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OpGen partners with UC Davis in 100K Genome Project
12-19-2012
by Kelsey Kaustinen  |  Email the author
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GAITHERSBURG, Md.OpGen, Inc. has announced the beginning of a scientific and technical partnership with the University of California, Davis (UC Davis) in cooperation with the 100K Genome Project, for the creation of high- resolution microbial genetic maps. UC Davis will integrate OpGen's Argus Whole Genome Mapping System into its current DNA sequencing workflow for sequence assembly and genome validation.
 
"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," sad Bart C. Weimer, Ph.D., professor in the Department of Population and Reproduction, School of Veterinary Medicine, UC Davis, and 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. Final Whole Genome Maps will assist health agencies in outbreak management of food borne diseases which cause tremendous risk to public health."  
 
The 100K Genome Project began this July between UC Davis, the U.S. Food and Drug Administration (FDA) and Agilent Technologies. The five-year initiative seeks to sequence the genomes of 100,000 infectious microorganisms in hopes of accelerating diagnosis of food-borne illnesses. The sequencing is taking place at the BGI@UC Davis facility.
 
Additional collaborators include the U.S. Centers for Disease Control and Prevention (CDC) and the U.S. Department of Agriculture's Food Safety and Inspection Service. The FDA will be providing more than 500 complete Salmonella whole-genome draft sequences in addition to thousands of food pathogen strains for sequencing, with the CDC providing additional strains and expertise. The U.S. Department of Agriculture's Food Safety and Inspection Service will also provide strains for UC Davis to sequence, and Agilent Technologies will contribute funding while UC Davis forms a consortium of additional project partners. Once sequences are completed, they will be stored in the National Institutes of Health's National Center for Biotechnology Information's public database.  
 
The addition of OpGen's Whole Genome Mapping technology will allow the project to create a new standard for high-quality microbial reference genomes, which will be used to monitor and manage international food-borne microbial outbreaks and establish a global reference database for microbial genomes of pathogens such as Salmonella, Listeria and E. coli. Completed and validated genomes will be published, and the FDA is calling for strict quality-control standards for the database, including validation of the gathered genomic data by two independent methods.  
 
"We are pleased to be a partner in this collaboration with UC Davis and the FDA in helping to set a high-quality, validated standard for this important reference database of microbes, which pose the greatest threats to food safety and public health," said Douglas White, Chief Executive Officer of OpGen. "OpGen is committed to advancing public health and providing actionable information to the healthcare community. "  
 
According to the CDC, approximately 48 million people contract food-borne diseases each year in the United States alone, with 128,000 resultant hospitalizations and 3,000 deaths. So far, there are 31 known food-borne pathogens, which includes familiar strains such as Salmonella, Listeria and E. coli, many of which are tracked by public health systems.
 
Code: E12191201

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