Students test new genomic technology
For most of history studying the genome, a complete set of genes, of an organism has required a lab with expensive and cumbersome equipment. Today, it is becoming accessible as this technology can fit in a pocket and be used by anyone with a laptop. Students will be using this technology during the MinION Hackathon, which started Oct. 23.
The MinION Hackathon is a short workshop organized by evolutionary biology professor Devin Drown. Students will use a pocket-sized DNA sequencing device called a MinION, the same model sent up to the International Space Station over the summer. All of the students have the opportunity to set up their own DNA sequencing experiment, get experience in a laboratory setting and analyze the data they collect with Drown’s help. While the workshop is full now, Drown has plans to do more in the spring semester.
“The technology is cool,” Jonilee Polanco, a biology student participating in the workshop, said. “The fact that we’ve come so far, we used to have these huge gigantic processors and now we can do it in the palm of our hand.”
The 2016 Hackathon is the second one to occur at UAF.
Drown organized a pilot version of the workshop in April of 2016 with six students, which he received funds from URSA to buy supplies. During that workshop the students sequenced a stew Drown made with several different Alaskan animals. The student were able to determine all of the different animals in the stew by identifying what DNA was in the stew. They presented their findings at last year’s UAF Research Day.
During that time they only had one DNA sequencer to work with, despite Drown’s hopes for all of the students to get to work with their own. The sequencer was sent to UAF after Ian Herriott, the Core Lab coordinator, signed up for the MinIon Access Program.
“It’s nice that UAF is able to provide free workshops like this,” Hannah Gerrish, a biology student participating in the workshop, said. “I think it’s a good opportunity … and it can be applicable in lots of different circumstances.”
For the Hackathon this fall Drown was able to get funding from Biomedical Learning and Student Training, commonly referred to as “BLaST.” The students now have ten MinION sequencers for their use.
The MinION, also called the Oxford Nanopore, is about half the size of an iPhone and plugs directly into a computer via USB cable. It was also used to monitor the Ebola and Zika outbreaks.
“A lot of traditional sequencing works by having a DNA strand and essentially rebuilding it,” Drown said. “This is different from that method.”
The MinIon sequencer works through a process called “nanopore sequencing.”
The device has a membrane, or a thin layer made up of proteins, with small holes in it. The DNA strands, which are made of a strand of four different “bases,” are then threaded through those holes and the hole gets bigger or smaller depending on which of the four bases that passed through. The computer can then identify which bases passed through depending on the size of the hole.
What makes this exciting is that nanopore sequencing is much faster and more efficiently than the sequencers that we’re currently using, according to Drown.
“Next Gen sequencing, which you may have heard about in the news, are sequencing chunks of DNA that are 300 to 600 bases long,” Drown said. “[Nanopore sequencing] can do 200,000 base pairs long, that’s a lot. You don’t have to be super talented, I’m not giving you the upper range of ideal laboratory conditions. We’ve done it here in the lab.”
Using traditional sequencers is like putting together a very large jigsaw puzzle with with small pieces and no corners to help you, whereas nanopore sequencing is like having the toddler version of that puzzle with large easy to assemble pieces, according to Drown.
The portability of the device is also a large benefit since it can be used in the field and is easily accessible for students in the classroom, particularly because of its affordability, currently the device costs about $500, according to Drown
“You can spend a whole summer at a field camp and not just collect samples that you’re sending back to a lab, you can be the lab out there,” Drown said.
This technology will allow students to do research with genomics whether that’s in a lab on campus or up in the Arctic, according to Devin Drown, a professor of evolutionary biology.
“I’m pretty excited about genomics and what kind of information we can learn about the world from understanding the genes and genomes of organisms,” Drown said.