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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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