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DNAStar to Use $400K NHGRI Grant to Further Develop Clinical GWAS Analysis Pipeline


DNAStar was recently awarded a $485,000 Small Business Innovation Research grant from the National Human Genome Research Institute to continue developing a new research analysis pipeline for genome-wide association studies in clinical settings.

This is the second round of funding that the Madison, Wis.-based firm has received from the National Institutes of Health under the agency's fast-track program. Last year, the company received $150,000 from the NHGRI for the first phase of development which wrapped up in June (BI 9/28/2012). According to the grant abstract, the yet-to-be named pipeline will include components from existing software developed by DNAStar as well as newly developed capabilities.

Specifically, it will consist of two modules that are already available in DNAStar's SeqMan NGen and ArrayStar software packages. The former, which is a genome assembly and analysis program, forms the front end of the pipeline and will provide capabilities for verifying "putative variations" in sequence data. On the back end, ArrayStar, a tool for analyzing gene expression experiments and sequence variation across samples, will provide multiple sample comparison and analysis capabilities.

In addition, DNAStar is working on a mechanism for pulling in information from external databases to help with sample comparisons. Tom Schwei, the company's vice president and general manager, told BioInform that it is currently mulling a few options including aggregating data from multiple resources into a single database and providing that as part of the project. Alternatively, they might provide links to relevant resources within the product and let customers search the data themselves, he said.

The company is also partnering with Douglas McNeel, a professor of medicine in the University of Wisconsin, Madison's division of hematology and oncology. McNeel is developing and testing a vaccine for prostate cancer and will provide 30 to 40 samples from clinical trial participants, Schwei said. These samples will undergo exome sequencing and the data will be used to test the pipeline's capabilities. DNAStar has a second unnamed collaborator who is also providing prostate cancer samples for testing.

Clinical research is a new playing field for DNAStar, which historically has developed and sold software solutions to research markets targeting customers using sequencing technologies, microarrays, and proteomics technologies. Besides SeqMan NGen and ArrayStar, the company's product portfolio includes the Lasergene suite, which offers tools for things like sequence assembly, alignment, and analysis, and macromolecular structure analysis; and NovaFold, which is used for protein structure prediction (BI 8/2/2013). The firm also recently launched a new cloud service based on Amazon web services to improve access to its Lasergene suite (BI 5/17/2013).

Current customers of the company's products include University of Nebraska Medical Center who purchased a site license for Lasergene earlier this year (BI 3/15/2013). Lasergene is also being used by researchers at Heidelberg University's Center for Molecular Biology for next-generation sequence data assembly and analysis (BI 6/8/2012).

Schwei told BioInform that his firm made the decision to enter the clinical arena because of the potential benefits NGS technologies can bring to the space. "We realize that as NGS is maturing and the tools are getting better, that the real opportunity for using it for great benefit is probably more in the clinical market, whether it's clinical research or clinical diagnostics," he said.

This current phase of the project is expected to wrap up in summer 2015, however DNAstar expects to launch the first version of its new pipeline as early as next year. "It won't have all the capabilities … but it will be something that clinical researchers can begin to work with effectively," Schwei said. Customers will be able to run it on both the cloud and internal hardware clusters, he said.