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

Author:

Allen SophieORCID,Loong Lucy,Garrett AliceORCID,Torr BethanyORCID,Durkie Miranda,Drummond James,Callaway Alison,Robinson Rachel,Burghel George JORCID,Hanson HelenORCID,Field Joanne,McDevitt Trudi,McVeigh Terri P,Bedenham Tina,Bowles Christopher,Bradshaw Kirsty,Brooks Claire,Butler Samantha,Del Rey Jimenez Juan Carlos,Hawkes Lorraine,Stinton Victoria,MacMahon Suzanne,Owens Martina,Palmer-Smith Sheila,Smith Kenneth,Tellez James,Valganon-Petrizan Mikel,Waskiewicz Erik,Yau Michael,Eccles Diana MORCID,Tischkowitz Marc,Goel Shilpi,McRonald Fiona,Antoniou Antonis CORCID,Morris Eva,Hardy Steven,Turnbull ClareORCID

Abstract

BackgroundNational 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.MethodsIn 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).ResultsWidely 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.ConclusionThe 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.

Funder

NIHR Cambridge Biomedical Research Centre

Cancer Research UK

Publisher

BMJ

Subject

Genetics (clinical),Genetics

Reference28 articles.

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3. Landmark strategy launched to cement UK’s position as global leader in genomics. Department of Health and Social Care, 2020.

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5. Karczewski KJ , Francioli LC , Tiao G . The mutational constraint spectrum quantified from variation in 141,456 humans. Genomics [Preprint]. doi:10.1101/531210

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