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Allen S, Loong L, Garrett A, Torr B, Durkie M, Drummond J, Callaway A, Robinson R, Burghel GJ, Hanson H, Field J, McDevitt T, McVeigh TP, Bedenham T, Bowles C, Bradshaw K, Brooks C, Butler S, Del Rey Jimenez JC, Hawkes L, Stinton V, MacMahon S, Owens M, Palmer-Smith S, Smith K, Tellez J, Valganon-Petrizan M, Waskiewicz E, Yau M, Eccles DM, Tischkowitz M, Goel S, McRonald F, Antoniou AC, Morris E, Hardy S, Turnbull C. Recommendations for laboratory workflow that better support centralised amalgamation of genomic variant data: findings from CanVIG-UK national molecular laboratory survey. J Med Genet 2024; 61:305-312. [PMID: 38154813 PMCID: PMC10982625 DOI: 10.1136/jmg-2023-109645] [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: 09/18/2023] [Accepted: 10/28/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND National and international amalgamation of genomic data offers opportunity for research and audit, including analyses enabling improved classification of variants of uncertain significance. Review of individual-level data from National Health Service (NHS) testing of cancer susceptibility genes (2002-2023) submitted to the National Disease Registration Service revealed heterogeneity across participating laboratories regarding (1) the structure, quality and completeness of submitted data, and (2) the ease with which that data could be assembled locally for submission. METHODS In May 2023, we undertook a closed online survey of 51 clinical scientists who provided consensus responses representing all 17 of 17 NHS molecular genetic laboratories in England and Wales which undertake NHS diagnostic analyses of cancer susceptibility genes. The survey included 18 questions relating to 'next-generation sequencing workflow' (11), 'variant classification' (3) and 'phenotypical context' (4). RESULTS Widely differing processes were reported for transfer of variant data into their local LIMS (Laboratory Information Management System), for the formatting in which the variants are stored in the LIMS and which classes of variants are retained in the local LIMS. Differing local provisions and workflow for variant classifications were also reported, including the resources provided and the mechanisms by which classifications are stored. CONCLUSION The survey responses illustrate heterogeneous laboratory workflow for preparation of genomic variant data from local LIMS for centralised submission. Workflow is often labour-intensive and inefficient, involving multiple manual steps which introduce opportunities for error. These survey findings and adoption of the concomitant recommendations may support improvement in laboratory dataflows, better facilitating submission of data for central amalgamation.
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Affiliation(s)
- Sophie Allen
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Lucy Loong
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Alice Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Bethany Torr
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, NEY Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - James Drummond
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Rachel Robinson
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Helen Hanson
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Joanne Field
- Genomics and Molecular Medicine Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Trudi McDevitt
- Department of Clinical Genetics, CHI at Crumlin, Dublin, Ireland
| | - Terri P McVeigh
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Tina Bedenham
- West Midlands, Oxford and Wessex Genomic Laboratory Hub, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christopher Bowles
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Kirsty Bradshaw
- East Midlands and East of England Genomics Laboratory, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Claire Brooks
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Samantha Butler
- Central and South Genomic Laboratory Hub, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Lorraine Hawkes
- South East Genomics Laboratory Hub, Guy's Hospital, London, UK
| | - Victoria Stinton
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Suzanne MacMahon
- Centre for Molecular Pathology, Institute of Cancer Research Sutton, Sutton, UK
- Department of Molecular Diagnostics, The Royal Marsden NHS Foundation Trust, London, UK
| | - Martina Owens
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sheila Palmer-Smith
- Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Kenneth Smith
- South West Genomic Laboratory Hub, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - James Tellez
- North East and Yorkshire Genomic Laboratory Hub, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mikel Valganon-Petrizan
- Centre for Molecular Pathology, Institute of Cancer Research Sutton, Sutton, UK
- Department of Molecular Diagnostics, The Royal Marsden NHS Foundation Trust, London, UK
| | - Erik Waskiewicz
- Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Michael Yau
- South East Genomics Laboratory Hub, Guy's Hospital, London, UK
| | - Diana M Eccles
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Shilpi Goel
- NHS England, National Disease Registration Service, London, UK
- Health Data Insight CIC, Cambridge, UK
| | - Fiona McRonald
- NHS England, National Disease Registration Service, London, UK
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, University of Cambridge Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Eva Morris
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Steven Hardy
- NHS England, National Disease Registration Service, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
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Nolan J, Buchanan J, Taylor J, Almeida J, Bedenham T, Blair E, Broadgate S, Butler S, Cazeaux A, Craft J, Cranston T, Crawford G, Forrest J, Gabriel J, George E, Gillen D, Haeger A, Hastings Ward J, Hawkes L, Hodgkiss C, Hoffman J, Jones A, Karpe F, Kasperaviciute D, Kovacs E, Leigh S, Limb E, Lloyd-Jani A, Lopez J, Lucassen A, McFarlane C, O'Rourke AW, Pond E, Sherman C, Stewart H, Thomas E, Thomas S, Thomas T, Thomson K, Wakelin H, Walker S, Watson M, Williams E, Ormondroyd E. Secondary (additional) findings from the 100,000 Genomes Project: Disease manifestation, health care outcomes, and costs of disclosure. Genet Med 2024; 26:101051. [PMID: 38131308 DOI: 10.1016/j.gim.2023.101051] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE The UK 100,000 Genomes Project offered participants screening for additional findings (AFs) in genes associated with familial hypercholesterolemia (FH) or hereditary cancer syndromes including breast/ovarian cancer (HBOC), Lynch, familial adenomatous polyposis, MYH-associated polyposis, multiple endocrine neoplasia (MEN), and von Hippel-Lindau. Here, we report disclosure processes, manifestation of AF-related disease, outcomes, and costs. METHODS An observational study in an area representing one-fifth of England. RESULTS Data were collected from 89 adult AF recipients. At disclosure, among 57 recipients of a cancer-predisposition-associated AF and 32 recipients of an FH-associated AF, 35% and 88%, respectively, had personal and/or family history evidence of AF-related disease. During post-disclosure investigations, 4 cancer-AF recipients had evidence of disease, including 1 medullary thyroid cancer. Six women with an HBOC AF, 3 women with a Lynch syndrome AF, and 2 individuals with a MEN AF elected for risk-reducing surgery. New hyperlipidemia diagnoses were made in 6 FH-AF recipients and treatment (re-)initiated for 7 with prior hyperlipidemia. Generating and disclosing AFs in this region cost £1.4m; £8680 per clinically significant AF. CONCLUSION Generation and disclosure of AFs identifies individuals with and without personal or familial evidence of disease and prompts appropriate clinical interventions. Results can inform policy toward secondary findings.
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Affiliation(s)
- Joshua Nolan
- Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, University of Oxford, United Kingdom
| | - John Taylor
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joao Almeida
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Tina Bedenham
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Suzanne Broadgate
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Samantha Butler
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Angela Cazeaux
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Judith Craft
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Treena Cranston
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Gillian Crawford
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Jamie Forrest
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; University of Manchester, Manchester, United Kingdom
| | - Jessica Gabriel
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Elaine George
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Donna Gillen
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Ash Haeger
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | | | - Lara Hawkes
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Claire Hodgkiss
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Jonathan Hoffman
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Alan Jones
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Fredrik Karpe
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Dalia Kasperaviciute
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Erika Kovacs
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Sarah Leigh
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Limb
- Population Health Research Institute, St George's University of London, London, United Kingdom
| | - Anjali Lloyd-Jani
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Javier Lopez
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Anneke Lucassen
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Centre for Personalised Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Carlos McFarlane
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Anthony W O'Rourke
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Emily Pond
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Catherine Sherman
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Ellen Thomas
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Simon Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Tessy Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate Thomson
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Hannah Wakelin
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Susan Walker
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Melanie Watson
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Eleanor Williams
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Ormondroyd
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
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Loong L, Huntley C, McRonald F, Santaniello F, Pethick J, Torr B, Allen S, Tulloch O, Goel S, Shand B, Rahman T, Luchtenborg M, Garrett A, Barber R, Bedenham T, Bourn D, Bradshaw K, Brooks C, Bruty J, Burghel GJ, Butler S, Buxton C, Callaway A, Callaway J, Drummond J, Durkie M, Field J, Jenkins L, McVeigh TP, Mountford R, Nyanhete R, Petrides E, Robinson R, Scott T, Stinton V, Tellez J, Wallace AJ, Yarram-Smith L, Sahan K, Hallowell N, Eccles DM, Pharoah P, Tischkowitz M, Antoniou AC, Evans DG, Lalloo F, Norbury G, Morris E, Burn J, Hardy S, Turnbull C. Germline mismatch repair (MMR) gene analyses from English NHS regional molecular genomics laboratories 1996-2020: development of a national resource of patient-level genomics laboratory records. J Med Genet 2023; 60:669-678. [PMID: 36572524 PMCID: PMC10359571 DOI: 10.1136/jmg-2022-108800] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/18/2022] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To describe national patterns of National Health Service (NHS) analysis of mismatch repair (MMR) genes in England using individual-level data submitted to the National Disease Registration Service (NDRS) by the NHS regional molecular genetics laboratories. DESIGN Laboratories submitted individual-level patient data to NDRS against a prescribed data model, including (1) patient identifiers, (2) test episode data, (3) per-gene results and (4) detected sequence variants. Individualised per-laboratory algorithms were designed and applied in NDRS to extract and map the data to the common data model. Laboratory-level MMR activity audit data from the Clinical Molecular Genetics Society/Association of Clinical Genomic Science were used to assess early years' missing data. RESULTS Individual-level data from patients undergoing NHS MMR germline genetic testing were submitted from all 13 English laboratories performing MMR analyses, comprising in total 16 722 patients (9649 full-gene, 7073 targeted), with the earliest submission from 2000. The NDRS dataset is estimated to comprise >60% of NHS MMR analyses performed since inception of NHS MMR analysis, with complete national data for full-gene analyses for 2016 onwards. Out of 9649 full-gene tests, 2724 had an abnormal result, approximately 70% of which were (likely) pathogenic. Data linkage to the National Cancer Registry demonstrated colorectal cancer was the most frequent cancer type in which full-gene analysis was performed. CONCLUSION The NDRS MMR dataset is a unique national pan-laboratory amalgamation of individual-level clinical and genomic patient data with pseudonymised identifiers enabling linkage to other national datasets. This growing resource will enable longitudinal research and can form the basis of a live national genomic disease registry.
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Affiliation(s)
- Lucy Loong
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Catherine Huntley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Fiona McRonald
- NHS Digital, National Disease Registration Service, London, UK
| | - Francesco Santaniello
- NHS Digital, National Disease Registration Service, London, UK
- Health Data Insight CIC, Cambridge, UK
| | - Joanna Pethick
- NHS Digital, National Disease Registration Service, London, UK
| | - Bethany Torr
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Sophie Allen
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Oliver Tulloch
- NHS Digital, National Disease Registration Service, London, UK
- Health Data Insight CIC, Cambridge, UK
| | - Shilpi Goel
- NHS Digital, National Disease Registration Service, London, UK
- Health Data Insight CIC, Cambridge, UK
| | - Brian Shand
- NHS Digital, National Disease Registration Service, London, UK
- Health Data Insight CIC, Cambridge, UK
| | - Tameera Rahman
- NHS Digital, National Disease Registration Service, London, UK
- Health Data Insight CIC, Cambridge, UK
| | - Margreet Luchtenborg
- NHS Digital, National Disease Registration Service, London, UK
- Centre for Cancer, Society & Public Health, King's College London, London, UK
| | - Alice Garrett
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Richard Barber
- Central and South Genomic Laboratory Hub, West Midlands Regional Genetics Laboratory, Birmingham, UK
| | - Tina Bedenham
- West Midlands, Oxford and Wessex Genomic Laboratory Hub, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Bourn
- North East and Yorkshire Genomic Laboratory Hub, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Kirsty Bradshaw
- East Midlands and East of England Genomics Laboratory, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Claire Brooks
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jonathan Bruty
- East Genomic Laboratory Hub, Cambridge University Hospitals Genomic Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Samantha Butler
- Central and South Genomic Laboratory Hub, West Midlands Regional Genetics Laboratory, Birmingham, UK
| | - Chris Buxton
- Bristol Genetics Laboratory, Southmead Hospital, Bristol, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury Hospital NHS Foundation Trust, Salisbury, UK
| | - Jonathan Callaway
- Wessex Regional Genetics Laboratory, Salisbury Hospital NHS Foundation Trust, Salisbury, UK
| | - James Drummond
- East Genomic Laboratory Hub, Cambridge University Hospitals Genomic Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, North East and Yorkshire Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Joanne Field
- East Midlands and East of England Genomics Laboratory, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Lucy Jenkins
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Terri P McVeigh
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
- Cancer Genetics Unit, Royal Marsden Hospital NHS Trust, London, UK
| | - Roger Mountford
- North West Genomic Laboratory Hub (Liverpool), Manchester Centre for Genomic Medicine, Liverpool, UK
| | - Rodney Nyanhete
- Sheffield Diagnostic Genetics Service, North East and Yorkshire Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Evgenia Petrides
- West Midlands, Oxford and Wessex Genomic Laboratory Hub, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rachel Robinson
- Yorkshire and North East Genomic Laboratory Hub, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Tracy Scott
- Yorkshire and North East Genomic Laboratory Hub, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Victoria Stinton
- North West Genomic Laboratory Hub (Liverpool), Manchester Centre for Genomic Medicine, Liverpool, UK
| | - James Tellez
- North East and Yorkshire Genomic Laboratory Hub, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Kate Sahan
- The Ethox Centre and Wellcome Centre for Ethics and Humanities, Nuffield Department of Population Health, University of Oxford Ethox Centre, Oxford, UK
| | - Nina Hallowell
- The Ethox Centre and Wellcome Centre for Ethics and Humanities, Nuffield Department of Population Health, University of Oxford Ethox Centre, Oxford, UK
| | - Diana M Eccles
- Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Paul Pharoah
- Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Antonis C Antoniou
- Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution & Genomic Sciences, The University of Manchester, Manchester, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gail Norbury
- South East Genomic Laboratory Hub, Guy's and St Thomas' Hospitals NHS Trust, London, UK
| | - Eva Morris
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - John Burn
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Steven Hardy
- NHS Digital, National Disease Registration Service, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
- Cancer Genetics Unit, Royal Marsden Hospital NHS Trust, London, UK
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Murphy A, Solomons J, Risby P, Gabriel J, Bedenham T, Johnson M, Atkinson N, Bailey AA, Bird‐Lieberman E, Leedham SJ, East JE, Biswas S. Germline variant testing in serrated polyposis syndrome. J Gastroenterol Hepatol 2022; 37:861-869. [PMID: 35128723 PMCID: PMC9305167 DOI: 10.1111/jgh.15791] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 12/13/2021] [Accepted: 01/12/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND AND AIM Serrated polyposis syndrome (SPS) is now known to be the commonest polyposis syndrome. Previous analyses for germline variants have shown no consistent positive findings. To exclude other polyposis syndromes, 2019 British Society of Gastroenterology (BSG) guidelines advise gene panel testing if the patient is under 50 years, there are multiple affected individuals within a family, or there is dysplasia within any of the polyps. METHODS A database of SPS patients was established at the Oxford University Hospitals NHS Foundation Trust. Patients were referred for genetic assessment based on personal and family history and patient preference. The majority were tested for a hereditary colorectal cancer panel including MUTYH, APC, PTEN, SMAD4, BMPR1A, STK11, NTLH1, POLD1, POLE, GREM1 (40-kb duplication), PMS2, and Lynch syndrome mismatch repair genes. RESULTS One hundred and seventy-three patients were diagnosed with SPS based on World Health Organization 2019 criteria between February 2010 and December 2020. The mean age of diagnosis was 54.2 ± 16.8 years. Seventy-three patients underwent genetic testing and 15/73 (20.5%) were found to have germline variants, of which 7/73 (9.6%) had a pathogenic variant (MUTYH n = 2, SMAD4 n = 1, CHEK2 n = 2, POLD1 n = 1, and RNF43 n = 1). Only 60% (9/15) of these patients would have been recommended for gene panel testing according to current BSG guidelines. CONCLUSIONS A total of 20.5% of SPS patients tested were affected by heterozygous germline variants, including previously unreported associations with CHEK2 and POLD1. This led to a change in management in seven patients (9.6%). Current recommendations may miss SPS associated with germline variants, which is more common than previously anticipated.
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Affiliation(s)
- Aisling Murphy
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Joyce Solomons
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Peter Risby
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Jessica Gabriel
- Oxford Regional Genetics Laboratories, Churchill HospitalOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Tina Bedenham
- Oxford Regional Genetics Laboratories, Churchill HospitalOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Michael Johnson
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Nathan Atkinson
- New Zealand Familial Gastrointestinal Cancer RegistryAuckland City HospitalAucklandNew Zealand
| | - Adam A Bailey
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Elizabeth Bird‐Lieberman
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Simon J Leedham
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK,Intestinal Stem Cell Biology Lab, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - James E East
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Sujata Biswas
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK,Gastroenterology DepartmentBuckinghamshire Healthcare NHS TrustUK
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Pitts SA, Kullar HS, Stankovic T, Stewart GS, Last JI, Bedenham T, Armstrong SJ, Piane M, Chessa L, Taylor AM, Byrd PJ. hMRE11: genomic structure and a null mutation identified in a transcript protected from nonsense-mediated mRNA decay. Hum Mol Genet 2001; 10:1155-62. [PMID: 11371508 DOI: 10.1093/hmg/10.11.1155] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [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] [Indexed: 11/13/2022] Open
Abstract
We showed recently that mutation of the hMRE11 gene identified a new ataxia telangiectasia-like disorder (ATLD). In this report we describe the genomic organization of the hMRE11 gene and the analysis of a promoter region that appears to direct the divergent transcription of hMRE11 and the adjacent gene. The characterization of the genomic organization of the hMRE11 gene allowed us to determine the basis of an apparent null hMRE11 allele present in the mother and two patients in one of our two ATLD families. Polymorphic markers in the hMRE11 gene, including the promoter region, provided evidence that the mutated maternal allele was not deleted. An exon by exon search revealed the presence of a missense mutation in exon 15, the effect of which was to create a premature termination codon. Transcripts derived from the mutant allele were found to be subject to nonsense-mediated mRNA decay (NMD). Therefore, this allele was effectively null, because little if any mRNA from it was available for translation. The ATLD patients carrying this protein-truncating hMRE11 mutation have survived because the null allele they inherited from their mother is present with a missense mutation inherited from their father, which is expressed as normal levels of partially functional MRE11 protein. The mutation in the maternal hMRE11 allele of family 2 was also identified in a further unrelated Italian family with ATLD and also found to be subject to NMD.
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Affiliation(s)
- S A Pitts
- The University of Birmingham CRC Institute for Cancer Studies, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK
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6
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Abstract
BACKGROUND Patients with the inherited disorder ataxia telangiectasia (A-T) have an increased susceptibility to lymphoid malignancies. In these patients mutations affect both alleles of the A-T gene (ATM). We have looked for mutations in the ATM gene in sporadic cases of B-cell chronic lymphocytic leukaemia (B-CLL). METHODS 32 cases of B-CLL were analysed by restriction endonuclease fingerprinting to detect mutations within ATM. In six of the cases in which mutations were detected in tumour samples, germline DNA was screened to assess ATM carrier status. The samples in 20 cases were also studied by western blot for abnormal expression of ATM protein. FINDINGS Expression of the ATM protein was impaired in eight (40%) of the 20 tumours analysed, being absent in three and decreased in five. Mutations within ATM were detected in six (18%) of the 32 patients. These point mutations, deletions, and one insertion were distributed across the coding sequence of ATM. Germline mutations, which indicate ATM carrier status, were found in two of these six patients compared with a frequency within the general population of below 1 in 200. INTERPRETATION Abnormal expression of ATM protein is a frequent finding in B-CLL. Although the precise function of this protein is unknown, it is thought to have a role in programmed cell death, a deficiency of which would fit with the characteristic phenotype of prolonged cell survival seen in B-CLL tumour cells. Our results also suggest that carriers of ATM mutations may be at a particular risk for the development of B-CLL and this may partly explain the known genetic susceptibility to this disease.
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Affiliation(s)
- T Stankovic
- CRC Institute for Cancer Studies, Medical School, University of Birmingham, Edgbaston, UK
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Stankovic T, Kidd AM, Sutcliffe A, McGuire GM, Robinson P, Weber P, Bedenham T, Bradwell AR, Easton DF, Lennox GG, Haites N, Byrd PJ, Taylor AM. ATM mutations and phenotypes in ataxia-telangiectasia families in the British Isles: expression of mutant ATM and the risk of leukemia, lymphoma, and breast cancer. Am J Hum Genet 1998; 62:334-45. [PMID: 9463314 PMCID: PMC1376883 DOI: 10.1086/301706] [Citation(s) in RCA: 272] [Impact Index Per Article: 10.5] [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] [Indexed: 02/06/2023] Open
Abstract
We report the spectrum of 59 ATM mutations observed in ataxia-telangiectasia (A-T) patients in the British Isles. Of 51 ATM mutations identified in families native to the British Isles, 11 were founder mutations, and 2 of these 11 conferred a milder clinical phenotype with respect to both cerebellar degeneration and cellular features. We report, in two A-T families, an ATM mutation (7271T-->G) that may be associated with an increased risk of breast cancer in both homozygotes and heterozygotes (relative risk 12.7; P=. 0025), although there is a less severe A-T phenotype in terms of the degree of cerebellar degeneration. This mutation (7271T-->G) also allows expression of full-length ATM protein at a level comparable with that in unaffected individuals. In addition, we have studied 18 A-T patients, in 15 families, who developed leukemia, lymphoma, preleukemic T-cell proliferation, or Hodgkin lymphoma, mostly in childhood. A wide variety of ATM mutation types, including missense mutations and in-frame deletions, were seen in these patients. We also show that 25% of all A-T patients carried in-frame deletions or missense mutations, many of which were also associated with expression of mutant ATM protein.
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Affiliation(s)
- T Stankovic
- CRC Institute for Cancer Studies, The Medical School, University of Birmingham, United Kingdom
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