Genome sequencing with gene panel-based analysis for rare inherited conditions in a publicly funded healthcare system: implications for future testing

Hocking, L. J. et al. (2023) Genome sequencing with gene panel-based analysis for rare inherited conditions in a publicly funded healthcare system: implications for future testing. European Journal of Human Genetics, 31(2), pp. 231-238. (doi: 10.1038/s41431-022-01226-3) (PMID:36474026) (PMCID:PMC9905562)

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Abstract

NHS genetics centres in Scotland sought to investigate the Genomics England 100,000 Genomes Project diagnostic utility to evaluate genome sequencing for in rare, inherited conditions. Four regional services recruited 999 individuals from 394 families in 200 rare phenotype categories, with negative historic genetic testing. Genome sequencing was performed at Edinburgh Genomics, and phenotype and sequence data were transferred to Genomics England for variant calling, gene-based filtering and variant prioritisation. NHS Scotland genetics laboratories performed interpretation, validation and reporting. New diagnoses were made in 23% cases – 19% in genes implicated in disease at the time of variant prioritisation, and 4% from later review of additional genes. Diagnostic yield varied considerably between phenotype categories and was minimal in cases with prior exome testing. Genome sequencing with gene panel filtering and reporting achieved improved diagnostic yield over previous historic testing but not over now routine trio-exome sequence tests. Re-interpretation of genomic data with updated gene panels modestly improved diagnostic yield at minimal cost. However, to justify the additional costs of genome vs exome sequencing, efficient methods for analysis of structural variation will be required and / or cost of genome analysis and storage will need to decrease.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Doherty, Mrs Jill and Williams, Miss Nicola and McGowan, Ruth and Westwood, dr Paul
Authors: Hocking, L. J., Andrews, C., Armstrong, C., Ansari, M., Baty, D., Berg, J., Bradley, T., Clark, C., Diamond, A., Doherty, J., Lampe, A., McGowan, R., Moore, D. J., O'Sullivan, D., Purvis, A., Santoyo-Lopez, J., Westwood, P., Abbott, M., Williams, N., Scottish Genomes Partnership, , Aitman, T. J., and Miedzybrodzka, Z.
College/School:College of Medical Veterinary and Life Sciences > School of Cancer Sciences
College of Medical Veterinary and Life Sciences > School of Medicine, Dentistry & Nursing
Journal Name:European Journal of Human Genetics
Publisher:Springer Nature
ISSN:1018-4813
ISSN (Online):1476-5438
Published Online:06 December 2022
Copyright Holders:Copyright © 2022 The Authors
First Published:First published in European Journal of Human Genetics 31(2): 231-238
Publisher Policy:Reproduced under a Creative Commons License

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