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November 15, 2010 (Vol. 30, No. 20)

Solving the Next-Gen Sequencing Data Crunch

Eureka Genomics' Bioinformatics Platform Takes Aim at Computational Bottlenecks

  • Breakthroughs

    Eureka Genomics recently demonstrated that its technology is capable of generating data from nanogram quantities of genomic DNA from plant, animal, and microbial cells. Most protocols for today’s sequencing instruments call for microgram amounts of a sample. However, it may be difficult to extract this much genomic material from environmental, clinical, and forensic samples. “This is a breakthrough because it represents a 1,000-fold reduction in the amount of sample needed to generate sequence data for analysis,” explains Dr. Koshinsky.

    Among other projects, the company worked with scientists at the University of California, Davis to characterize a previously undefined viral disease that threatens California vineyards. Known as Syrah Decline, the disease has baffled researchers for 20 years. Eureka Genomics isolated RNA from both infected and healthy grapevines, then compared about five million short reads from infected plants to two million short reads from uninfected plants. Sequences unique to the diseased plants were assembled and analyzed with BLAST searches and the GenBank database.

    They discovered a mixed infection of Grapevine rupestris stem pitting-associated fovea virus strains that contains two novel members. The information could help to contain or eliminate Syrah Decline. Grapevines imported into California are routinely quarantined and tested for diseases, and the nucleic acid signatures of the newly identified disease organisms may be added to the protocol. The technology readily extends to other areas of agriculture, cleantech, and human disease.

    In another collaboration, Eureka Genomics teamed up with Glycos Biotechnologies to sequence the genome of a bacterium used in the biorefinery industry. The new bacterial strain plays a key role in efforts at Glycos Biotechnologies to commercialize microbial strains to produce high-margin biochemicals from a variety of feedstocks and byproduct streams considered as low value or waste.

    The bacterial strains will make ethanol produced from corn and other biomass more economically sustainable by providing benefits to the biorefinery industry, according to the firms. Glycos Biotechnologies reported that working with Eureka Genomics saved it two years of research time and money.

    These same tools help researchers at Eureka Genomics to detect unknown pathogens that cause human illnesses. “We’re working on finding a virus suspected of causing colorectal cancer and cardiovascular disease,” says Didier. When disease-associated pathogens are detected,  Eureka Genomics will create intellectual property related to screening and diagnostic tools, therapeutics, and vaccines in collaboration with appropriate companies.

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