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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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Møller H, Riaz SP, Holmberg L, Jakobsen E, Lagergren J, Page R, Peake MD, Pearce N, Purushotham A, Sullivan R, Vedsted P, Luchtenborg M. High lung cancer surgical procedure volume is associated with shorter length of stay and lower risks of re-admission and death: National cohort analysis in England. Eur J Cancer 2016; 64:32-43. [PMID: 27328450 DOI: 10.1016/j.ejca.2016.05.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 04/05/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/14/2022]
Abstract
It is debated whether treating cancer patients in high-volume surgical centres can lead to improvement in outcomes, such as shorter length of hospital stay, decreased frequency and severity of post-operative complications, decreased re-admission, and decreased mortality. The dataset for this analysis was based on cancer registration and hospital discharge data and comprised information on 15,738 non-small-cell lung cancer patients resident and diagnosed in England in 2006-2010 and treated by surgical resection. The number of lung cancer resections was computed for each hospital in each calendar year, and patients were assigned to a hospital volume quintile on the basis of the volume of their hospital. Hospitals with large lung cancer surgical resection volumes were less restrictive in their selection of patients for surgical management and provided a higher resection rate to their geographical population. Higher volume hospitals had shorter length of stay and the odds of re-admission were 15% lower in the highest hospital volume quintile compared with the lowest quintile. Mortality risks were 1% after 30 d and 3% after 90 d. Patients from hospitals in the highest volume quintile had about half the odds of death within 30 d than patients from the lowest quintile. Variations in outcomes were generally small, but in the same direction, with consistently better outcomes in the larger hospitals. This gives support to the ongoing trend towards centralisation of clinical services, but service re-organisation needs to take account of not only the size of hospitals but also referral routes and patient access.
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Affiliation(s)
- Henrik Møller
- King's College London, Cancer Epidemiology, Population and Global Health, Research Oncology, 3rd Floor Bermondsey Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK; Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, Barts and The London School of Medicine and Dentistry, Charterhouse Square, London EC1M 6BQ, UK; Public Health England, UK National Cancer Analysis and Registration Service, 2nd Floor Skipton House, 80 London Road, London SE1 6LH, UK; Research Unit for General Practice and Research Centre for Cancer Diagnosis in Primary Care (CaP), Aarhus University, Bartholins Allé 2, DK-8000 Aarhus C, Denmark.
| | - Sharma P Riaz
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, Barts and The London School of Medicine and Dentistry, Charterhouse Square, London EC1M 6BQ, UK.
| | - Lars Holmberg
- King's College London, Cancer Epidemiology, Population and Global Health, Research Oncology, 3rd Floor Bermondsey Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
| | - Erik Jakobsen
- The Danish Lung Cancer Registry, Department of Thoracic Surgery, Odense University Hospital, Sdr. Boulevard 29, 5000 Odense C, Denmark.
| | - Jesper Lagergren
- King's College London, Cancer Epidemiology, Population and Global Health, Research Oncology, 3rd Floor Bermondsey Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK; Department of Molecular Medicine and Surgery (MMK), K1, Upper Gastrointestinal Research, Övre gastrointestinal forskning, NS 67, Institutionen för molekylär medicin och kirurgi, Karolinska Institutet, 171 76 Stockholm, Sweden.
| | - Richard Page
- Liverpool Heart and Chest Hospital, Thomas Drive, Liverpool L14 3PE, UK.
| | - Michael D Peake
- Public Health England, UK National Cancer Analysis and Registration Service, 2nd Floor Skipton House, 80 London Road, London SE1 6LH, UK.
| | - Neil Pearce
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
| | - Arnie Purushotham
- King's College London, Cancer Epidemiology, Population and Global Health, Research Oncology, 3rd Floor Bermondsey Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
| | - Richard Sullivan
- King's College London, Cancer Epidemiology, Population and Global Health, Research Oncology, 3rd Floor Bermondsey Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
| | - Peter Vedsted
- Research Unit for General Practice and Research Centre for Cancer Diagnosis in Primary Care (CaP), Aarhus University, Bartholins Allé 2, DK-8000 Aarhus C, Denmark.
| | - Margreet Luchtenborg
- King's College London, Cancer Epidemiology, Population and Global Health, Research Oncology, 3rd Floor Bermondsey Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK; Public Health England, UK National Cancer Analysis and Registration Service, 2nd Floor Skipton House, 80 London Road, London SE1 6LH, UK.
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