1
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, Sant DW, Stark Z, Whiffin N, Rehm HL, Ware JS. Toward robust clinical genome interpretation: Developing a consistent terminology to characterize Mendelian disease-gene relationships-allelic requirement, inheritance modes, and disease mechanisms. Genet Med 2024; 26:101029. [PMID: 37982373 PMCID: PMC11039201 DOI: 10.1016/j.gim.2023.101029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023] Open
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here, we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both Sequence Ontology (SO) and Human Phenotype Ontology (HPO) ontologies. Gene Curation Coalition member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom.
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Katherine S Josephs
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, United Kingdom
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom; Open Targets, Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David W Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia; University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, United Kingdom
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
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2
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Josephs KS, Roberts AM, Theotokis P, Walsh R, Ostrowski PJ, Edwards M, Fleming A, Thaxton C, Roberts JD, Care M, Zareba W, Adler A, Sturm AC, Tadros R, Novelli V, Owens E, Bronicki L, Jarinova O, Callewaert B, Peters S, Lumbers T, Jordan E, Asatryan B, Krishnan N, Hershberger RE, Chahal CAA, Landstrom AP, James C, McNally EM, Judge DP, van Tintelen P, Wilde A, Gollob M, Ingles J, Ware JS. Beyond gene-disease validity: capturing structured data on inheritance, allelic requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions. Genome Med 2023; 15:86. [PMID: 37872640 PMCID: PMC10594882 DOI: 10.1186/s13073-023-01246-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND As the availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than domain-specific experts. Demand is rising for laboratories to accurately classify variants in inherited cardiac condition (ICC) genes, including secondary findings. METHODS We analyse evidence for inheritance patterns, allelic requirement, disease mechanism and disease-relevant variant classes for 65 ClinGen-curated ICC gene-disease pairs. We present this information for the first time in a structured dataset, CardiacG2P, and assess application in genomic variant filtering. RESULTS For 36/65 gene-disease pairs, loss of function is not an established disease mechanism, and protein truncating variants are not known to be pathogenic. Using the CardiacG2P dataset as an initial variant filter allows for efficient variant prioritisation whilst maintaining a high sensitivity for retaining pathogenic variants compared with two other variant filtering approaches. CONCLUSIONS Access to evidence-based structured data representing disease mechanism and allelic requirement aids variant filtering and analysis and is a pre-requisite for scalable genomic testing.
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Affiliation(s)
- Katherine S Josephs
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Angharad M Roberts
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Great Ormond Street Hospital, NHS Foundation Trust, London, UK
| | - Pantazis Theotokis
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Roddy Walsh
- Amsterdam University Medical Centre, University of Amsterdam, Heart Center, Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | | | - Matthew Edwards
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andrew Fleming
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason D Roberts
- Population Health Research Institute, McMaster University, and Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Melanie Care
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Division of Cardiology, Toronto General Hospital, Toronto, Canada
| | - Wojciech Zareba
- Clinical Cardiovascular Research Center, University of Rochester, Rochester, NY, USA
| | - Arnon Adler
- Division of Cardiology, Peter Munk Cardiac Centre, University Health Network and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute, and Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Valeria Novelli
- Unit of Immunology and Functional Genomics, Centro Cardiologico Monzino IRCCS, Milano, Italy
| | - Emma Owens
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lucas Bronicki
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Genetics, CHEO, Ottawa, Ontario, Canada
| | - Olga Jarinova
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Genetics, CHEO, Ottawa, Ontario, Canada
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Stacey Peters
- Department of Cardiology and Genomic Medicine, Royal Melbourne Hospital, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Tom Lumbers
- Barts Health & University College London Hospitals NHS Trusts, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Elizabeth Jordan
- Divisions of Human Genetics and Cardiovascular Medicine, The Ohio State University, Columbus, OH, USA
| | - Babken Asatryan
- Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neesha Krishnan
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, The Ohio State University, Columbus, OH, USA
| | - C Anwar A Chahal
- Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, PA, USA
- Cardiac Electrophysiology and Inherited Cardiovascular Diseases, Cardiovascular Division, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
| | - Andrew P Landstrom
- Department of Pediatrics and Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Cynthia James
- Johns Hopkins Center for Inherited Heart Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Dept of Medicine (Cardiology), Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Daniel P Judge
- Medical University of South Carolina, Charleston, SC, USA
| | - Peter van Tintelen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arthur Wilde
- Department of Cardiology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
| | - Michael Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology, University of Toronto, Toronto, ON, Canada
| | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK.
- MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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3
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Josephs KS, Roberts AM, Theotokis P, Walsh R, Ostrowski PJ, Edwards M, Fleming A, Thaxton C, Roberts JD, Care M, Zareba W, Adler A, Sturm AC, Tadros R, Novelli V, Owens E, Bronicki L, Jarinova O, Callewaert B, Peters S, Lumbers T, Jordan E, Asatryan B, Krishnan N, Hershberger RE, Chahal CAA, Landstrom AP, James C, McNally EM, Judge DP, van Tintelen P, Wilde A, Gollob M, Ingles J, Ware JS. Beyond gene-disease validity: capturing structured data on inheritance, allelic-requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions. medRxiv 2023:2023.04.03.23287612. [PMID: 37066275 PMCID: PMC10104233 DOI: 10.1101/2023.04.03.23287612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Background As availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than domain-specific experts. Demand is rising for laboratories to accurately classify variants in inherited cardiac condition (ICC) genes, including as secondary findings. Methods We analyse evidence for inheritance patterns, allelic requirement, disease mechanism and disease-relevant variant classes for 65 ClinGen-curated ICC gene-disease pairs. We present this information for the first time in a structured dataset, CardiacG2P, and assess application in genomic variant filtering. Results For 36/65 gene-disease pairs, loss-of-function is not an established disease mechanism, and protein truncating variants are not known to be pathogenic. Using CardiacG2P as an initial variant filter allows for efficient variant prioritisation whilst maintaining a high sensitivity for retaining pathogenic variants compared with two other variant filtering approaches. Conclusions Access to evidence-based structured data representing disease mechanism and allelic requirement aids variant filtering and analysis and is pre-requisite for scalable genomic testing.
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Affiliation(s)
- Katherine S Josephs
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London UK
| | - Angharad M Roberts
- National Heart and Lung Institute, Imperial College London, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Roddy Walsh
- Amsterdam University Medical Centre, University of Amsterdam, Heart Center, Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | | | - Matthew Edwards
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London UK
| | - Andrew Fleming
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London UK
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason D Roberts
- Population Health Research Institute, McMaster University, and Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Melanie Care
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Division of Cardiology, Toronto General Hospital, Toronto, Canada
| | - Wojciech Zareba
- Clinical Cardiovascular Research Center, University of Rochester, Rochester, New York, USA
| | - Arnon Adler
- Division of Cardiology, Peter Munk Cardiac Centre, University Health Network and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Amy C Sturm
- 23andMe, Sunnyvale, California, Genomic Health
| | - Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute, and Faculty of Medicine, Université de Montréal
| | - Valeria Novelli
- Unit of Immunology and Functional Genomics, Centro Cardiologico Monzino IRCCS, Milano, Italy
| | - Emma Owens
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lucas Bronicki
- CHEO Research Institute, University of Ottawa, Ontario, Canada
| | - Olga Jarinova
- CHEO Research Institute, University of Ottawa, Ontario, Canada
- Department of Genetics, CHEO, Ontario, Canada
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital
- Department of Biomolecular Medicine, Ghent University
| | - Stacey Peters
- Department of Cardiology and Genomic Medicine, Royal Melbourne Hospital, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Tom Lumbers
- Barts Health & University College London Hospitals NHS Trusts, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Elizabeth Jordan
- Division of Human Genetics, The Ohio State University, Columbus, Ohio USA
| | - Babken Asatryan
- Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neesha Krishnan
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - Ray E Hershberger
- Division of Human Genetics, The Ohio State University, Columbus, Ohio USA
| | - C Anwar A Chahal
- Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, PA USA
- Cardiac Electrophysiology and Inherited Cardiovascular Diseases, Cardiovascular Division, Hospital of the University of Pennsylvania, Philadelphia, PA USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN USA
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
| | - Andrew P Landstrom
- Department of Pediatrics and Cell Biology, Duke University School of Medicine, Durham, North Carolina, US
| | - Cynthia James
- Johns Hopkins Center for Inherited Heart Diseases, Department of Medicine, Johns Hopkins
| | - Elizabeth M McNally
- Center for Genetic Medicine, Dept of Medicine (Cardiology), Northwestern University Feinberg School of Medicine, Chicago, IL US
| | - Daniel P Judge
- Medical University of South Carolina, Charleston, SC USA
| | - Peter van Tintelen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arthur Wilde
- Amsterdam UMC location University of Amsterdam, Department of Cardiology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences, Heart Failure and arrhythmias, Amsterdam, the Netherlands
| | - Michael Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology, University of Toronto, Toronto ON Canada
| | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London UK
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, van Sant D, Stark Z, Whiffin N, Rehm HL, Ware JS. Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms. medRxiv 2023:2023.03.30.23287948. [PMID: 37066232 PMCID: PMC10104222 DOI: 10.1101/2023.03.30.23287948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation, and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition (GenCC) members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both sequence ontology (SO) and human phenotype ontology (HPO) ontologies. GenCC member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Rooney Riggs
- Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA
| | - Katherine S Josephs
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC, 27599
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Ada Hamosh
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, EC1M 6BQ, UK
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
- Open Targets, Cambridge, UK
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA
| | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David van Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia
- University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - James S Ware
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
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5
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Mansour S, Josephs KS, Ostergaard P, Gordon K, Van Zanten M, Pearce J, Jeffery S, Keeley V, Riches K, Kreuter A, Wieland U, Hägerling R, Ratnam L, Sackey E, Grigoriadis D, Ho B, Smith F, Rauter E, Mortimer P, Macallan D. Redefining WILD syndrome: a primary lymphatic dysplasia with congenital multisegmental lymphoedema, cutaneous lymphovascular malformation, CD4 lymphopaenia and warts. J Med Genet 2023; 60:84-90. [PMID: 34916230 PMCID: PMC9811088 DOI: 10.1136/jmedgenet-2021-107820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 11/10/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Primary lymphoedema (PL) syndromes are increasingly recognised as presentations of complex genetic disease, with at least 20 identified causative genes. Recognition of clinical patterns is key to diagnosis, research and therapeutics. The defining criteria for one such clinical syndrome, 'WILD syndrome' (Warts, Immunodeficiency, Lymphoedema and anogenital Dysplasia), have previously depended on a single case report. METHODS AND RESULTS We present 21 patients (including the first described case) with similar clinical and immunological phenotypes. All had PL affecting multiple segments, with systemic involvement (intestinal lymphangiectasia/pleural or pericardial effusions) in 70% (n=14/20). Most (n=20, 95%) had a distinctive cutaneous lymphovascular malformation on the upper anterior chest wall. Some (n=10, 48%) also had hyperpigmented lesions resembling epidermal naevi (but probably lymphatic in origin). Warts were common (n=17, 81%) and often refractory. In contrast to the previous case report, anogenital dysplasia was uncommon-only found in two further cases (total n=3, 14%). Low CD4 counts and CD4:CD8 ratios typified the syndrome (17 of 19, 89%), but monocyte counts were universally normal, unlike GATA2 deficiency. CONCLUSION WILD syndrome is a previously unrecognised, underdiagnosed generalised PL syndrome. Based on this case series, we redefine WILD as 'Warts, Immunodeficiency, andLymphatic Dysplasia' and suggest specific diagnostic criteria. The essential criterion is congenital multisegmental PL in a 'mosaic' distribution. The major diagnostic features are recurrent warts, cutaneous lymphovascular malformations, systemic involvement (lymphatic dysplasia), genital swelling and CD4 lymphopaenia with normal monocyte counts. The absence of family history suggests a sporadic condition, and the random distribution of swelling implicates mosaic postzygotic mutation as the cause.
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Affiliation(s)
- Sahar Mansour
- Lymphovascular Research Unit, Molecular and Clinical Sciences Research Institute, University of London St George's, London, UK,SW Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Katherine S Josephs
- Lymphovascular Research Unit, Molecular and Clinical Sciences Research Institute, University of London St George's, London, UK,SW Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Pia Ostergaard
- Lymphovascular Research Unit, Molecular and Clinical Sciences Research Institute, University of London St George's, London, UK
| | - Kristiana Gordon
- Dermatology and Lymphovascular Medicine, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Malou Van Zanten
- Lymphovascular Research Unit, Molecular and Clinical Sciences Research Institute, University of London St George's, London, UK
| | - Julian Pearce
- Dermatology and Lymphovascular Medicine, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Steve Jeffery
- Lymphovascular Research Unit, Molecular and Clinical Sciences Research Institute, University of London St George's, London, UK
| | - Vaughan Keeley
- Lymphedema Clinic, Derby Hospitals NHS Foundation Trust, Derby, UK
| | - Katie Riches
- Lymphedema Clinic, Derby Hospitals NHS Foundation Trust, Derby, UK
| | - Alexander Kreuter
- Department of Dermatology, Venereology and Allergology, Helios St Elisabeth Hospital Oberhausen, University Witten-Herdecke, Oberhausen, Germany
| | - Ulrike Wieland
- National Reference Center for Papilloma and Polyomaviruses, Institute of Virology, Uniklinik Koln, University of Cologne, Cologne, Germany
| | - René Hägerling
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Lakshmi Ratnam
- Radiology Department, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Ege Sackey
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
| | - Dionysios Grigoriadis
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
| | - Bernard Ho
- Dermatology and Lymphovascular Medicine, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Frances Smith
- Viapath Haematology Laboratory, King's College Hospital NHS Foundation Trust, London, UK
| | - Elisabeth Rauter
- Viapath Haematology Laboratory, King's College Hospital NHS Foundation Trust, London, UK
| | - Peter Mortimer
- Dermatology and Lymphovascular Medicine, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Derek Macallan
- Infection Care Group, St George's University Hospitals NHS Foundation Trust, London, UK,Institute for Infection and Immunity, St George's University of London, London, UK
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6
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Garrett A, Talukdar S, Izatt L, Brady AF, Whyte S, Josephs KS, Shanmugasundaram M, Guillemot LS, Vakili D, Ey S, Ahmed M. Results from London Regional Clinical Genetics services over a 5-year period on germline TP53 testing in women diagnosed with breast cancer at <30 years. J Med Genet 2021; 59:554-558. [PMID: 34266904 DOI: 10.1136/jmedgenet-2021-107742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/06/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND The most common cancer diagnosed in germline TP53 pathogenic variant (PV) carriers is premenopausal breast cancer. An increased rate of breast tumour HER2 positivity has been reported in this group. Screening for breast/other cancers is recommended in PV carriers. OBJECTIVES 1. To assess the frequency of germline TP53 PVs reported diagnostically in women with breast cancer at <30 years of age.2. To evaluate the impact of personal/family history and HER2 status on the likelihood of germline TP53 pathogenic/likely pathogenic variant (PV/LPV) identification. METHODS Genetic test results from patients undergoing diagnostic germline TP53 tests between 2012 and 2017 in the four London Regional Clinical Genetics Services were reviewed. Clinical/pathology data and family history were extracted from genetics files for women diagnosed with breast cancer at <30 years. RESULTS The overall germline TP53 PV/LPV variant detection rate was 9/270=3.3% in all women diagnosed with breast cancer at <30 years and 2/171=1.2% in those with no second/subsequent cancer diagnosis or family history of TP53-spectrum cancers. Breast cancers were significantly more likely to be HER2-positive in TP53 PV/LPV carriers than in non-carriers (p=0.00006). CONCLUSIONS Germline TP53 PVs/LPVs are uncommon among women diagnosed with breast cancer aged <30 years without other relevant personal or family cancer history but have an important clinical impact when identified.
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Affiliation(s)
- Alice Garrett
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sabrina Talukdar
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Louise Izatt
- South East Thames Regional Genetics Service, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Angela F Brady
- North West Thames Regional Genetics Service, London North West University Healthcare NHS Trust, Harrow, UK
| | - Sinead Whyte
- North West Thames Regional Genetics Service, London North West University Healthcare NHS Trust, Harrow, UK
| | - Katherine S Josephs
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Monisha Shanmugasundaram
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Li Shan Guillemot
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Dara Vakili
- Institute of Child Health, University College London, London, UK
| | - Shevaun Ey
- Australian National University Medical School, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Munaza Ahmed
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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7
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Martin-Almedina S, Ogmen K, Sackey E, Grigoriadis D, Karapouliou C, Nadarajah N, Ebbing C, Lord J, Mellis R, Kortuem F, Dinulos MB, Polun C, Bale S, Atton G, Robinson A, Reigstad H, Houge G, von der Wense A, Becker WH, Jeffery S, Mortimer PS, Gordon K, Josephs KS, Robart S, Kilby MD, Vallee S, Gorski JL, Hempel M, Berland S, Mansour S, Ostergaard P. Correction: Janus-faced EPHB4-associated disorders: novel pathogenic variants and unreported intrafamilial overlapping phenotypes. Genet Med 2021; 23:1376-1377. [PMID: 34040196 PMCID: PMC8257488 DOI: 10.1038/s41436-021-01202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | - Kazim Ogmen
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Ege Sackey
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Dionysios Grigoriadis
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Christina Karapouliou
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Noeline Nadarajah
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Cathrine Ebbing
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | | | - Rhiannon Mellis
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Fanny Kortuem
- Institute of Human Genetics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Mary Beth Dinulos
- Departments of Pediatrics - Section of Genetics and Child Development, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.,Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Cassandra Polun
- Department of Child Health, University of Missouri School of Medicine, Columbia, MO, USA
| | - Sherri Bale
- GeneDx, 207 Perry Parkway, Gaithersburg, MD, USA
| | - Giles Atton
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Alexandra Robinson
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.,University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Hallvard Reigstad
- Neonatal intensive care unit, Children's Department, Haukeland University Hospital, Bergen, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Axel von der Wense
- Department of Neonatology and Paediatric Intensive Care, Altona Children's Hospital, Hamburg, Germany
| | | | - Steve Jeffery
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Peter S Mortimer
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.,Dermatology & Lymphovascular Medicine, St George's Universities NHS Foundation Trust, London, UK
| | - Kristiana Gordon
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.,Dermatology & Lymphovascular Medicine, St George's Universities NHS Foundation Trust, London, UK
| | - Katherine S Josephs
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.,South West Thames Regional Genetics Service, St George's NHS Foundation Trust, London, UK
| | - Sarah Robart
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Mark D Kilby
- The Institute of Metabolism & Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK.,West Midlands Fetal Medicine Centre, Birmingham Women's & Children's Foundation Trust, Birmingham, UK
| | - Stephanie Vallee
- Departments of Pediatrics - Section of Genetics and Child Development, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Jerome L Gorski
- Department of Child Health, University of Missouri School of Medicine, Columbia, MO, USA
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Sahar Mansour
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK. .,South West Thames Regional Genetics Service, St George's NHS Foundation Trust, London, UK.
| | - Pia Ostergaard
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.
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8
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Martin-Almedina S, Ogmen K, Sackey E, Grigoriadis D, Karapouliou C, Nadarajah N, Ebbing C, Lord J, Mellis R, Kortuem F, Dinulos MB, Polun C, Bale S, Atton G, Robinson A, Reigstad H, Houge G, von der Wense A, Becker WH, Jeffery S, Mortimer PS, Gordon K, Josephs KS, Robart S, Kilby MD, Vallee S, Gorski JL, Hempel M, Berland S, Mansour S, Ostergaard P. Janus-faced EPHB4-associated disorders: novel pathogenic variants and unreported intrafamilial overlapping phenotypes. Genet Med 2021; 23:1315-1324. [PMID: 33864021 PMCID: PMC8257501 DOI: 10.1038/s41436-021-01136-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 01/13/2023] Open
Abstract
Purpose Several clinical phenotypes including fetal hydrops, central conducting lymphatic anomaly or capillary malformations with arteriovenous malformations 2 (CM-AVM2) have been associated with EPHB4 (Ephrin type B receptor 4) variants, demanding new approaches for deciphering pathogenesis of novel variants of uncertain significance (VUS) identified in EPHB4, and for the identification of differentiated disease mechanisms at the molecular level. Methods Ten index cases with various phenotypes, either fetal hydrops, CM-AVM2, or peripheral lower limb lymphedema, whose distinct clinical phenotypes are described in detail in this study, presented with a variant in EPHB4. In vitro functional studies were performed to confirm pathogenicity. Results Pathogenicity was demonstrated for six of the seven novel EPHB4 VUS investigated. A heterogeneity of molecular disease mechanisms was identified, from loss of protein production or aberrant subcellular localization to total reduction of the phosphorylation capability of the receptor. There was some phenotype–genotype correlation; however, previously unreported intrafamilial overlapping phenotypes such as lymphatic-related fetal hydrops (LRFH) and CM-AVM2 in the same family were observed. Conclusion This study highlights the usefulness of protein expression and subcellular localization studies to predict EPHB4 variant pathogenesis. Our accurate clinical phenotyping expands our interpretation of the Janus-faced spectrum of EPHB4-related disorders, introducing the discovery of cases with overlapping phenotypes.
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Affiliation(s)
| | - Kazim Ogmen
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Ege Sackey
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Dionysios Grigoriadis
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Christina Karapouliou
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Noeline Nadarajah
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Cathrine Ebbing
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | | | - Rhiannon Mellis
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Fanny Kortuem
- Institute of Human Genetics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Mary Beth Dinulos
- Departments of Pediatrics - Section of Genetics and Child Development, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.,Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Cassandra Polun
- Department of Child Health, University of Missouri School of Medicine, Columbia, MO, USA
| | - Sherri Bale
- GeneDx, 207 Perry Parkway, Gaithersburg, MD, USA
| | - Giles Atton
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Alexandra Robinson
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.,University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Hallvard Reigstad
- Neonatal intensive care unit, Children's Department, Haukeland University Hospital, Bergen, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Axel von der Wense
- Department of Neonatology and Paediatric Intensive Care, Altona Children's Hospital, Hamburg, Germany
| | | | - Steve Jeffery
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Peter S Mortimer
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.,Dermatology & Lymphovascular Medicine, St George's Universities NHS Foundation Trust, London, UK
| | - Kristiana Gordon
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.,Dermatology & Lymphovascular Medicine, St George's Universities NHS Foundation Trust, London, UK
| | - Katherine S Josephs
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.,South West Thames Regional Genetics Service, St George's NHS Foundation Trust, London, UK
| | - Sarah Robart
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Mark D Kilby
- The Institute of Metabolism & Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK.,West Midlands Fetal Medicine Centre, Birmingham Women's & Children's Foundation Trust, Birmingham, UK
| | - Stephanie Vallee
- Departments of Pediatrics - Section of Genetics and Child Development, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Jerome L Gorski
- Department of Child Health, University of Missouri School of Medicine, Columbia, MO, USA
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Sahar Mansour
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK. .,South West Thames Regional Genetics Service, St George's NHS Foundation Trust, London, UK.
| | - Pia Ostergaard
- Molecular and Clinical Sciences Institute, St George's University of London, London, UK.
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9
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Cordeddu V, Macke EL, Radio FC, Lo Cicero S, Pantaleoni F, Tatti M, Bellacchio E, Ciolfi A, Agolini E, Bruselles A, Brunetti-Pierri N, Suri M, Josephs KS, McEntagart M, Lanpher B, Nickels KC, Haworth A, Reed L, Cappuccio G, Mammi I, Tarnowski JM, Novelli A, Melis D, Callewaert B, Dallapiccola B, Klee E, Tartaglia M. Refinement of the clinical and mutational spectrum of UBE2A deficiency syndrome. Clin Genet 2020; 98:172-178. [PMID: 32415735 DOI: 10.1111/cge.13775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/13/2022]
Abstract
UBE2A deficiency, that is, intellectual disability (ID) Nascimento type (MIM 300860), is an X-linked syndrome characterized by developmental delay, moderate to severe ID, seizures, dysmorphisms, skin anomalies, and urogenital malformations. Forty affected subjects have been reported thus far, with 31 cases having intragenic UBE2A variants. Here, we report on additional eight affected subjects from seven unrelated families who were found to be hemizygous for previously unreported UBE2A missense variants (p.Glu62Lys, p.Arg95Cys, p.Thr99Ala, and p.Arg135Trp) or small in-frame deletions (p.Val81_Ala83del, and p.Asp101del). A wide phenotypic spectrum was documented in these subjects, ranging from moderate ID associated with mild dysmorphisms to severe features including congenital heart defects (CHD), severe cognitive impairment, and pineal gland tumors. Four variants affected residues (Glu62, Arg95, Thr99 and Asp101) that contribute to stabilizing the structure of the E3 binding domain. The three-residue in-frame deletion, p.Val81_Ala83del, resulted from aberrant processing of the transcript. This variant and p.Arg135Trp mapped to regions of the protein located far from the E3 binding region, and caused variably accelerated protein degradation. By reviewing available clinical information, we revise the clinical and molecular profile of the disorder and document genotype-phenotype correlations. Pineal gland cysts/tumors, CHD and hypogammaglobulinemia emerge as recurrent features.
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Affiliation(s)
- Viviana Cordeddu
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCSS, Rome, Italy
| | - Massimo Tatti
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCSS, Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCSS, Rome, Italy
| | - Emanuele Agolini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCSS, Rome, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Mohnish Suri
- Regional Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | | | | | - Brendan Lanpher
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Laura Reed
- Congenica, Wellcome Genome Campus, Cambridge, UK
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | | | - Antonio Novelli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCSS, Rome, Italy
| | -
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Daniela Melis
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana", Università di Salerno, Salerno, Italy
| | - Bert Callewaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCSS, Rome, Italy
| | - Eric Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCSS, Rome, Italy
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10
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Josephs KS, Berner A, George A, Scott RH, Firth HV, Tatton-Brown K. Genomics: the power, potential and pitfalls of the new technologies and how they are transforming healthcare. Clin Med (Lond) 2019; 19:269-272. [PMID: 31308101 PMCID: PMC6752247 DOI: 10.7861/clinmedicine.19-4-269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Powerful new genomic technologies are transforming healthcare. The faster, cheaper generation of genomic data is driving the integration of genomics into all healthcare specialties. Within the next decade, healthcare professionals will be using genomic data to diagnose and manage their patients.However, despite these exciting advances, few clinicians are aware of or prepared for this genomics-based future. Through five patient-focused scenarios with accompanying interviews, this article showcases new genomic technologies while highlighting the inherent challenges associated with complex genomic data.
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Affiliation(s)
- Katherine S Josephs
- South West Thames Regional Genetic Services, London, UK and St George's, University of London, London, UK
| | - Alison Berner
- Barts Cancer Institute, London, UK and clinical research fellow, Genomics England, London, UK
| | | | - Richard H Scott
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK and clinical lead for rare disease, 100,000 Genome Project, Genomics England, London, UK
| | - Helen V Firth
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK and Wellcome Sanger Institute, Cambridge, UK and Joint Committee on Genomics in Medicine, Royal College of Physicians, London, UK
| | - Katrina Tatton-Brown
- St George's University Hospitals NHS Foundation Trust, London, UK and professor in clinical genetics and genomic education, St George's, University of London, London, UK and Joint Committee on Genomics in Medicine, Royal College of Physicians, London, UK
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