GigaScience Paper Demonstrates Pathogen Detection on the MinION

By Bio-IT World Staff 

March 27, 2015 | A team of researchers led by Andy Kilianski of Maryland’s Edgewood Chemical Biological Center has published a paper demonstrating the use of the MinION nanopore sequencer to accurately identify strains of bacteria and viruses. Distinguishing between microbes based on small DNA samples, especially in a clinical setting, is one of the most highly anticipated applications of the MinION, a three-inch-long DNA sequencer that plugs into a laptop and can be run with minimal lab equipment. (See, “Nanopore Sequencing Is Here to Stay.”)

The new paper, published in the open access journal GigaScience, targeted the bacterium E. coli and three closely-related viruses in the poxvirus family. Rather than sequencing raw DNA samples, the authors sequenced PCR amplicons from regions of the genome useful for species and strain identification, meaning their methods, while generalizable to a wide range of pathogens, are not fully sample agnostic. Still, the MinION’s ability to correctly distinguish species and strains after a six-hour sequencing run is promising for clinical applications. This is especially so because the authors, like many other members of the early access program for the MinION, saw high error rates in base calling and relied on alignment software designed for very different sequencing instruments — suggesting there is significant room for better performance with custom software and new generations of MinION hardware and chemistry.

“By utilizing amplicon sequencing as a method for bacterial and viral detection and differentiation, accurate depictions of what agents are in a sample can be generated,” the authors conclude. “Importantly, this is a practical use for the technology as it exists now, and the methods described here will only become more accurate as nanopore sequencing technology evolves.”

As has been common among early MinION adopters, the authors of this paper have made their data freely available for anyone to view and use. (See also, “Early Data on Human Sequencing with Oxford Nanopore MinION.”)