Accès ouvert déclaré 2023 article

Recommendations for laboratory workflow that better support centralised amalgamation of genomic variant data: findings from CanVIG-UK national molecular laboratory survey

Sophie Allen, Lucy Loong, Alice Garrett, Bethany Torr, Miranda Durkie, James P. Drummond, Alison Callaway, Rachel Maya Robinson, George J. Burghel, HELEN LOUISE HANSON, Joanne Field, Trudi McDevitt, Terri Patricia McVeigh, Tina Bedenham, Christopher T. Bowles, Kirsty Bradshaw, Claire Brooks, Samantha Butler, Juan Carlos Del Rey Jimenez, Lorraine Hawkes, Victoria Stinton, Suzanne MacMahon, Martina Owens, Sheila Palmer-Smith, Kenneth C. Smith, James O. Tellez, Mikel Valganon-Petrizan, Erik Waskiewicz, Michael Yau, Diana Eccles, Marc D. Tischkowitz, Shilpi Goel, Fiona E. McRonald, Antonis C. Antoniou, Eva J.A. Morris, Steven A. Hardy

6Citations signalées, ce qui n’est pas une note de qualité

39Institutions déclarées

5Pays d’affiliation déclarés

Rattachement africain : gb, ru, us, ie, it. Niveau de preuve : code pays fourni par la source.

Le résumé fourni par la source

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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Le contrôle bibliographique ouvert

DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.

Titre Crossref: Recommendations for laboratory workflow that better support centralised amalgamation of genomic variant data: findings from CanVIG-UK national molecular laboratory survey
Date Crossref: 22/12/2023
Éditeur: BMJ
Type: journal-article

Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.

Où se fait cette recherche

Institute of Cancer Research Division of Genetics and Epidemiology pays non établi dans la notice
Université ou école supérieure
Institute of Cytology and Genetics pays non établi dans la notice
Structure de recherche
St George’s University Hospitals NHS Foundation Trust Department of Clinical Genetics pays non établi dans la notice
Établissement de santé
Sheffield Children's NHS Foundation Trust pays non établi dans la notice
Établissement de santé
Anglian Water Services (United Kingdom) pays non établi dans la notice
Entreprise
Cambridge University Hospitals NHS Foundation Trust East Anglian Medical Genetics Service pays non établi dans la notice
Organisme public
University Hospital Southampton NHS Foundation Trust Wessex Regional Genetics Laboratory pays non établi dans la notice
Établissement de santé
Wessex Regional Genetics Laboratory pays non établi dans la notice
Structure de recherche
Leeds Teaching Hospitals NHS Trust Yorkshire Regional Genetics Service pays non établi dans la notice
Établissement de santé
University of Manchester pays non établi dans la notice
Université ou école supérieure
Manchester University Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub pays non établi dans la notice
Université ou école supérieure
Nottingham University Hospitals NHS Trust Genomics and Molecular Medicine Service pays non établi dans la notice
Établissement de santé

Division of Genetics and Epidemiology — Institute of Cancer Research, Institute of Cytology and Genetics et Department of Clinical Genetics — St George’s University Hospitals NHS Foundation Trust, avec 9 autres affiliations.

Une affiliation ne permet pas de déduire la nationalité d’un auteur.

Les sujets associés

Genomics and Rare DiseasesCancer Genomics and DiagnosticsBRCA gene mutations in cancer

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