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NMSU professor among scientists worldwide testing miniaturized genome sequencer

It fits in the palm of your hand but might someday match the performance of genetic testing instruments hundreds of times its size. A New Mexico State University professor is one of a limited group of scientists around the world now beta testing a handheld genome sequencer.

Head and shoulders of man holding small device
NMSU biology professor Brook Milligan holds the Oxford Nanopore MinION. Milligan is among a limited group of scientists around the world testing the handheld genome sequencer. (NMSU photo by Darren Phillips)

“NMSU is lucky to have the opportunity,” said Brook Milligan, biology professor in the College of Arts and Sciences. “This is the cutting edge, the frontier.”

Oxford Nanopore’s MinION is designed to gather data on hundreds of molecules simultaneously and return results quickly. Milligan received two of the miniaturized genome sequencers this summer and will continue to test them throughout the fall semester.

“It’s very simple,” Milligan said as he described the device’s operation. “There’s a cassette that fits inside. You open it, load your sample into it and plug it into the USB port of a laptop.

“The sensor is like a set of pores, a sieve. As molecules go through the pores, they change the electrical current, which the electronic sensors can detect. The device sends signals to the computer, which sends the files off to the cloud and they are returned as sequences of nucleotides.”

In 2008, NMSU acquired a then state-of-the-art pyrosequencer with the help of a $1.2 million National Science Foundation grant co-led by Milligan. That pyrosequencer could process more than one million molecules in the same time it took for even older machines to process 96 samples. That process, however, took significant preparation, a fully equipped lab and skilled technicians to properly execute. Similarly, other sequencing technologies demand large investments and skilled personnel.

The MinION is poised to transform that by being more accessible and more cost-effective.

Milligan says if Oxford Nanopore’s device works as expected, this new instrument set to retail for under $1,000 could not only reduce the turn around time for data but also dramatically expand access to genetic testing.

“Not all sequencing will be done on handheld devices, but this opens up some opportunities that haven’t existed before,” Milligan said. “All over the world you can empower people in developing countries who might never have access to the kind of large-scale equipment needed to do genetic testing for diseases.

“This device could be used at the border for monitoring food security. A USDA or customs officer wouldn’t need a lot of training to use this device. We could also take these into high school biology labs. You could easily train middle school students to use it. There are many possibilities.”

Milligan is most interested in tracking illegal trade in wildlife, timber and fisheries. He spent a year in the U.S. State Department working on international conservation issues such as poaching and wildlife trafficking. He explained that insurgencies in Africa are funded by poaching, especially elephants for ivory trade, rhinos for their horns and tigers for their skins.

“Illegal wildlife trade is probably the third largest illegal trade in the world. It’s up there with guns and drugs,” said Milligan. “Genetic patterns can help identify not just what species it is but also the location of origin.”

Milligan is already involved with applications to test timber for a project in Peru, which has a major problem with illegally harvested mahogany and Spanish cedar. He also has genetic samples of tigers from Nepal and elephants from Laos to test in the handheld sequencer.

“With a device like this you can get an army of people mapping the geographic genetic differentiation. This could give NGOs interested in tracking illegal trade an additional tool. It could be used for enforcement. It could also be used by timber companies that have complex supply chains, for example, to prove where they are getting their products.”

Handheld genetic sequencing equipment will not completely replace the larger industrial machines, according to Milligan. But if scientists find the Oxford Nanopore device works well during the beta test period, its size, simplicity and price tag could save researchers both money and time.

“Literally you load this, turn it on and within less than five minutes you have data,” Milligan said. “Not all the data certainly, as it just keeps coming. The longer you run it, the more data you get. An individual lab could have one of these or 10 of them, whatever corresponds to the work they are doing. It’s much more scaled to the size of the operations.”