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Genetics Group, Analytics Firm Collaborate on Diagnostics

DNA Strands (NIST.gov)

(NIST.gov)

19 March 2014. A genetics research center at University of Utah in Salt Lake City and Omicia Inc., a genomic analytics company in Oakland, California are developing systems to make genomic analysis a routine medical diagnostic procedure. The $6 million in funding for the USTAR Center for Genetic Discovery comes from the university and Utah Science Technology and Research (USTAR) an initiative of the state government.

The USTAR Center is directed by Utah genetics professor Mark Yandell and Gabor Marth, a computer scientist who recently joined the Utah medical faculty from Boston College. Their goal is to make it possible to quickly sequence an individual’s entire genome to uncover underlying genetic causes for disease. The results would make it possible, say Yandell and Marth, to prescribe more customized and cost-effective treatments for the patient’s condition, as well as prevent further disorders.

While the time and cost of sequencing the human genome are much lower than 10 years ago, the mountain of data generated from sequencing still need a good deal of analysis and interpretation to make them useful for clinicians. “Current systems,” says Marth in a university statement, “are not prepared for the increasing amounts of data we will be seeing within the next few years.”

Yandell’s lab wrote an algorithm called the Variant Annotation, Analysis and Search Tool or VAAST, now in its second version, that identifies with probability processes genetic variations and damaged genes in an individual’s genome as potential causes of disease. The university says VAAST is in use at more than 250 institutions.

Omicia is working with Yandell and Marth to further develop the company’s cloud-based genomic analysis toolkit, called Opal. In 2012, Omicia received a Small Business Innovation Research grant from National Human Genome Research Institute, part of NIH, to integrate VAAST into Opal. The company launched Opal that same year.

Opal, says the company, analyzes genomes to find disease-causing variants and damaged genes, making the highlighted causes easier to identify, and presented in a format useful for physicians, with cross-references to scientific literature. The system, says Omicia, can process exomes — the regions of the genome translated into proteins — in under one hour, while whole genomes can be processed in under three hours.

The USTAR Center is collaborating as well with the Utah Genome Project, an undertaking that combines genealogical and health records dating back to pioneer days to find genetic causes of cancer, cardiovascular diseases, and immune disorders. The center expects to eventually commercialize its full line of genetic software.

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