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Array, Sequencing Firms to Benefit from $10M UK Tumor Profiling and Data Capture Initiative

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By Justin Petrone

Affymetrix, Almac Diagnostics, and Oxford Gene Technology are among the firms that have been awarded funding to develop new approaches for tumor profiling and data capture.

The UK's Technology Strategy Board announced last week that it would provide £6 million ($9.7 million) for the R&D projects. Companies heading other funded projects include Aridhia Informatics, IDBS, Life Technologies, and Source BioScience.

The funding is being made available as part of the UK's Stratified Medicine Innovation Platform, a five-year, £60 million personalized medicine initiative. The Technology Strategy Board is leading the project.

Of the six projects named, only one will specifically rely on arrays. That project, called "Developing a robust, reliable multiplex clinical tool for guiding tumor therapy," involves Affy, Almac, and researchers at the Leeds Institute of Molecular Medicine.

Karen Keating, biomarker research manager at Craigavon, UK-based Almac, said that the group aims to develop and validate a "rapid, robust and sensitive product suitable for therapeutic selection for patients" as well as generate "substantial additional research data" in six cancer settings — lung, breast, colorectal, prostate, ovarian, and melanoma.

The resulting product will be developed from "microarray technology already established in Affymetrix research labs that can generate high-quality somatic mutation, SNP, and copy number data from very small amounts of formalin-fixed, paraffin-embedded tissue, " Keating told BioArray News.

Keating was referring to Affy's OncoScan FFPE Express product, the second version of which was launched in April (BAN 4/5/2011).

Dara Wright, vice president of clinical marketing at Affy, told BioArray News this week that the ultimate goal of the 3-year project is to develop a multiplex genetic test that "must work with FFPE tissue samples, detect a minimum set of target cancer genes with actionable somatic mutations, and meet a target price point."

Wright said the project will use OncoScan FFPE Express technology to develop the "customized clinical derivative."

Almac's Keating added that the new project will "encompass the transfer of this technology, [and the] refinement and automation of the technology to address the specific requirements of the TSB competition." In addition, "suitable algorithms will be developed to ensure accurate and efficient assessment of raw data, as well as facilitate separation of clinically relevant data from additional data for research use," she said.

According to Keating, the test will be among the first in a "new class" of diagnostics that can provide clinically relevant information to inform clinicians as to the best possible treatment for patients, and also generate a "huge amount" of additional genetic information to support research.

Keating noted that Almac and its partners anticipate the new test will be adopted by the UK's National Health Service. Almac will establish the technology in house and contribute to the selection of markers suitable for the test, she said.
She declined to describe the specific roles of the different partners, and also declined to discuss how much of the TSB funding would be allotted toward the project.

The path to NHS use seems assured. Results from the new projects will support the aims of Cancer Research UK's Stratified Medicines Program, which aims to test up to 9,000 tumor samples in order to show how molecular diagnosis of NHS patient tumors could be scaled up to provide a national service, according to the TSB.

Iain Gray, chief executive of the TSB, said in a statement that the projects will "lead to the development of products or services which can be readily adopted by [National Health Service] commissioners for the improvement of patient outcomes."

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'Outside the Scope'

In perhaps a sign of the times, Oxford Gene Technology, which was founded on the intellectual property estate of microarray pioneer Edwin Southern, will not be using array technology to carry out its TSB-funded project.

OGT's partners in the effort, entitled "Development of a fully integrated service for sequencing-based tumor profiling including data interpretation and commercialization of assay panel kit products," are the University of Southampton, the University of Birmingham, and CIS Healthcare.

James Clough, vice president of clinical and genomic solutions at OGT, told BioArray News this week that the OGT-led TSB project aims to develop a tumor-profiling assay based on in-solution targeted panel enrichment and next-gen sequencing.

This capture assay will be "commercialized as a product for sales to existing clinical labs that have their own sequencing platforms, and offered as a centralized, high-throughput, validated service" via OGT's laboratories. OGT expanded its Genefficiency services to include next-gen sequencing last month (BAN 5/31/2011).

According to Clough, the envisioned assay will be built into a "fully integrated innovative workflow, from sample submission to interpretation of the patient’s tumor profile and transfer of the data into an automated prescription-management system." He said that the "final step" of the project will be to "ensure that the output of profiling can be closely coupled to drug prescription, ensuring accuracy and consistency of care and delivering significant cost savings to the healthcare provider."

According to Clough, CIS Healthcare will contribute to the project by facilitating the adoption of profiling by clinicians. CIS Healthcare's ChemoCare system already helps manage more than 70 percent of cancer patients in the UK, and results from the molecular-profiling assay will be integrated into the ChemoCare diagnostic module, he added.

OGT and CIS Healthcare will be working with academic partners at the University of Southampton and the University of Birmingham to bring "additional clinical and technical expertise" allowing the development and "comparison of assays," including genotyping, mutation scanning, loss of heterozygosity, gene fusions, and gene expression, to "ensure the most accurate and informative test is delivered," said Clough.

Since the partners are affiliated with the UK's National Genetics Reference Laboratory in Salisbury and the West Midlands Regional Genetics Lab in Birmingham, they can validate the resulting assays in-house in a clinical setting, using their own sequencing platforms, said Clough.

While Clough said that microarray technology is "outside the scope of this particular project," the firm will rely on its "expertise in probe design, data analysis and quality control, plus clinical product and service delivery generated though our CytoSure and Genefficiency products and services" in carrying it out.

The Other Projects

Of the other four projects funded by TSB, two concern bioinformatics development and two involve next-gen sequencing.

Edinburgh, UK-based software developer Aridhia Informatics will work with partners at the University of Dundee in Scotland, NHS Tayside, and the University of Edinburgh on a project entitled, "The Dundee Edinburgh Cancer Informatics Programme: Harnessing Excellent Research [DECIPHER]."

Data management shops IDBS and Quantix, meantime, will work with researchers at Kings College London and Manchester University on a project called, "Acropolis," an acronym for Advanced Collaborative Research for Oncology Platform for Improved Outcomes, Learnings, Insight, and Science.

On the next-gen sequencing front, Life Technologies, the University of Oxford, and pharma companies AstraZeneca and Johnson & Johnson have been awarded funds to carry out a project called, "Next Generation Sequencing Analysis: A Clinical Study to Implement an Innovative Cancer Care Model in the UK, with Health and Economic Benefits."

Also, Source Bioscience, the Barts Cancer Institute, and Illumina will conduct "Tumour Mutation Profiling Using Illumina Massively Parallel Sequencing."


Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com

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