Oxford Gene Technology (OGT), provider of innovative genetics research and biomarker solutions to advance molecular medicine, has launched a new solid tumour profiling next-generation sequencing service to advance vital research into personalised cancer care. OGT is the first commercial facility in the UK to offer this service.
OGT’s SureSeq Solid Tumour Panel Sequencing Service profiles the mutations of patient tumours for 58 cancer-associated genes prioritised by Cancer Research UK and leading cancer researchers. The genes include those important in breast, prostate, ovarian, lung and colorectal cancers, many with currently actionable mutations. OGT also offers researchers the flexibility to further customise the panel by adding additional genes of interest.
The panel of 58 genes was developed in collaboration with researchers at the Salisbury and Birmingham NHS Regional Genetics Laboratories as part of a £1.16 million funding award from the UK Government-backed Technology Strategy Board’s Stratified Medicines programme. The ultimate aim of the programme is to improve patient care and achieve significant cost savings over the single gene tests currently available. OGT has applied its extensive expertise in probe design to Agilent’s industry-leading SureSelect hybridisation methodology, to deliver an assay with unparalleled uniformity of targeted sequence enrichment, excellent accuracy and sensitivity of variant detection across full genes, and robust performance with FFPE samples. All results are delivered in a comprehensive interactive web-based report to enable informed interpretation of results.
Dr Mike Evans, CEO at OGT said: “We are committed to tackling cancer by developing tools for cancer research, such as biomarkers for early detection and tumour profiling assays, such as SureSeq. This comprehensive, full-gene assay allows clinical researchers to accurately identify known and de novo mutations, enabling the development of informed, personalised cancer treatment strategies. We are proud to be working alongside the Technology Strategy Board and NHS in order to revolutionise cancer profiling and treatment.”
The project partners, including Salisbury and Birmingham NHS Regional Genetics Laboratories, validated the tumour profiling assay with fresh, frozen and formalin-fixed, paraffin-embedded (FFPE) samples. In a blind study of previously genotyped clinical samples, the assay accurately detected all variants present. Through expert probe design by OGT and improved uniformity of sequence enrichment, the assay also delivered an improved likelihood of variant discovery across all regions of the genes, enabling the detection of low-frequency somatic variants in heterogeneous cancer samples.
Dr Alasdair Gaw, Lead Technologist, Stratified Medicine at the UK’s innovation agency, the Technology Strategy Board said: “We are pleased with the progress made by OGT and its partners in the development of this new tumour profiling assay. We are confident that the implementation of such assays will significantly advance our understanding of cancer, enabling stratified medicine and the development of personalised cancer treatment regimes that will significantly improve patient care.”
The SureSeq Solid Tumour Panel Sequencing Service utilises an enrichment panel comprising the full coding regions of 58 prioritised cancer genes. The aim of the panel is to improve cancer care by providing individualised patient profiles facilitating the implementation of personalised treatment strategies. The panel was research-validated for use with fresh, frozen and formalin-fixed, paraffin-embedded (FFPE) samples and focuses on breast, prostate, ovarian, lung and colorectal cancers. OGT also offers the user flexibility to add genes of interest to the panel as part of the service.
The panel was validated against blinded, previously genotyped samples, confirming that the assay accurately detects all variants present. OGT’s expert probe design was found to deliver significantly better uniformity of enrichment than standard design models. A key metric of uniformity, the percentage of bases covered to at least twenty per cent of the mean coverage, increased from 72% in the standard design, to >97.5% in OGT’s current panel.
The assay is optimised to detect low copy variants such as those found in heterogeneous cancer samples so that even low-level changes are classified. The assay called low frequency variants representing between 1% and 2% of bases, at read depths of 600x to 1300x. This feature is enhanced by two factors – firstly the design of the panel and secondly, optimisation of OGT’s Somatic Variant Analysis pipeline to ensure that low-frequency variants are called correctly. OGT’s powerful NGS report provides an integrated end-to-end workflow translating raw results into informed interpretation.
OGT received a funding award of £1.16 million in June 2011 from the UK’s innovation agency, the Technology Strategy Board, as part of a five year programme in stratified medicine research and development involving over £60 million of government funding. Led by OGT, the project is a partnership with the Universities of Southampton and Birmingham, including, West Midlands Regional genetics Laboratory and Birmingham United Molecular Pathology and the Wessex regional Genetics Laboratory and National genetics reference Laboratory in Salisbury.
Another partner in the project, CIS Healthcare develops chemotherapy prescription management software. Results from the tumour profiling assay will be integrated into the Company’s ChemoCare diagnostic module providing clinicians with accurate and up-to-date information on which to base treatment decisions.
Founded by Professor Ed Southern, Oxford Gene Technology (OGT) provides innovative genetics research and biomarker solutions to advance molecular medicine.
The Technology Strategy Board is the UK’s innovation agency. Its goal is to accelerate economic growth by stimulating and supporting business-led innovation.