discussion / Sensors  / 24 March 2016

Portable DNA Sequencer

This might be interesting for anyone looking a DNA and need a field version:


Wonder if it could be used for tracking all animal or plant matter..




Thanks, Adam, for initating a discussion about the MinION. It certainly seems to have a lot of promise, however the scientists who are currently field testing it detect very high error rates. It's been on my radar as a possible field kit for extracting DNA out of wood as it gets processed into various forest products through the supply chain. The implication here is that the part of a tree that is made into forest products is made up of dead cells and thus it is very difficult to extract quality and quantity DNA out of wood. This, combined with the high error rates makes it 'still very much in development' for forest products - but perhaps it'd be suitable sooner for other applications in the conservation world.  There's a professor at New Mexico State Univ. who has been working with the MinION for a while now on wood - Brook Milligan. He recently gave a talk at the 'London Calling' Oxford Nanopore (maker of the Minion) conference that is worth watching: https://londoncallingconf.co.uk/2015/videos/view/241

Hi John and Adam, 

I've been hearing a lot about Oxford Nanopore Technologies and MinION over the last few months, and while it sounds fanastic, it's been difficult to get an understanding about the potential and limitations of this piece of tech, particularly as relates to conservaiton applications. So hearing your experiences, John, is really interesting. 

For anyone interested in learning more about MinION and nanopore technology, I've just came across a thorough article in the Atlantic about the sequencer that was helpful for me as a total novice (though a very interested one!) in the world of nanotechnology and eDNA. It gives context to the MinION in terms of history, current applications and potential applications.  It also features one of our community members, Jon Whetton, who is also a USAID Wildlife Crime Tech Challenge Winner, talking about the potential applications to conservation:

The etymology of VolTRAX may be farcical, but its purpose is not. This domino-sized add-on for the MinION is designed to prepare a biological sample—say bodily fluids, or swabs of soil—for sequencing. It moves liquid through a network of fine channels, bombards it with chemical reagents to extract DNA, and loads that DNA into the MinION. “We spend a lot more time in the lab preparing samples than we do sequencing,” says Loman. “If, and it’s a big if, you could drop the clinical sample onto the chip that does it all for you, it would be hugely advantageous.”

VolTRAX is set to go out to early users this summer. Jon Wetton, a geneticist and forensic scientist at the University of Leicester, wants to use it to fight illegal wildlife trafficking, by sequencing telltale genes that act as identity badges for different species. Conservationists have already used this technique, known as DNA barcoding, to track sources of elephant ivory or identify whale meat posing as sushi. But samples must be shipped for analysis, and “you’re looking at weeks or months to get the results back,” says Wetton. “That can’t be done on anything perishable, or if you’ve got a suspect in custody. But with an on-the-spot test, you could confiscate, arrest, or do something about it.”

With a nanopore sequencer, inspectors could tell the difference between a cut of beef or bushmeat from threatened apes and monkeys. They could analyze the blood on a suspected poacher’s tools to reveal the identity of the last animals it cut. They could work out if seized caviar belong to legitimate fish species or endangered sturgeon. “You could answer a whole slew of serious wildlife crime issues with the same test,” says Wetton.

That still leaves the significant problem of parsing the data, but Oxford Nanopore has a solution for that, too: an online hub called Metrichor, where people can connect to ready-made apps for analyzing DNA sequences. One such app, developed by Oxford Nanopore itself, is called “What’s In My Pot?” or WIMP. It takes sequences and identifies the organisms they belong to. The team have already field-tested it on microbes from a sewage-contaminated river behind their own building, and on unpasteurized milk from the back of a New York lorry.