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, and Anna, Schuh
Background 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. Methods and findings 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. Conclusions 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., Sarah Wordsworth and colleagues study the feasibility of employing next-generation sequencing of tumor DNA in clinical practice., Author summary Why was this study done? Healthcare planners and oncologists require real world evidence that next generation sequencing (NGS) technologies improve gene mutation detection and enable more appropriate use of targeted drug therapies. With a range of genomic testing options available for cancer patients, we need to know whether healthcare systems can afford to implement cancer panels in routine clinical care, even if they are effective. What did the researchers do and find? This study assessed a 46-gene hotspot cancer panel assay allowing multiple gene testing of small diagnostic cancer biopsies in the context of the UK National Health Service. Tumour samples (including non-small-cell lung cancer, melanoma, and colorectal carcinoma) from 351 patients who treating clinicians thought might benefit from more extensive genetic analysis underwent NGS using the panel. A clinical report was produced with a median turnaround time of seven working days that indicated all mutations detected, including those with potential diagnostic, prognostic, therapeutic, or clinical trial entry implications. Clinical data were collected for patients whose tumour samples underwent sequencing in order to assess changes to clinical management resulting from this test. An accompanying detailed cost analysis was performed to determine the affordability of the panel compared to existing single gene testing options. The panel demonstrated at least one mutation in 87% (296/342) of successfully sequenced tumours. Forty patients in this cohort received targeted treatments on the basis of genetic data obtained using the panel. For 22 of these patients, there was no alternative genetic test available locally to produce this data. Mutation detection with the panel costs £339 (US$449) per patient, compared with single gene testing ranging from £71 to £141 (US$94–US$187) per test, depending on the mutation type. If more than two or three genes are examined (depending on the cancer type), using the panel is less expensive than single gene testing. What do these findings mean? The panel assay is a useful method to identify genetic mutations in tumours that can extend the range of therapeutic options available to patients. In terms of costs and affordability, the panel may be a justifiable option if 2–3 or more genes need to be examined. Further data need to be collected on the clinical outcomes of patients accessing drugs as a result of more extensive sequencing data outside the scope of single gene/mutation tests. In addition to supporting routine clinical care, the panel can be used to support research studies where treatment choices are genetically determined.