title: Clinical applicability and cost of a 46-gene panel for genomic analysis of solid tumours: Retrospective validation and prospective audit in the UK National Health Service.
abstract: Single gene tests to predict whether cancers respond to specific targeted therapies are performed increasingly often. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean the entire cancer genome or parts of it can now be sequenced at speed with increased depth and sensitivity. However, translation of NGS into routine cancer care has been slow. Healthcare stakeholders are unclear about the clinical utility of NGS and are concerned it could be an expensive addition to cancer diagnostics, rather than an affordable alternative to single gene testing.
  
  
  
  We validated a 46-gene hotspot cancer panel assay allowing multiple gene testing from small diagnostic biopsies. From 1 January 2013 to 31 December 2013, solid tumour samples (including non-small-cell lung carcinoma [NSCLC], colorectal carcinoma, and melanoma) were sequenced in the context of the UK National Health Service from 351 consecutively submitted prospective cases for which treating clinicians thought the patient had potential to benefit from more extensive genetic analysis. Following histological assessment, tumour-rich regions of formalin-fixed paraffin-embedded (FFPE) sections underwent macrodissection, DNA extraction, NGS, and analysis using a pipeline centred on Torrent Suite software. With a median turnaround time of seven working days, an integrated clinical report was produced indicating the variants detected, including those with potential diagnostic, prognostic, therapeutic, or clinical trial entry implications. Accompanying phenotypic data were collected, and a detailed cost analysis of the panel compared with single gene testing was undertaken to assess affordability for routine patient care. Panel sequencing was successful for 97% (342/351) of tumour samples in the prospective cohort and showed 100% concordance with known mutations (detected using cobas assays). At least one mutation was identified in 87% (296/342) of tumours. A locally actionable mutation (i.e., available targeted treatment or clinical trial) was identified in 122/351 patients (35%). Forty patients received targeted treatment, in 22/40 (55%) cases solely due to use of the panel. Examination of published data on the potential efficacy of targeted therapies showed theoretically actionable mutations (i.e., mutations for which targeted treatment was potentially appropriate) in 66% (71/107) and 39% (41/105) of melanoma and NSCLC patients, respectively. At a cost of £339 (US$449) per patient, the panel was less expensive locally than performing more than two or three single gene tests. Study limitations include the use of FFPE samples, which do not always provide high-quality DNA, and the use of "real world" data: submission of cases for sequencing did not always follow clinical guidelines, meaning that when mutations were detected, patients were not always eligible for targeted treatments on clinical grounds.
  
  
  
  This study demonstrates that more extensive tumour sequencing can identify mutations that could improve clinical decision-making in routine cancer care, potentially improving patient outcomes, at an affordable level for healthcare providers.
authors.affiliation: Molecular Diagnostics Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.|National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Angela
authors.initials: A
authors.lastname: Hamblin
authors.affiliation: National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom.
authors.forename: Sarah
authors.initials: S
authors.lastname: Wordsworth
authors.affiliation: Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Jilles M
authors.initials: JM
authors.lastname: Fermont
authors.affiliation: Molecular Diagnostics Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.|National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Suzanne
authors.identifier: 0000-0002-3117-4156
authors.initials: S
authors.lastname: Page
authors.affiliation: National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Kulvinder
authors.initials: K
authors.lastname: Kaur
authors.affiliation: National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Carme
authors.initials: C
authors.lastname: Camps
authors.affiliation: National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Pamela
authors.initials: P
authors.lastname: Kaisaki
authors.affiliation: Department of Oncology, University of Oxford, Oxford, United Kingdom.
authors.forename: Avinash
authors.initials: A
authors.lastname: Gupta
authors.affiliation: National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Department of Oncology, University of Oxford, Oxford, United Kingdom.
authors.forename: Denis
authors.initials: D
authors.lastname: Talbot
authors.affiliation: National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Department of Oncology, University of Oxford, Oxford, United Kingdom.
authors.forename: Mark
authors.initials: M
authors.lastname: Middleton
authors.affiliation: Molecular Diagnostics Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.|National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Shirley
authors.initials: S
authors.lastname: Henderson
authors.affiliation: Molecular Diagnostics Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.|National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Anthony
authors.initials: A
authors.lastname: Cutts
authors.affiliation: Molecular Diagnostics Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.|National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Dimitrios V
authors.initials: DV
authors.lastname: Vavoulis
authors.affiliation: Molecular Diagnostics Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.|National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Nick
authors.initials: N
authors.lastname: Housby
authors.affiliation: National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Ian
authors.identifier: 0000-0003-3037-1470
authors.initials: I
authors.lastname: Tomlinson
authors.affiliation: National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
authors.forename: Jenny C
authors.initials: JC
authors.lastname: Taylor
authors.affiliation: Molecular Diagnostics Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.|National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.|Department of Oncology, University of Oxford, Oxford, United Kingdom.
authors.forename: Anna
authors.initials: A
authors.lastname: Schuh
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002289:Carcinoma, Non-Small-Cell Lung / Q000175:diagnosis* / Q000191:economics / Q000235:genetics / Q000628:therapy; D002648:Child; D000066491:Clinical Decision-Making; D015179:Colorectal Neoplasms / Q000175:diagnosis* / Q000191:economics / Q000235:genetics / Q000628:therapy; D005260:Female; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008545:Melanoma / Q000175:diagnosis* / Q000191:economics / Q000235:genetics / Q000628:therapy; D008875:Middle Aged; D009313:National Health Programs; D010336:Pathology / Q000379:methods* / Q000592:standards*; D011446:Prospective Studies; D012189:Retrospective Studies; D006113:United Kingdom; D055815:Young Adult