OpGen partners with UC Davis in 100K Genome Project

OpGen's Argus Whole Genome Mapping System to be used in sequencing efforts

Kelsey Kaustinen
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GAITHERSBURG, Md.—OpGen, Inc. has announced the beginning ofa scientific and technical partnership with the University of California, Davis(UC Davis) in cooperation with the 100K Genome Project, for the creation ofhigh-resolution microbial genetic maps. UC Davis will integrate OpGen's ArgusWhole Genome Mapping System into its current DNA sequencing workflow forsequence assembly and genome validation.
"OpGen's technology allows us to complete sequencing andprovide quality control of genomes drafted by data produced using short readnext-generation sequencing methods," sad Bart C. Weimer, Ph.D., professor inthe Department of Population and Reproduction, School of Veterinary Medicine,UC Davis, and director of The 100K Pathogen Genome Project. "Whole GenomeMapping provides an independent method to detect sequence variations andmisassemblies, and aids us in closing the gaps. Final Whole Genome Maps willassist health agencies in outbreak management of food borne diseases whichcause 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. Thefive-year initiative seeks to sequence the genomes of 100,000 infectiousmicroorganisms in hopes of accelerating diagnosis of food-borne illnesses. Thesequencing is taking place at the BGI@UC Davis facility.
Additionalcollaborators 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 draftsequences in addition to thousands of food pathogen strains for sequencing,with the CDC providing additional strains and expertise. The U.S. Department ofAgriculture's Food Safety and Inspection Service will also provide strains forUC Davis to sequence, and Agilent Technologies will contribute funding while UCDavis forms a consortium of additional project partners. Once sequences arecompleted, they will be stored in the National Institutes of Health's NationalCenter for Biotechnology Information's public database.
The addition of OpGen's Whole Genome Mapping technology willallow the project to create a new standard for high-quality microbial referencegenomes, which will be used to monitor and manage international food-bornemicrobial outbreaks and establish a global reference database for microbialgenomes 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 withUC Davis and the FDA in helping to set a high-quality, validated standard forthis important reference database of microbes, which pose the greatest threatsto food safety and public health," said Douglas White, Chief Executive Officerof OpGen. "OpGen is committed to advancing public health and providingactionable information to the healthcare community."
According to the CDC, approximately 48 million peoplecontract food-borne diseases each year in the United States alone, with 128,000resultant hospitalizations and 3,000 deaths. So far, there are 31 knownfood-borne pathogens, which includes familiar strains such as Salmonella,Listeria and E. coli, many of which aretracked by public health systems.

Kelsey Kaustinen

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