NEW YORK (GenomeWeb) – Recently, Oxford Gene Technology said that it had been awarded a £200,000 (around $338,000) phase one development contract by the Small Business Research Initiative (SBRI) healthcare competition to develop user-friendly software for analyzing variants found in whole-genome sequence data.
The grant comes from the jointly run UK Department of Health and Genomics England collaborative. They operate a funding competition that supports the development of innovative technologies, including bioinformatics tool and analysis algorithms, which will address the requirements of the 100K Genome Project.
The partners award contracts in two phases. In the first phase, groups receive resources to demonstrate the technical feasibility of their proposed products. Then, if they are successful, they are eligible to apply for a second phase of funding to further develop and test the product.
Dietrich Lueerssen, OGT's director of computational biology, told BioInform that his firm will use the funds to develop software that will, among other things, provide simple workflows that clinical laboratories can use to identify actionable mutations, compare multiple samples, and share data with other researchers within their labs and institutions.
The proposed system will also include a database of variants from samples analyzed in previous studies that can be used for comparison purposes, a mechanism to update the database as new variant information becomes available, and tools for generating and sharing reports.
In developing its new product, OGT will rely on the experience its internal informatics team has gleaned from years of developing software first for the microarray market and, more recently, for the next-generation sequencing market. Existing software products from OGT include CytoSure Interpret, a software solution that the company markets alongside its CytoSure arrays product line.
The software provides capabilities for analyzing and annotating data from arrayCGH experiments including tools for identifying both copy number variation and loss of heterozygosity. It also includes a database that contains results from previously analyzed samples, to which users can compare the results of new samples.
The company's informatics unit also developed software that OGT provides as part of its NGS service, which launched about four years ago. The software offers simple to use tools for things like data quality checking and simplifies the process of sorting through long variant lists to identify those that are most meaningful.
In addition to using internally developed algorithms, Lueerssen's team is also exploring open-source software options that might be a good fit for the product, he said. OGT has spoken "extensively," Lueerssen said, to current customers and potential customers as well as collaborators to ensure that it is creating a system that meets current and potential customers' requirements and addresses pertinent analysis pain points.
"I think the best way to describe what we are proposing here for this software is that we want to bring to NGS what we did for arrays when we introduced CytoSure Interpret software," he said. "We have a lot of experience in not only making that software robust, but also in supporting our customers here and everywhere in the world."
OGT hopes to have its new software on the market by next year. It intends to sell the solution as a standalone desktop product. However, it is not disclosing further details of its commercialization plans for the product at this time.
When it does bring the product to market, OGT's solution will have to contend with companies such as Ingenuity Systems — now Qiagen Redwood City — and Omicia, who also develop and sell variant interpretation software for the clinical laboratory market.
But Lueerssen believes that OGT can compete favorably in the space. "There are different models that can work for different people," he said. For example, some other companies provide solutions where users have to move their data to external servers, but that does not work for all customers, some of whom might be worried about data exiting their firewalls. With a desktop solution, all the data stays local and so any privacy concerns are addressed, he said.