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Hand-Held DNA Sequencer IDs Bacteria, Viruses

MinIon device

MinIon device (Biomed Central)

26 March 2015. A palm-sized DNA sequencing device was able to identify a number of bacteria and viruses, and discriminate between closely related species in about 6 hours. Tests of the MinIon device, made by Oxford Nanopore Technologies in Oxford, U.K., were reported today in the journal GigaScience.

Oxford Nanopore is developing the MinIon as a portable disease surveillance system that analyzes DNA from blood samples in the field, and operates as a plug-in peripheral on a laptop computer. The company makes early versions of the system available to researchers for hands-on testing, and the GigaScience article reports on results by testers at the U.S. Army’s Edgewood Chemical Biological Center in Aberdeen, Maryland and the company Signature Science LLC in Austin, Texas.

Oxford Nanopore is a spin-off from University of Oxford, founded in 2005 and licensing technology from research by biochemistry professor Hagan Bayley. The company’s technology is based on straining and isolating individual DNA strands through nanoscale pores in a membrane that allows for electronic sequencing processes to identify the base components of DNA passing through the pore. These nanopores were originally formed in proteins in a lipid membrane, but the company since introduced synthetic materials for nanopores, including graphene.

The team from Edgewood and Signature Science analyzed lab samples of E. coli bacteria and 3 types of pox viruses: cowpox and 2 closely related strains of vaccinia, used to develop smallpox vaccines. Data generated by the MinIon were then analyzed with software performing polymerase chain reactions that amplify single copies of DNA into amplicons, providing multiple copies of sequences.

The use of amplicons makes it possible, say the authors, to overcome a limitation of the MinIon, namely a high read error rate of 30 percent. The multiple sequences provide a more robust analytical pool after about 6 hours that the researchers could then compare to known reference sequences for E. coli and the 3 pox viruses. The results show the system was able to successfully identify the 4 samples, including the individual strain of E. coli and distinguish between the 2 closely related vaccinia samples.

Oxford Nanopore says additional analyses of MinIon data from can be performed through cloud-based software. The following 4 minute video tells more about the MinIon.

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