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Macken WL, Falabella M, McKittrick C, Pizzamiglio C, Ellmers R, Eggleton K, Woodward CE, Patel Y, Labrum R, Phadke R, Reilly MM, DeVile C, Sarkozy A, Footitt E, Davison J, Rahman S, Houlden H, Bugiardini E, Quinlivan R, Hanna MG, Vandrovcova J, Pitceathly RDS, Hubbard TJP, Jackson R, Jones LJ, Kasperaviciute D, Kayikci M, Kousathanas A, Lahnstein L, Lakey A, Leigh SEA, Leong IUS, Lopez FJ, Maleady-Crowe F, McEntagart M, Minneci F, Mitchell J, Moutsianas L, Mueller M, Murugaesu N, Need AC, O’Donovan P, Odhams CA, Patch C, Perez-Gil D, Pereira MB, Pullinger J, Rahim T, Rendon A, Rogers T, Savage K, Sawant K, Scott RH, Siddiq A, Sieghart A, Smith SC, Sosinsky A, Stuckey A, Tanguy M, Taylor Tavares AL, Thomas ERA, Thompson SR, Tucci A, Welland MJ, Williams E, Witkowska K, Wood SM, Zarowiecki M, Phadke R, Reilly MM, DeVile C, Sarkozy A, Footitt E, Davison J, Rahman S, Houlden H, Bugiardini E, Quinlivan R, Hanna MG, Vandrovcova J, Pitceathly RDS. Specialist multidisciplinary input maximises rare disease diagnoses from whole genome sequencing. Nat Commun 2022; 13:6324. [PMID: 36344503 PMCID: PMC9640711 DOI: 10.1038/s41467-022-32908-7] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Diagnostic whole genome sequencing (WGS) is increasingly used in rare diseases. However, standard, semi-automated WGS analysis may overlook diagnoses in complex disorders. Here, we show that specialist multidisciplinary analysis of WGS, following an initial 'no primary findings' (NPF) report, improves diagnostic rates and alters management. We undertook WGS in 102 adults with diagnostically challenging primary mitochondrial disease phenotypes. NPF cases were reviewed by a genomic medicine team, thus enabling bespoke informatic approaches, co-ordinated phenotypic validation, and functional work. We enhanced the diagnostic rate from 16.7% to 31.4%, with management implications for all new diagnoses, and detected strong candidate disease-causing variants in a further 3.9% of patients. This approach presents a standardised model of care that supports mainstream clinicians and enhances diagnostic equity for complex disorders, thereby facilitating access to the potential benefits of genomic healthcare. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project: http://www.genomicsengland.co.uk .
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Affiliation(s)
- William L. Macken
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK ,grid.436283.80000 0004 0612 2631NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Micol Falabella
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Caroline McKittrick
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Chiara Pizzamiglio
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK ,grid.436283.80000 0004 0612 2631NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Rebecca Ellmers
- Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Kelly Eggleton
- Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Cathy E. Woodward
- grid.436283.80000 0004 0612 2631NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK ,Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Yogen Patel
- Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Robyn Labrum
- grid.436283.80000 0004 0612 2631NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK ,Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | | | - Rahul Phadke
- grid.424537.30000 0004 5902 9895Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Mary M. Reilly
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Catherine DeVile
- grid.424537.30000 0004 5902 9895Department of Neurosciences, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Anna Sarkozy
- grid.424537.30000 0004 5902 9895Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Emma Footitt
- grid.424537.30000 0004 5902 9895Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - James Davison
- grid.424537.30000 0004 5902 9895Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK ,grid.420468.cNational Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Shamima Rahman
- grid.424537.30000 0004 5902 9895Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK ,grid.83440.3b0000000121901201Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Henry Houlden
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Enrico Bugiardini
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK ,grid.436283.80000 0004 0612 2631NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Rosaline Quinlivan
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK ,grid.436283.80000 0004 0612 2631NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK ,grid.424537.30000 0004 5902 9895Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Michael G. Hanna
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK ,grid.436283.80000 0004 0612 2631NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Robert D. S. Pitceathly
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK ,grid.436283.80000 0004 0612 2631NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
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Shoemark A, Griffin H, Wheway G, Hogg C, Lucas JS, Camps C, Taylor J, Carroll M, Loebinger MR, Chalmers JD, Morris-Rosendahl D, Mitchison HM, De Soyza A, Brown D, Ambrose JC, Arumugam P, Bevers R, Bleda M, Boardman-Pretty F, Boustred CR, Brittain H, Caulfield MJ, Chan GC, Fowler T, Giess A, Hamblin A, Henderson S, Hubbard TJP, Jackson R, Jones LJ, Kasperaviciute D, Kayikci M, Kousathanas A, Lahnstein L, Leigh SEA, Leong IUS, Lopez FJ, Maleady-Crowe F, McEntagart M, Minneci F, Moutsianas L, Mueller M, Murugaesu N, Need AC, O'Donovan P, Odhams CA, Patch C, Perez-Gil D, Pereira MB, Pullinger J, Rahim T, Rendon A, Rogers T, Savage K, Sawant K, Scott RH, Siddiq A, Sieghart A, Smith SC, Sosinsky A, Stuckey A, Tanguy M, Taylor Tavares AL, Thomas ERA, Thompson SR, Tucci A, Welland MJ, Williams E, Witkowska K, Wood SM. Genome sequencing reveals underdiagnosis of primary ciliary dyskinesia in bronchiectasis. Eur Respir J 2022; 60:13993003.00176-2022. [PMID: 35728977 DOI: 10.1183/13993003.00176-2022] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/12/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Bronchiectasis can result from infectious, genetic, immunological and allergic causes. 60-80% of cases are idiopathic, but a well-recognised genetic cause is the motile ciliopathy, primary ciliary dyskinesia (PCD). Diagnosis of PCD has management implications including addressing comorbidities, implementing genetic and fertility counselling and future access to PCD-specific treatments. Diagnostic testing can be complex; however, PCD genetic testing is moving rapidly from research into clinical diagnostics and would confirm the cause of bronchiectasis. METHODS This observational study used genetic data from severe bronchiectasis patients recruited to the UK 100,000 Genomes Project and patients referred for gene panel testing within a tertiary respiratory hospital. Patients referred for genetic testing due to clinical suspicion of PCD were excluded from both analyses. Data were accessed from the British Thoracic Society audit, to investigate whether motile ciliopathies are underdiagnosed in people with bronchiectasis in the UK. RESULTS Pathogenic or likely pathogenic variants were identified in motile ciliopathy genes in 17 (12%) out of 142 individuals by whole-genome sequencing. Similarly, in a single centre with access to pathological diagnostic facilities, 5-10% of patients received a PCD diagnosis by gene panel, often linked to normal/inconclusive nasal nitric oxide and cilia functional test results. In 4898 audited patients with bronchiectasis, <2% were tested for PCD and <1% received genetic testing. CONCLUSIONS PCD is underdiagnosed as a cause of bronchiectasis. Increased uptake of genetic testing may help to identify bronchiectasis due to motile ciliopathies and ensure appropriate management.
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Affiliation(s)
- Amelia Shoemark
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, Dundee, UK
- Royal Brompton Hospital and NHLI, Imperial College London, London, UK
- Newcastle University and NIHR Biomedical Research Centre for Ageing, Freeman Hospital, Newcastle upon Tyne, UK
| | - Helen Griffin
- Primary Immunodeficiency Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Newcastle University and NIHR Biomedical Research Centre for Ageing, Freeman Hospital, Newcastle upon Tyne, UK
| | - Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Claire Hogg
- Royal Brompton Hospital and NHLI, Imperial College London, London, UK
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | | | - Carme Camps
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Clinical Informatics Research Office, John Radcliffe Hospital, Oxford, UK
| | - Jenny Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Clinical Informatics Research Office, John Radcliffe Hospital, Oxford, UK
| | - Mary Carroll
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - James D Chalmers
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, Dundee, UK
| | - Deborah Morris-Rosendahl
- Clinical Genetics and Genomics, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust and NHLI, Imperial College London, London, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, UK
- These authors contributed equally to this manuscript
| | - Anthony De Soyza
- Newcastle University and NIHR Biomedical Research Centre for Ageing, Freeman Hospital, Newcastle upon Tyne, UK
- These authors contributed equally to this manuscript
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Chaudhry A, Noor A, Degagne B, Baker K, Bok LA, Brady AF, Chitayat D, Chung BH, Cytrynbaum C, Dyment D, Filges I, Helm B, Hutchison HT, Jeng LJB, Laumonnier F, Marshall CR, Menzel M, Parkash S, Parker MJ, Raymond LF, Rideout AL, Roberts W, Rupps R, Schanze I, Schrander-Stumpel CTRM, Speevak MD, Stavropoulos DJ, Stevens SJC, Thomas ERA, Toutain A, Vergano S, Weksberg R, Scherer SW, Vincent JB, Carter MT. Phenotypic spectrum associated withPTCHD1deletions and truncating mutations includes intellectual disability and autism spectrum disorder. Clin Genet 2014; 88:224-33. [DOI: 10.1111/cge.12482] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 11/28/2022]
Affiliation(s)
- A. Chaudhry
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
| | - A. Noor
- Department of Pathology and Laboratory Medicine; The Hospital for Sick Children; Toronto Ontario Canada
- Molecular Neuropsychiatry and Development Lab; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health; Toronto Ontario Canada
| | - B. Degagne
- Molecular Neuropsychiatry and Development Lab; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health; Toronto Ontario Canada
| | - K. Baker
- Department of Medical Genetics; Cambridge UK
- Institute for Medical Research Wellcome Trust; University of Cambridge; Cambridge UK
| | - L. A. Bok
- Department of Clinical Genetics, Unit of Cytogenetics; Maastricht University Medical Center; Maastricht The Netherlands
| | - A. F. Brady
- North West Thames Regional Genetics Service; Northwick Park Hospital; Harrow UK
| | - D. Chitayat
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital; University of Toronto; Toronto Ontario Canada
| | - B. H. Chung
- Department of Pediatrics and Adolescent Medicine, Department of Obstetrics and Gynaecology, Centre for Reproduction, Development and Growth, Centre for Genomic Sciences; The University of Hong Kong; Pok Fu Lam, Hong Kong
| | - C. Cytrynbaum
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
- Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - D. Dyment
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
| | - I. Filges
- Division of Medical Genetics, Department of Biomedicine; University Hospital Basel; Basel Switzerland
| | - B. Helm
- Division of Medical Genetics and Metabolism; Children's Hospital of The King's Daughters/Eastern Virginia Medical School; Norfolk VA USA
| | - H. T. Hutchison
- Departments of Neurology and Pediatrics; UCSF Fresno Medical Education Program; San Francisco CA USA
| | - L. J. B. Jeng
- Department of Laboratory Medicine; University of California; San Francisco CA USA
| | - F. Laumonnier
- UMR_INSERM U930 Faculté de Médecine; Université François Rabelais; Tours France
| | - C. R. Marshall
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Ontario Canada
| | | | - S. Parkash
- Maritime Medical Genetics Service; IWK Health Centre; Halifax Nova Scotia Canada
- Dalhousie University Halifax; Nova Scotia Canada
| | - M. J. Parker
- Sheffield Clinical Genetics Service; Sheffield Children's Hospital; Western Bank Sheffield UK
| | - L. F. Raymond
- Department of Medical Genetics; Cambridge UK
- Institute for Medical Research Wellcome Trust; University of Cambridge; Cambridge UK
| | - A. L. Rideout
- Maritime Medical Genetics Service; IWK Health Centre; Halifax Nova Scotia Canada
| | - W. Roberts
- Autism Research Unit; The Hospital for Sick Children; Toronto Ontario Canada
| | - R. Rupps
- Department of Medical Genetics, Children's and Women's Health Centre; University of British Columbia; Vancouver BC Canada
| | - I. Schanze
- Institute of Human Genetics; University Hospital Magedeburg; Magedeburg Germany
| | - C. T. R. M. Schrander-Stumpel
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW); Maastricht UMC+; Maastricht The Netherlands
| | - M. D. Speevak
- Credit Valley Site, Trillium Health Partners, Department of Laboratory Medicine and Pathobiology; University of Toronto; Toronto Onatario Canada
| | - D. J. Stavropoulos
- Department of Pathology and Laboratory Medicine; The Hospital for Sick Children; Toronto Ontario Canada
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Ontario Canada
| | - S. J. C. Stevens
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW); Maastricht UMC+; Maastricht The Netherlands
| | - E. R. A. Thomas
- Clinical Genetics Department; Guy's and St Thomas' NHS Foundation Trust; London UK
| | - A. Toutain
- UMR_INSERM U930 Faculté de Médecine; Université François Rabelais; Tours France
- Service de Génétique; Centre Hospitalo-Universitaire; Tours France
| | - S. Vergano
- Division of Medical Genetics and Metabolism; Children's Hospital of The King's Daughters/Eastern Virginia Medical School; Norfolk VA USA
| | - R. Weksberg
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
- Institute of Medical Science; Toronto Ontario Canada
- McLaughlin Centre and Department of Molecular Genetics; Toronto Ontario Canada
| | - S. W. Scherer
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Ontario Canada
- Institute of Medical Science; Toronto Ontario Canada
- McLaughlin Centre and Department of Molecular Genetics; Toronto Ontario Canada
| | - J. B. Vincent
- Molecular Neuropsychiatry and Development Lab; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health; Toronto Ontario Canada
- Institute of Medical Science; Toronto Ontario Canada
- Department of Psychiatry; University of Toronto; Toronto Ontario Canada
| | - M. T. Carter
- Department of Pediatrics; Division of Clinical and Metabolic Genetics; The Hospital for Sick Children; Toronto Ontario Canada
- Autism Research Unit; The Hospital for Sick Children; Toronto Ontario Canada
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