This article has been updated from a version posted June 15 to include additional information from CLC Bio.
CLC Bio announced this week that it has teamed up with Ion Torrent and Aarhus University Hospital, Denmark, to develop an integrated software and hardware solution for use in sequencing-based molecular diagnostics.
The project received a $2 million grant from the Danish National Advanced Technology Foundation.
The companies plan to develop a user-friendly IT infrastructure to analyze data produced by high-throughput sequencers to faster and more accurately analyze and diagnose patients based on their DNA samples.
The project, which is expected to take three years to complete, aims to develop an IT solution that can be used for molecular diagnostics research as well as for clinical diagnostics in hospitals and outpatient clinics.
For its part, CLC Bio will be modifying its research-based Genomics Workbench and Genomics Server to ensure that the tools meet the requirements of the molecular diagnostic workflow.
One feature of the new software will be a secure data-management module, CLC CEO Thomas Knudsen told BioInform. With this feature, the software will be able to track user activity so that multiple users can re-analyze the same data from scratch. This feature will also ensure that the system conforms to the US Food and Drug Administration's requirements for diagnostics software Knudsen said.
Other modules will be able to provide more specialized information about gene activities associated with disease. For example, the software would be able to identify specific biomarkers for different types of colon cancer that indicate increased risk for the disease.
Although the company is partnering with Ion Torrent for this project, like its research-based counterpart, the software will work with sequence data produced on multiple platforms. This is in keeping with CLC Bio’s overarching strategy to be platform-independent so that it can handle datasets from rapidly evolving sequencing platforms as well as accommodate new players in the industry, Knudsen said.
Currently the company’s general-purpose research software can handle data produced by sequencers from Illumina, Life Technologies, and Roche. In February, Pacific Biosciences included CLC Bio in a list of partners to provide supporting software for its sequencing platform, which is scheduled to hit the market in the second half of this year (BioInform 2/19/2010).
Furthermore, this isn’t the first project CLC Bio and Ion Torrent have partnered on. Earlier this year, the companies announced that they would work together to ensure that CLC Bio’s IT infrastructure is compatible with Ion Torrent's sequencing platform, which is scheduled to launch later this year (BioInform 4/30/2010).
In addition to working with Ion Torrent, Knudsen said that the company will work closely with doctors at the Aarhus University Hospital to gain a better understanding of the diagnostics process.
“Their role in this project is to explain their workflows so that we can make software that supports their full workflow in the diagnostics process,” he said. “It will, of course, [involve] mutations, genomic rearrangements, and genetic repeats. In terms of analysis we will be looking at different genetic traits on the patient DNA compared to similar patients versus people without those diseases.”
Based on that knowledge, CLC will create “specialized extensions” for the Genomics Workbench and Genomics Server. These extensions will automatically analyze patient data and provide detailed analysis about genetic links to disease, he said.
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Lasse Görlitz, CLC Bio’s head of global PR and marketing, told BioInform that over the three-year period, the company will develop a series of smaller modules that the hospital will test using anonymized data.
“We will make them available in beta version so that we will get feedback. Eventually within this three-year period we will end up with a full suite of tools that will accommodate molecular diagnostics,” he said.
He added that the company aims to make the software user friendly so that buyers don’t need to have a detailed knowledge of informatics in order to operate it. The company expects to have smaller modules ready for testing within a year.
When it is completed, the software will have workflow pipelines set up to register and analyze sequence data as it is produced, compare the results with existing patient data stored in the system, and generate a detailed report. It is hoped that based on analysis of the datasets, clinics can make treatment decisions best suited for their patients.
Ion Torrent could not be reached before press time to comment on its role in the partnership.
Neither Knudsen nor Görlitz would comment directly on Ion Torrent’s specific role in developing the software or why the company was chosen for the project, though Knudsen did note that Ion Torrent has claimed that its sequencer will reduce the amount of time for a run to an hour or two, as opposed to a week for other technologies.
“If a patient has some acute disease, [you want an] answer within a few hours [rather] than waiting a week,” he said.
CLC expects that once its software is ready for the market, it will be adopted by hospitals and clinics globally.
“I think eventually you are going to see some kind of sequencing apparatus and a small computer tied to it in every PI's office,” said Görlitz.