NEW YORK (GenomeWeb) – Oxford Gene Technology is one of five companies selected to receive a second small business research initiative grant from the UK's Genomics England project, which it will use to continue developing a variant interpretation solution as part of the second phase of the national project.
The company received £1.2 million (about $1.8 million) for this round which it will use to finish developing its software within the next 18 months – the lifetime of the current phase of the project – at which time it will launch the full solution, Dietrich Lueerssen, OGT's director of computational biology, told GenomeWeb.
The company has said previously that it plans to offer the software as a standalone desktop solution but has yet to release details about its commercialization plans. John Anson, OGT's executive vice president of research and development, told GenomeWeb that the company is currently discussing various commercial approaches including licensing and pay-per-click models but has yet to make a decision.
OGT received £200,000 last year for the first phase of the UK initiative, which aims to sequence 100,000 whole genomes from UK National Health Service patients. The company is working on software that it claims will provide simple workflows that clinical laboratories can use to identify and interpret actionable genetic mutations from whole genome sequence, compare multiple samples, and share data with other researchers within their labs and institutions. The planned system will 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. Users will also have access to information from both public and private databases that they can use to explore the results of these tests in context.
Part of OGT's efforts in phase I involved scoping out the need its solution is intended to address, Lueerssen told GenomeWeb. Rather than rely solely on its expertise and experience, the company asked for input from clinical researchers and clinicians, who are the primary target market for its solution, as well as other groups that use next-generation sequencing data in their projects, to get a better handle on what the current needs are as well as what sort of capabilities they would want to see in the full solution. They also developed a functional prototype of the planned system which they showed to both current and potential customers, he said.
By and large, the collected feedback confirmed the company's initial analysis of the market needs and did not result in major revisions to its initial development plans, Lueerssen said. There were some improvements made based on the customers' comments but the "broad strokes of what we perceived at the outset have remained unchanged." The customer-provided feedback did highlight some common themes including a need for more collaborative workflows as well as more intuitive ways of displaying variant data, he said. Customers also called for better tools to analyze variants after identification and cut down on the amount of time required for variant interpretation tasks, he said.
OGT will continue its conversations with customers during this next round of funding. Responses to the early prototype of the software were also positive, according to Lueerssen, with customers expressing interest in being part of OGT's development efforts moving forward. The company will also work on turning the prototype of its system into a fully functional and robust software solution, he said. They'll also make improvements to the user interface so that it can adapted to fit specific end user applications, he said. In the context of the Genomics England project, this will include providing capabilities and features that support cancer and rare disease research and activities.
OGT's system will also allow users to incorporate data from other testing platforms outside of NGS as well. In addition to NGS-based testing, customers will also be able to incorporate data from Sanger sequencing, microarrays, and fluorescence in situ hybridization-based tests. "I think it’s accepted that whole genome data is going to be powerful but it’s not necessarily going to give the whole picture," Anson said. "There's obviously an opportunity for companies that have the software and reagents like OGT does to bring together a united offering in this space."
In fact that’s one of the reasons why the Genomics England project was attractive to OGT, he told GenomeWeb. "It’s not just about whole genome sequencing, it’s also about how whole genome sequencing can be complemented with these other technologies" he said. "We know [for example] that quite a lot of Sanger sequencing is done to complement NGS, so all these different sources will be brought together and used holistically to make better clinical decisions based on the complex datasets that are going to be generated."
Other companies selected to receive grants under phase II of the Genomics England initiative include Congenica, which is developing the Sapientia analytics platform for the identification, annotation, and interpretation of whole-genome sequence data from patients with rare genetic disease; Genomics Ltd., which is creating statistical tools for population-scale clinical genome analysis; and Omixon UK, which is developing tools for human leukocyte antigen genotyping from NGS data. Also selected was Seven Bridges Genomics UK, which is using its funds to complete and commercialize a population-scale graph-based genome reference tool and a suite of related software for assembling and analyzing whole genome samples.