarsdottir U, Magnusdottir DN, Snorradottir S, Kristinsson K, Sobech E, Jonsson H, Geirsson AJ, Olafsson I, Jonsson P, Pedersen OB, Erikstrup C, Brunak S, Ostrowski SR, Thorleifsson G, Jonsson F, Melsted P, Jonsdottir I, Rafnar T, Holm H, Stefansson H, Saemundsdottir J, Gudbjartsson DF, Magnusson OT, Masson G, Thorsteinsdottir U, Helgason A, Jonsson H, Sulem P, Stefansson K. The sequences of 150,119 genomes in the UK Biobank. Nature 2022; 607:732-740. [PMID: 35859178 PMCID: PMC9329122 DOI: 10.1038/s41586-022-04965-x] [Citation(s) in RCA: 179] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/10/2022] [Indexed: 12/25/2022]
Abstract
Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data1,2. Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank3. This constitutes a set of high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% of all possible human single-nucleotide polymorphisms, and 58,707,036 indels. This large set of variants allows us to characterize selection based on sequence variation within a population through a depletion rank score of windows along the genome. Depletion rank analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UK Biobank: a large British Irish cohort, a smaller African cohort and a South Asian cohort. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large-scale whole-genome sequencing studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on whole-exome sequencing and/or imputation.
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Affiliation(s)
- Bjarni V Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland. .,School of Technology, Reykjavik University, Reykjavik, Iceland.
| | | | | | | | | | - Magnus O Ulfarsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Marteinn T Hardarson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | - Snaedis Kristmundsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Technology, Reykjavik University, Reykjavik, Iceland
| | - Brynja D Sigurpalsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Helgi Jonsson
- Landspitali-University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Palmi Jonsson
- Landspitali-University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ole Birger Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Christian Erikstrup
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Clinical Sciences, Copenhagen University, Copenhagen, Denmark
| | | | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
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14
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Capalbo A, Buonaiuto S, Figliuzzi M, Damaggio G, Girardi L, Caroselli S, Poli M, Patassini C, Cetinkaya M, Yuksel B, Azad A, Grøndahl M, Hoffmann E, Simón C, Colonna V, Kahraman S. A standardized approach for case selection and genomic data analysis of maternal exomes for the diagnosis of oocyte maturation and early embryonic developmental arrest in IVF. Reprod Biomed Online 2022; 45:508-518. [DOI: 10.1016/j.rbmo.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/17/2022] [Indexed: 11/15/2022]
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15
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Buonaiuto S, Biase ID, Aleotti V, Ravaei A, Marino AD, Damaggio G, Chierici M, Pulijala M, D'Ambrosio P, Esposito G, Ayub Q, Furlanello C, Greco P, Capalbo A, Rubini M, Biase SD, Colonna V. Prioritization of putatively detrimental variants in euploid miscarriages. Sci Rep 2022; 12:1997. [PMID: 35132093 PMCID: PMC8821623 DOI: 10.1038/s41598-022-05737-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/11/2022] [Indexed: 12/21/2022] Open
Abstract
Miscarriage is the spontaneous termination of a pregnancy before 24 weeks of gestation. We studied the genome of euploid miscarried embryos from mothers in the range of healthy adult individuals to understand genetic susceptibility to miscarriage not caused by chromosomal aneuploidies. We developed GP , a pipeline that we used to prioritize 439 unique variants in 399 genes, including genes known to be associated with miscarriages. Among the prioritized genes we found STAG2 coding for the cohesin complex subunit, for which inactivation in mouse is lethal, and TLE4 a target of Notch and Wnt, physically interacting with a region on chromosome 9 associated to miscarriages.
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Affiliation(s)
| | | | - Valentina Aleotti
- Department of Neurosciences and Rehabilitation, University of Ferrara, Ferrara, 44121, Italy
| | - Amin Ravaei
- Department of Neurosciences and Rehabilitation, University of Ferrara, Ferrara, 44121, Italy
| | | | | | | | - Madhuri Pulijala
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500, Bandar Sunway, Malaysia
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Malaysia
| | | | | | - Qasim Ayub
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500, Bandar Sunway, Malaysia
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Malaysia
| | | | - Pantaleo Greco
- Department of Medical Sciences, University of Ferrara, Ferrara, 44121, Italy
| | | | - Michele Rubini
- Department of Neurosciences and Rehabilitation, University of Ferrara, Ferrara, 44121, Italy
| | | | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy.
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16
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Population-level deficit of homozygosity unveils CPSF3 as an intellectual disability syndrome gene. Nat Commun 2022; 13:705. [PMID: 35121750 PMCID: PMC8817032 DOI: 10.1038/s41467-022-28330-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
AbstractPredicting the pathogenicity of biallelic missense variants can be challenging. Here, we use a deficit of observed homozygous carriers of missense variants, versus an expected number in a set of 153,054 chip-genotyped Icelanders, to identify potentially pathogenic genotypes. We follow three missense variants with a complete deficit of homozygosity and find that their pathogenic effect in homozygous state ranges from severe childhood disease to early embryonic lethality. One of these variants is in CPSF3, a gene not previously linked to disease. From a set of clinically sequenced Icelanders, and by sequencing archival samples targeted through the Icelandic genealogy, we find four homozygous carriers. Additionally, we find two homozygous carriers of Mexican descent of another missense variant in CPSF3. All six homozygous carriers of missense variants in CPSF3 show severe intellectual disability, seizures, microcephaly, and abnormal muscle tone. Here, we show how the absence of certain homozygous genotypes from a large population set can elucidate causes of previously unexplained recessive diseases and early miscarriage.
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17
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Bournazos AM, Riley LG, Bommireddipalli S, Ades L, Akesson LS, Al-Shinnag M, Alexander SI, Archibald AD, Balasubramaniam S, Berman Y, Beshay V, Boggs K, Bojadzieva J, Brown NJ, Bryen SJ, Buckley MF, Chong B, Davis MR, Dawes R, Delatycki M, Donaldson L, Downie L, Edwards C, Edwards M, Engel A, Ewans LJ, Faiz F, Fennell A, Field M, Freckmann ML, Gallacher L, Gear R, Goel H, Goh S, Goodwin L, Hanna B, Harraway J, Higgins M, Ho G, Hopper BK, Horton AE, Hunter MF, Huq AJ, Josephi-Taylor S, Joshi H, Kirk E, Krzesinski E, Kumar KR, Lemckert F, Leventer RJ, Lindsey-Temple SE, Lunke S, Ma A, Macaskill S, Mallawaarachchi A, Marty M, Marum JE, McCarthy HJ, Menezes MP, McLean A, Milnes D, Mohammad S, Mowat D, Niaz A, Palmer EE, Patel C, Patel SG, Phelan D, Pinner JR, Rajagopalan S, Regan M, Rodgers J, Rodrigues M, Roxburgh RH, Sachdev R, Roscioli T, Samarasekera R, Sandaradura SA, Savva E, Schindler T, Shah M, Sinnerbrink IB, Smith JM, Smith RJ, Springer A, Stark Z, Strom SP, Sue CM, Tan K, Tan TY, Tantsis E, Tchan MC, Thompson BA, Trainer AH, van Spaendonck-Zwarts K, Walsh R, Warwick L, White S, White SM, Williams MG, Wilson MJ, Wong WK, Wright DC, Yap P, Yeung A, Young H, Jones KJ, Bennetts B, Cooper ST. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genet Med 2021; 24:130-145. [PMID: 34906502 DOI: 10.1016/j.gim.2021.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/18/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Genetic variants causing aberrant premessenger RNA splicing are increasingly being recognized as causal variants in genetic disorders. In this study, we devise standardized practices for polymerase chain reaction (PCR)-based RNA diagnostics using clinically accessible specimens (blood, fibroblasts, urothelia, biopsy). METHODS A total of 74 families with diverse monogenic conditions (31% prenatal-congenital onset, 47% early childhood, and 22% teenage-adult onset) were triaged into PCR-based RNA testing, with comparative RNA sequencing for 19 cases. RESULTS Informative RNA assay data were obtained for 96% of cases, enabling variant reclassification for 75% variants that can be used for genetic counseling (71%), to inform clinical care (32%) and prenatal counseling (41%). Variant-associated mis-splicing was highly reproducible for 28 cases with samples from ≥2 affected individuals or heterozygotes and 10 cases with ≥2 biospecimens. PCR amplicons encompassing another segregated heterozygous variant was vital for clinical interpretation of 22 of 79 variants to phase RNA splicing events and discern complete from partial mis-splicing. CONCLUSION RNA diagnostics enabled provision of a genetic diagnosis for 64% of recruited cases. PCR-based RNA diagnostics has capacity to analyze 81.3% of clinically significant genes, with long amplicons providing an advantage over RNA sequencing to phase RNA splicing events. The Australasian Consortium for RNA Diagnostics (SpliceACORD) provide clinically-endorsed, standardized protocols and recommendations for interpreting RNA assay data.
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Affiliation(s)
- Adam M Bournazos
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Lisa G Riley
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Lesley Ades
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Lauren S Akesson
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Mohammad Al-Shinnag
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia; The University of Queensland, Herston, Queensland, Australia
| | - Stephen I Alexander
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Alison D Archibald
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Yemima Berman
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Northern Clinical School, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Victoria Beshay
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kirsten Boggs
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Australian Genomics Health Alliance, Parkville, Victoria, Australia; Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Jasmina Bojadzieva
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Natasha J Brown
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Samantha J Bryen
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | | | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Ruebena Dawes
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Martin Delatycki
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Liz Donaldson
- The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Lilian Downie
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Caitlin Edwards
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Matthew Edwards
- Department of Paediatrics, School of Medicine, Western Sydney University, Penrith South, New South Wales, Australia
| | - Amanda Engel
- ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia
| | - Lisa J Ewans
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; Central Clinical School, The University of Sydney, Camperdown, New South Wales, Australia
| | - Fathimath Faiz
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Andrew Fennell
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia
| | | | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Russell Gear
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Himanshu Goel
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia; The University of Newcastle, Callaghan, New South Wales, Australia
| | - Shuxiang Goh
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Linda Goodwin
- Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia
| | - Bernadette Hanna
- Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - James Harraway
- Sullivan Nicolaides Pathology, Bowen Hills, Queensland, Australia
| | - Megan Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Gladys Ho
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | | | - Ari E Horton
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia; Monash Heart and Monash Children's Hospital, Monash Health, Clayton, Victoria, Australia; Monash Cardiovascular Research Centre, Clayton, Victoria, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Aamira J Huq
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - Himanshu Joshi
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Edwin Kirk
- NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Emma Krzesinski
- Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Kishore R Kumar
- Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Translational Genomics, Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, New South Wales, Australia
| | - Frances Lemckert
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Neurology, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Suzanna E Lindsey-Temple
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Sebastian Lunke
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Alan Ma
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | | | - Amali Mallawaarachchi
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Melanie Marty
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Justine E Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Hugh J McCarthy
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Manoj P Menezes
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Alison McLean
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Shekeeb Mohammad
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - David Mowat
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Aram Niaz
- Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Elizabeth E Palmer
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Shilpan G Patel
- School of Medicine, The University of Auckland, Auckland, New Zealand
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Jason R Pinner
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia
| | - Sulekha Rajagopalan
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Matthew Regan
- Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Jonathan Rodgers
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Miriam Rodrigues
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand
| | | | - Rani Sachdev
- Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Tony Roscioli
- NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia, University of New South Wales, Randwick, New South Wales, Australia
| | - Ruvishani Samarasekera
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Sarah A Sandaradura
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Elena Savva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Tim Schindler
- School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia; Newborn Care, Royal Hospital for Women, Randwick, New South Wales, Australia
| | - Margit Shah
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Ingrid B Sinnerbrink
- Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia
| | - Janine M Smith
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Amanda Springer
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | | | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Kenneth Tan
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia; Monash Newborn, Monash Children's Hospital, Clayton, Victoria, Australia
| | - Tiong Y Tan
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Esther Tantsis
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Michel C Tchan
- Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia
| | - Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Alison H Trainer
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Rebecca Walsh
- NSW Health Pathology, Randwick, New South Wales, Australia
| | - Linda Warwick
- ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia
| | - Stephanie White
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Mark G Williams
- Mater Research Institute, The University of Queensland, South Brisbane, Queensland, Australia
| | - Meredith J Wilson
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Wui Kwan Wong
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Dale C Wright
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Patrick Yap
- Northern Hub, Genetic Health Service NZ, Auckland, New Zealand
| | - Alison Yeung
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Helen Young
- Department of Intensive Care, Austin Hospital, Heidelberg, Victoria, Australia
| | - Kristi J Jones
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Bruce Bennetts
- Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The Children's Medical Research Institute, Westmead, New South Wales, Australia.
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Martin EMMA, Enriquez A, Sparrow DB, Humphreys DT, McInerney-Leo AM, Leo PJ, Duncan EL, Iyer KR, Greasby JA, Ip E, Giannoulatou E, Sheng D, Wohler E, Dimartino C, Amiel J, Capri Y, Lehalle D, Mory A, Wilnai Y, Lebenthal Y, Gharavi AG, Krzemień GG, Miklaszewska M, Steiner RD, Raggio C, Blank R, Baris Feldman H, Milo Rasouly H, Sobreira NLM, Jobling R, Gordon CT, Giampietro PF, Dunwoodie SL, Chapman G. Heterozygous loss of WBP11 function causes multiple congenital defects in humans and mice. Hum Mol Genet 2021; 29:3662-3678. [PMID: 33276377 DOI: 10.1093/hmg/ddaa258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/09/2020] [Accepted: 11/25/2020] [Indexed: 12/31/2022] Open
Abstract
The genetic causes of multiple congenital anomalies are incompletely understood. Here, we report novel heterozygous predicted loss-of-function (LoF) and predicted damaging missense variants in the WW domain binding protein 11 (WBP11) gene in seven unrelated families with a variety of overlapping congenital malformations, including cardiac, vertebral, tracheo-esophageal, renal and limb defects. WBP11 encodes a component of the spliceosome with the ability to activate pre-messenger RNA splicing. We generated a Wbp11 null allele in mouse using CRISPR-Cas9 targeting. Wbp11 homozygous null embryos die prior to E8.5, indicating that Wbp11 is essential for development. Fewer Wbp11 heterozygous null mice are found than expected due to embryonic and postnatal death. Importantly, Wbp11 heterozygous null mice are small and exhibit defects in axial skeleton, kidneys and esophagus, similar to the affected individuals, supporting the role of WBP11 haploinsufficiency in the development of congenital malformations in humans. LoF WBP11 variants should be considered as a possible cause of VACTERL association as well as isolated Klippel-Feil syndrome, renal agenesis or esophageal atresia.
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Affiliation(s)
- Ella M M A Martin
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Annabelle Enriquez
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia.,Faculty of Medicine, UNSW, Sydney 2052, Australia
| | - Duncan B Sparrow
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia.,Faculty of Science, UNSW, Sydney 2052, Australia.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - David T Humphreys
- Faculty of Medicine, UNSW, Sydney 2052, Australia.,Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Aideen M McInerney-Leo
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane 4072, Australia
| | - Paul J Leo
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba 4102, Australia
| | - Emma L Duncan
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba 4102, Australia.,Department of Twin Research & Genetic Epidemiology, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King's College London, London SE1 7EH, UK.,Faculty of Medicine, University of Queensland, Herston 4006, Australia
| | - Kavitha R Iyer
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Joelene A Greasby
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Eddie Ip
- Faculty of Medicine, UNSW, Sydney 2052, Australia.,Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Eleni Giannoulatou
- Faculty of Medicine, UNSW, Sydney 2052, Australia.,Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Delicia Sheng
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore 21287, USA
| | - Clémantine Dimartino
- Laboratory of Embryology and Genetics of Human Malformations, Institute National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris 75015, France.,Paris Descartes-Sorbonne Paris Cité Université, Institut Imagine, Paris 75015, France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformations, Institute National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris 75015, France.,Paris Descartes-Sorbonne Paris Cité Université, Institut Imagine, Paris 75015, France.,Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris 75015, France
| | - Yline Capri
- Département de Génétique, Hôpital Robert Debré, Assistance Publique Hôpitaux de Paris, Paris 75019, France
| | - Daphné Lehalle
- Centre Hospitalier Intercommunal Créteil, Créteil 94000, France
| | - Adi Mory
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Yael Wilnai
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Yael Lebenthal
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.,Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Pediatric Endocrinology and Diabetes Unit, Tel Aviv 6423906, Israel
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Grażyna G Krzemień
- Department of Pediatrics and Nephrology, Warsaw Medical University, Warsaw 02-091, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Kraków 30-663, Poland
| | - Robert D Steiner
- Marshfield Clinic Health System, Marshfield, WI 54449, USA.,University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Cathy Raggio
- Hospital for Special Surgery, Pediatrics Orthopedic Surgery, New York, NY 10021, USA
| | - Robert Blank
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hagit Baris Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Milo Rasouly
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Nara L M Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore 21287, USA
| | - Rebekah Jobling
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G1X3, Canada
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformations, Institute National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris 75015, France.,Paris Descartes-Sorbonne Paris Cité Université, Institut Imagine, Paris 75015, France
| | - Philip F Giampietro
- Department of Pediatrics, University of Illinois-Chicago, Chicago, IL 60607, USA
| | - Sally L Dunwoodie
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia.,Faculty of Medicine, UNSW, Sydney 2052, Australia.,Faculty of Science, UNSW, Sydney 2052, Australia
| | - Gavin Chapman
- Development & Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia.,Faculty of Medicine, UNSW, Sydney 2052, Australia
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19
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Salnikova LE, Kolobkov DS, Sviridova DA, Abilev SK. An overview of germline variations in genes of primary immunodeficiences through integrative analysis of ClinVar, HGMD ® and dbSNP databases. Hum Genet 2021; 140:1379-1393. [PMID: 34272616 DOI: 10.1007/s00439-021-02316-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/10/2021] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PID) are a diverse group of genetic disorders caused by inadequate development and function of immune system. Identifying genetic etiology is important for genetic counselling and treatment decisions. Clinical relevance of genetic variants is a complex problem depending on gene-specific and variant specific genotype-phenotype interactions. To address this challenge, we aimed to characterize the pathogenic landscape of PID genes by combining the analysis of germline variations reported in ClinVar and HGMD® and identification of damaging variations available in dbSNP. We generated a joint ClinVar/HGMD database, which included 111,940 variants, among them 32,452 were classified as pathogenic/likely pathogenic. From a total of 5,415,794 bi- or multiallelic variants in PID genes recorded in dbSNP, we retrieved 38,291 high impact (HI) biallelic variants with presumably disruptive impact in the protein, of them 25,500 variants were not present in ClinVar/HGMD. Using a functional prediction algorithm, we additionally identified 28,507 deleterious and 56,016 neutral missense variants among dbSNP variants and created a collection of damaging and neutral variations in PID genes, not currently present in ClinVar/HGMD, with their allele frequencies and mappings to protein domains. The distribution of pathogenic variants from ClinVar/HGMD, HI variants and deleterious missense variants from dbSNP was analyzed in the context of hereditary pattern and gene specific metrics, such as pLI and haploinsufficiency. Our report summarized data on complex gene-specific variability in PID genes and might be useful for the identification of the most promising variants and gene regions for further study.
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Affiliation(s)
- Lyubov E Salnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, 117971, Russia. .,The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia. .,The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia.
| | - Dmitry S Kolobkov
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, 117971, Russia.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Darya A Sviridova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, 117971, Russia
| | - Serikbai K Abilev
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, 117971, Russia
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20
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Laisk T, Soares ALG, Ferreira T, Painter JN, Censin JC, Laber S, Bacelis J, Chen CY, Lepamets M, Lin K, Liu S, Millwood IY, Ramu A, Southcombe J, Andersen MS, Yang L, Becker CM, Børglum AD, Gordon SD, Bybjerg-Grauholm J, Helgeland Ø, Hougaard DM, Jin X, Johansson S, Juodakis J, Kartsonaki C, Kukushkina V, Lind PA, Metspalu A, Montgomery GW, Morris AP, Mors O, Mortensen PB, Njølstad PR, Nordentoft M, Nyholt DR, Lippincott M, Seminara S, Salumets A, Snieder H, Zondervan K, Werge T, Chen Z, Conrad DF, Jacobsson B, Li L, Martin NG, Neale BM, Nielsen R, Walters RG, Granne I, Medland SE, Mägi R, Lawlor DA, Lindgren CM. The genetic architecture of sporadic and multiple consecutive miscarriage. Nat Commun 2020; 11:5980. [PMID: 33239672 PMCID: PMC7689465 DOI: 10.1038/s41467-020-19742-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/23/2020] [Indexed: 12/17/2022] Open
Abstract
Miscarriage is a common, complex trait affecting ~15% of clinically confirmed pregnancies. Here we present the results of large-scale genetic association analyses with 69,054 cases from five different ancestries for sporadic miscarriage, 750 cases of European ancestry for multiple (≥3) consecutive miscarriage, and up to 359,469 female controls. We identify one genome-wide significant association (rs146350366, minor allele frequency (MAF) 1.2%, P = 3.2 × 10-8, odds ratio (OR) = 1.4) for sporadic miscarriage in our European ancestry meta-analysis and three genome-wide significant associations for multiple consecutive miscarriage (rs7859844, MAF = 6.4%, P = 1.3 × 10-8, OR = 1.7; rs143445068, MAF = 0.8%, P = 5.2 × 10-9, OR = 3.4; rs183453668, MAF = 0.5%, P = 2.8 × 10-8, OR = 3.8). We further investigate the genetic architecture of miscarriage with biobank-scale Mendelian randomization, heritability, and genetic correlation analyses. Our results show that miscarriage etiopathogenesis is partly driven by genetic variation potentially related to placental biology, and illustrate the utility of large-scale biobank data for understanding this pregnancy complication.
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Affiliation(s)
- Triin Laisk
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.
- Competence Centre on Health Technologies, Tartu, Estonia.
| | - Ana Luiza G Soares
- MRC Integrated Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Teresa Ferreira
- Big Data Institute, Li Ka Shing Center for Health for Health Information and Discovery, Oxford University, Oxford, UK
| | - Jodie N Painter
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Jenny C Censin
- Big Data Institute, Li Ka Shing Center for Health for Health Information and Discovery, Oxford University, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Samantha Laber
- Big Data Institute, Li Ka Shing Center for Health for Health Information and Discovery, Oxford University, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital Östra, Gothenburg, Sweden
| | - Chia-Yen Chen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maarja Lepamets
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Kuang Lin
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Siyang Liu
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Iona Y Millwood
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit (PHRU), University of Oxford, Oxford, UK
| | - Avinash Ramu
- Department of Genetics, Washington University in St. Louis, Saint Louis, MO, USA
| | - Jennifer Southcombe
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | | | - Ling Yang
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit (PHRU), University of Oxford, Oxford, UK
| | - Christian M Becker
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine and Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus University and University Hospital, Aarhus, Denmark
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Øyvind Helgeland
- Department of Genetics and Bioinformatics, Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, N-5020, Bergen, Norway
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China
| | - Stefan Johansson
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, N-5020, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, N-5021, Bergen, Norway
| | - Julius Juodakis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christiana Kartsonaki
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit (PHRU), University of Oxford, Oxford, UK
| | - Viktorija Kukushkina
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Andrew P Morris
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital - Psychiatry, Aarhus, Denmark
| | - Preben B Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Pål R Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, N-5020, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Copenhagen University Hospital, Mental Health Center Copenhagen, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Dale R Nyholt
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Margaret Lippincott
- Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Stephanie Seminara
- Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Andres Salumets
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
- Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Krina Zondervan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Zhengming Chen
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Donald F Conrad
- Department of Genetics, Washington University in St. Louis, Saint Louis, MO, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital Östra, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Liming Li
- Department of Epidemiology & Biostatistics, Peking University Health Science Centre, Peking University, Beijing, China
| | | | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Robin G Walters
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit (PHRU), University of Oxford, Oxford, UK
| | - Ingrid Granne
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Deborah A Lawlor
- MRC Integrated Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol National Institute of Health Research Biomedical Research Centre, Bristol, UK
| | - Cecilia M Lindgren
- Big Data Institute, Li Ka Shing Center for Health for Health Information and Discovery, Oxford University, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Program in Medical and Population Genetics, Broad Institute, Boston, MA, USA.
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21
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Capalbo A, Poli M, Riera-Escamilla A, Shukla V, Kudo Høffding M, Krausz C, Hoffmann ER, Simon C. Preconception genome medicine: current state and future perspectives to improve infertility diagnosis and reproductive and health outcomes based on individual genomic data. Hum Reprod Update 2020; 27:254-279. [PMID: 33197264 DOI: 10.1093/humupd/dmaa044] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/13/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Our genetic code is now readable, writable and hackable. The recent escalation of genome-wide sequencing (GS) applications in population diagnostics will not only enable the assessment of risks of transmitting well-defined monogenic disorders at preconceptional stages (i.e. carrier screening), but also facilitate identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting reproductive fitness. Through GS, the acquisition and curation of reproductive-related findings will warrant the expansion of genetic assessment to new areas of genomic prediction of reproductive phenotypes, pharmacogenomics and molecular embryology, further boosting our knowledge and therapeutic tools for treating infertility and improving women's health. OBJECTIVE AND RATIONALE In this article, we review current knowledge and potential development of preconception genome analysis aimed at detecting reproductive and individual health risks (recessive genetic disease and medically actionable secondary findings) as well as anticipating specific reproductive outcomes, particularly in the context of IVF. The extension of reproductive genetic risk assessment to the general population and IVF couples will lead to the identification of couples who carry recessive mutations, as well as sub-lethal conditions prior to conception. This approach will provide increased reproductive autonomy to couples, particularly in those cases where preimplantation genetic testing is an available option to avoid the transmission of undesirable conditions. In addition, GS on prospective infertility patients will enable genome-wide association studies specific for infertility phenotypes such as predisposition to premature ovarian failure, increased risk of aneuploidies, complete oocyte immaturity or blastocyst development failure, thus empowering the development of true reproductive precision medicine. SEARCH METHODS Searches of the literature on PubMed Central included combinations of the following MeSH terms: human, genetics, genomics, variants, male, female, fertility, next generation sequencing, genome exome sequencing, expanded carrier screening, secondary findings, pharmacogenomics, controlled ovarian stimulation, preconception, genetics, genome-wide association studies, GWAS. OUTCOMES Through PubMed Central queries, we identified a total of 1409 articles. The full list of articles was assessed for date of publication, limiting the search to studies published within the last 15 years (2004 onwards due to escalating research output of next-generation sequencing studies from that date). The remaining articles' titles were assessed for pertinence to the topic, leaving a total of 644 articles. The use of preconception GS has the potential to identify inheritable genetic conditions concealed in the genome of around 4% of couples looking to conceive. Genomic information during reproductive age will also be useful to anticipate late-onset medically actionable conditions with strong genetic background in around 2-4% of all individuals. Genetic variants correlated with differential response to pharmaceutical treatment in IVF, and clear genotype-phenotype associations are found for aberrant sperm types, oocyte maturation, fertilization or pre- and post-implantation embryonic development. All currently known capabilities of GS at the preconception stage are reviewed along with persisting and forthcoming barriers for the implementation of precise reproductive medicine. WIDER IMPLICATIONS The expansion of sequencing analysis to additional monogenic and polygenic traits may enable the development of cost-effective preconception tests capable of identifying underlying genetic causes of infertility, which have been defined as 'unexplained' until now, thus leading to the development of a true personalized genomic medicine framework in reproductive health.
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Affiliation(s)
- Antonio Capalbo
- Igenomix Italy, Marostica, Italy.,Igenomix Foundation, INCLIVA, Valencia, Spain
| | | | - Antoni Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Vallari Shukla
- Department of Cellular and Molecular Medicine, DRNF Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
| | - Miya Kudo Høffding
- Department of Cellular and Molecular Medicine, DRNF Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
| | - Csilla Krausz
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain.,Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Eva R Hoffmann
- Department of Cellular and Molecular Medicine, DRNF Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
| | - Carlos Simon
- Igenomix Foundation, INCLIVA, Valencia, Spain.,Department of Obstetrics and Gynecology, University of Valencia, Valencia, Spain.,Department of Obstetrics and Gynecology BIDMC, Harvard University, Cambridge, MA, USA
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22
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Ravenscroft G, Clayton JS, Faiz F, Sivadorai P, Milnes D, Cincotta R, Moon P, Kamien B, Edwards M, Delatycki M, Lamont PJ, Chan SH, Colley A, Ma A, Collins F, Hennington L, Zhao T, McGillivray G, Ghedia S, Chao K, O'Donnell-Luria A, Laing NG, Davis MR. Neurogenetic fetal akinesia and arthrogryposis: genetics, expanding genotype-phenotypes and functional genomics. J Med Genet 2020; 58:609-618. [PMID: 33060286 DOI: 10.1136/jmedgenet-2020-106901] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/16/2020] [Accepted: 07/05/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Fetal akinesia and arthrogryposis are clinically and genetically heterogeneous and have traditionally been refractive to genetic diagnosis. The widespread availability of affordable genome-wide sequencing has facilitated accurate genetic diagnosis and gene discovery in these conditions. METHODS We performed next generation sequencing (NGS) in 190 probands with a diagnosis of arthrogryposis multiplex congenita, distal arthrogryposis, fetal akinesia deformation sequence or multiple pterygium syndrome. This sequencing was a combination of bespoke neurogenetic disease gene panels and whole exome sequencing. Only class 4 and 5 variants were reported, except for two cases where the identified variants of unknown significance (VUS) are most likely to be causative for the observed phenotype. Co-segregation studies and confirmation of variants identified by NGS were performed where possible. Functional genomics was performed as required. RESULTS Of the 190 probands, 81 received an accurate genetic diagnosis. All except two of these cases harboured class 4 and/or 5 variants based on the American College of Medical Genetics and Genomics guidelines. We identified phenotypic expansions associated with CACNA1S, CHRNB1, GMPPB and STAC3. We describe a total of 50 novel variants, including a novel missense variant in the recently identified gene for arthrogryposis with brain malformations-SMPD4. CONCLUSIONS Comprehensive gene panels give a diagnosis for a substantial proportion (42%) of fetal akinesia and arthrogryposis cases, even in an unselected cohort. Recently identified genes account for a relatively large proportion, 32%, of the diagnoses. Diagnostic-research collaboration was critical to the diagnosis and variant interpretation in many cases, facilitated genotype-phenotype expansions and reclassified VUS through functional genomics.
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Affiliation(s)
- Gina Ravenscroft
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia .,Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Joshua S Clayton
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Fathimath Faiz
- PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
| | - Padma Sivadorai
- PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Rob Cincotta
- Maternal and Fetal Medicine, Mater Mothers' Hospital, Brisbane, Queensland, Australia
| | - Phillip Moon
- Department of Obstetrics, Redland Hospital, Cleveland, Queensland, Australia
| | - Ben Kamien
- Genetic Services WA, Women and Newborn Heath Service, Subiaco, Western Australia, Australia.,Hunter Genetics, Hunter New England Health, New Lambton, New South Wales, Australia
| | - Matthew Edwards
- Hunter Genetics, Hunter New England Health, New Lambton, New South Wales, Australia
| | - Martin Delatycki
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Phillipa J Lamont
- Neurology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Sophelia Hs Chan
- Paediatric Neurology Division, Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Alison Colley
- Clinical Genetics Services SWSLHD, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Alan Ma
- Department of Clinical Genetics, Children's Hospital Westmead, Sydney, New South Wales, Australia
| | - Felicity Collins
- Clinical Genetics Department, Western Sydney Genetics Program, Children's Hospitalat Westmead, Westmead, New South Wales, Australia
| | - Lucinda Hennington
- Mercy Health, Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Austin Health, Melbourne, Victoria, Australia.,Alfred Health, Melbourne, Victoria, Australia
| | - Teresa Zhao
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - George McGillivray
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sondhya Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Katherine Chao
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Anne O'Donnell-Luria
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia.,PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
| | - Mark R Davis
- PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
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23
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Abstract
Identifying the molecular mechanisms that control differential gene expression (DE) is a major goal of basic and disease biology. We develop a systems biology model to predict DE, and mine the biological basis of the factors that influence predicted gene expression, in order to understand how it may be generated. This model, called DEcode, utilizes deep learning to predict DE based on genome-wide binding sites on RNAs and promoters. Ranking predictive factors from the DEcode indicates that clinically relevant expression changes between thousands of individuals can be predicted mainly through the joint action of post-transcriptional RNA-binding factors. We also show the broad potential applications of DEcode to generate biological insights, by predicting DE between tissues, differential transcript-usage, and drivers of aging throughout the human lifespan, of gene coexpression relationships on a genome-wide scale, and of frequently DE genes across diverse conditions. Researchers can freely utilize DEcode to identify influential molecular mechanisms for any human expression data - www.differentialexpression.org.
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24
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Abramovs N, Brass A, Tassabehji M. Hardy-Weinberg Equilibrium in the Large Scale Genomic Sequencing Era. Front Genet 2020; 11:210. [PMID: 32231685 PMCID: PMC7083100 DOI: 10.3389/fgene.2020.00210] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Abstract
Hardy-Weinberg Equilibrium (HWE) is used to estimate the number of homozygous and heterozygous variant carriers based on its allele frequency in populations that are not evolving. Deviations from HWE in large population databases have been used to detect genotyping errors, which can result in extreme heterozygote excess (HetExc). However, HetExc might also be a sign of natural selection since recessive disease causing variants should occur less frequently in a homozygous state in the population, but may reach high allele frequency in a heterozygous state, especially if they are advantageous. We developed a filtering strategy to detect these variants and applied it on genome data from 137,842 individuals. The main limitations of this approach were quality of genotype calls and insufficient population sizes, whereas population structure and inbreeding can reduce sensitivity, but not precision, in certain populations. Nevertheless, we identified 161 HetExc variants in 149 genes, most of which were specific to African/African American populations (∼79.5%). Although the majority of them were not associated with known diseases, or were classified as clinically "benign," they were enriched in genes associated with autosomal recessive diseases. The resulting dataset also contained two known recessive disease causing variants with evidence of heterozygote advantage in the sickle-cell anemia (HBB) and cystic fibrosis (CFTR). Finally, we provide supporting in silico evidence of a novel heterozygote advantageous variant in the chromodomain helicase DNA binding protein 6 gene (CHD6; involved in influenza virus replication). We anticipate that our approach will aid the detection of rare recessive disease causing variants in the future.
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Affiliation(s)
- Nikita Abramovs
- School of Computer Science, University of Manchester, Manchester, United Kingdom
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew Brass
- School of Computer Science, University of Manchester, Manchester, United Kingdom
- Faculty of Biology, Medicine and Health, School of Health Sciences, University of Manchester, Manchester, United Kingdom
| | - May Tassabehji
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, United Kingdom
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Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D. Human and mouse essentiality screens as a resource for disease gene discovery. Nat Commun 2020; 11:655. [PMID: 32005800 PMCID: PMC6994715 DOI: 10.1038/s41467-020-14284-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery.
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Grants
- UM1 HG008900 NHGRI NIH HHS
- UM1 HG006504 NHGRI NIH HHS
- MC_UP_1502/1 Medical Research Council
- UM1 HG006542 NHGRI NIH HHS
- UM1 OD023221 NIH HHS
- MC_U142684171 Medical Research Council
- MR/S006753/1 Medical Research Council
- UM1 HG006370 NHGRI NIH HHS
- UM1 HG006493 NHGRI NIH HHS
- U54 HG006370 NHGRI NIH HHS
- U54 HG006364 NHGRI NIH HHS
- MC_U142684172 Medical Research Council
- UM1 HG006348 NHGRI NIH HHS
- U42 OD011174 NIH HHS
- U42 OD011175 NIH HHS
- Wellcome Trust
- This work was supported by NIH grant U54 HG006370. IMPC-related mouse production and phenotyping was funded by the Government of Canada through Genome Canada and Ontario Genomics (OGI-051) for NorCOMM2 (C.M.) and the National Institutes of Health and OD, NCRR, NIDDK and NHLBI for KOMP and KOMP2 Projects U42 OD011175 and UM1OD023221 (C.M., K.C.K.L), Infrafrontier grant 01KX1012, EU Horizon2020: IPAD-MD funding 653961 (M.H.d.A); EUCOMM: LSHM-CT-2005-018931, EUCOMMTOOLS: FP7-HEALTH-F4-2010-261492 (W.G.W). UM1 HG006348; U42 OD011174; U54 HG005348 (A.L.B), NIH U54706HG006364 (A.L.B). Wellcome Trust grants WT098051 and WT206194 (D.A). The French National Centre for Scientific Research (CNRS), the French National Institute of Health and Medical Research (INSERM), the University of Strasbourg and the “Centre Europeen de Recherche en Biomedecine”, and the French state funds through the “Agence Nationale de la Recherche” under the frame programme Investissements d’Avenir labelled (ANR-10-IDEX-0002-02, ANR-10-LABX-0030-INRT, ANR-10-INBS-07 PHENOMIN (J.H.). This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. We are also grateful for the data access provided by the DDD and CMG projects. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003], a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute [grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. The Centers for Mendelian Genomics are funded by the National Human Genome Research Institute, the National Heart, Lung, and Blood Institute, and the National Eye Institute. Broad Institute (UM1 HG008900), Johns Hopkins University School of Medicine/Baylor College of Medicine (UM1 HG006542), University of Washington (UM1 HG006493), Yale University (UM1 HG006504).
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Affiliation(s)
- Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Mary E Dickinson
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | | | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ann M Flenniken
- The Centre for Phenogenomics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5T 3H7, Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Henrik Westerberg
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tomasz Konopka
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Chih-Wei Hsu
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Audrey Christiansen
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Denise G Lanza
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404, Illkirch, France
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tertius Hough
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
- Department of Developmental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85764, Neuherberg, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, 80336, Munich, Germany
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - John R Seavitt
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | | | - Colin McKerlie
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404, Illkirch, France
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA, 95618, USA
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
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