Research Article: 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

Date Published: February 14, 2017

Publisher: Public Library of Science

Author(s): Angela Hamblin, Sarah Wordsworth, Jilles M. Fermont, Suzanne Page, Kulvinder Kaur, Carme Camps, Pamela Kaisaki, Avinash Gupta, Denis Talbot, Mark Middleton, Shirley Henderson, Anthony Cutts, Dimitrios V. Vavoulis, Nick Housby, Ian Tomlinson, Jenny C. Taylor, Anna Schuh, Marc Ladanyi

Abstract: BackgroundSingle 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.Methods and findingsWe 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.ConclusionsThis 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.

Partial Text: Historically, the standard approach to testing for somatic mutations in cancers has been single gene testing using methods such as Sanger sequencing. With such methods, candidate genes are examined for mutations, and, as a result, patients may become eligible to enter a clinical trial or receive targeted drug therapies [1–3]. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean that the entire cancer genome (whole genome sequencing [WGS]) or parts of it (via targeted panels or whole exome sequencing [WES]) can now be sequenced in hours and at great depth and increasing sensitivity. However, while NGS offers high-throughput, rapid, and accurate testing of multiple genes, it remains to be proven whether it also leads to more appropriate use of targeted drug therapies and an enhanced ability to identify patients who are more likely to benefit from treatment compared with single gene sequencing.

We have validated and clinically implemented an NGS assay that detects relevant mutations across mutational hotspots of 46 genes from minimal quantities of FFPE-derived highly fragmented tumour DNA, allowing routine testing of multiple genes from small biopsies. Its performance has been validated across a variety of tumour types for single nucleotide variants and indels and has been shown to have an enhanced sensitivity compared with conventional diagnostic techniques. Treatment data revealed that surprisingly few patients (~40%) received any pharmacological treatment, targeted or otherwise, confounding the fact that for most patients the indication for mutation analysis should be to inform whether treatment should be conventional chemotherapy or targeted agents. Examination of individual cases showed that, in contravention of operational policy, many samples were not from metastatic or unresectable malignancies. Whilst early testing in the diagnostic pathway may be desirable, many targeted therapies are indicated only for metastatic or unresectable disease, such as erlotinib in NSCLC. Additionally, differences in side effects between conventional chemotherapy and targeted agents are such that some elderly patients may be deemed suitable for the latter but not the former, meaning that if no actionable mutation is identified there is no appropriate treatment.



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