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December 19, 2012

100K Genome Project, OpGen Tackle Foodborne Illnesses

  • OpGen is teaming up with the University of California, Davis, (UC Davis) in cooperation with the FDA-supported 100K Genome Project to create high-resolution microbial genetic maps.

    The 100K Genome Project is a collaboration that was initiated earlier this year by the U.S. Food and Drug Administration (FDA), UC Davis, and Agilent Technologies to sequence the genetic code of at least 100,000 infectious organisms including Salmonella, Listeria, and E. coli, and accelerate the diagnosis of foodborne illnesses. UC Davis will integrate OpGen’s Argus Whole Genome Mapping System into its current DNA sequencing workflow for sequence assembly and validation of the genomes.

    Through the integration of OpGen’s Whole Genome Mapping technology, The 100K Genome Project aims to create a new standard for microbial reference genomes. These data will reportedly be used in the surveillance and management of international foodborne microbial outbreaks, and to establish a high-fidelity global reference database for microbial genomes. The 100K Genome Project will publish the genomes that are completed and validated using OpGen’s Whole Genome Maps to a database, providing access to the genomic maps for public health agencies throughout the world. The FDA is advocating rigorous quality control standards for this reference database whereby genomic information should be validated by two independent methods.

    “OpGen’s technology allows us to complete sequencing and provide quality control of genomes drafted by data produced using short-read next-generation sequencing methods,” said Bart C. Weimer, Ph.D., who is a professor in the department of population and reproduction at UC Davis' School of Veterinary Medicine, and the director of the 100K Pathogen Genome Project. “Whole Genome Mapping provides an independent method to detect sequence variations and misassemblies, and aids us in closing the gaps.”

    The Argus Whole Genome Mapping System has been gaining popularity lately, as, according to OpGen, the Genome Institute at Washington University, St. Louis, MO; the Genome Analysis Centre (TGAC) in Norwich, UK; Genoscope in Evry, France; the National High-throughput DNA Sequencing Center at the Center for GeoGenetics, Copenhagen, Denmark; and the Genome Institute of Singapore have all recently adopted the technology.

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