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Columbia University Team Uses MinIon to Bring DNA Sequencing to Classroom

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This article has been updated to correct that the researchers did not use Oxford Nanopore's WIMP software for the projects described.

NEW YORK (GenomeWeb) – Researchers affiliated with Columbia University and the New York Genome Center have used Oxford Nanopore Technologies' portable MinIon sequencer to bring DNA sequencing to the classroom.

This fall, the team, led by Yaniv Erlich, an assistant professor of computer science at Columbia and a faculty member of the New York Genome Center, for the first time offered a course for undergraduate and graduate students at Columbia that included two hands-on MinIon sequencing projects, called "hackathons," that were organized by his postdoc Sophie Zaaijer. The course was supported by Oxford Nanopore, which donated five MinIon devices, 20 flowcells, and reagents for the course.

Last week at Oxford Nanopore's MinIon Community user meeting, held at the New York Genome Center, Zaaijer reported on the team's experience, including challenges they encountered and how the course influenced students' attitudes about the future of mobile sequencing.

The Columbia course is among the first to explore the MinIon for educational purposes. The device distinguishes itself from other massively parallel sequencers by its small size and portability, low cost, ease of use, and fast data generation, making it suitable for such projects, even though sample preparation and data analysis currently still require significant expertise. Oxford Nanopore is working on making the front and back ends of the sequencing process more user friendly by developing the VolTrax device for automated sample preparation and new software applications for its Metrichor environment.

Another scientist presenting at the meeting, Karen James of the Mount Desert Island Biological Laboratory in Maine, has used the MinIon as part of summer courses for high school students. In collaboration with Oxford Nanopore, James is working on defining how the company can support educators going forward and is currently surveying teachers, students, citizen scientists, science communicators, and others about their ideas and needs for using the MinIon in educational settings. The company, for its part, is launching an education-focused web portal for MinIon users to share ideas about and post completed educational projects. 

For their course, called "Ubiquitous Genomics", which started in September and runs until later this month, the Columbia researchers signed up a total of 20 students — an equal number of undergraduates and graduates — more than half of them with a computer science background, in addition to other sciences.

The curriculum included two single-afternoon "hackathons," held in a meeting room at the New York Genome Center, to allow students to gain hands-on experience with MinIon sequencing. After analyzing the data at home, student teams presented their results in class a few weeks later.

The goal of the first hackathon, called "Snack to Sequence," was to identify the source of DNA prepared from supermarket food. Zaaijer said this project was inspired by a food scandal in Europe a few years ago where meat products labeled as beef were tainted with horse meat, which raised consumers' awareness for what goes into their food.

For this project, two student groups received DNA from samples containing tomato and ground beef, one group got DNA from samples that contained kale, mussels, and shrimp, and a fourth group obtained DNA from a sample with bacon and salmon. Groups received no information about what foods were in their sample.

For the second, more challenging hackathon, dubbed "CSI Columbia," five student groups were each given a human DNA sample and asked to identify the person it came from, or at least figure out their ancestry or some phenotypic traits. Students were told that the DNA could originate from one of four individuals — Yaniv Erlich, Craig Venter, James Watson, or a specific HapMap sample. The actual samples contained DNA from one of these, except Watson.

Zaaijer had prepared the sequencing libraries for both projects in advance and tested their functionality, so they were ready to go when the students arrived. She also kept some extra library material available in case students dropped their sample prior to loading it into the MinIon device, though that did not happen. Just in case, she had also performed a few sequencing runs ahead of the hackathons to be able to provide the students with backup data for analysis in case their in-class projects failed.

In addition, Zaaijer had to come up with five Windows-operated computers to run the MinIons, which was a bit of a challenge because the New York Genome Center, like many other scientific institutions, predominantly runs Macs. However, Oxford Nanopore is working on making the MinIon MinKnow software compatible with Apple computers, she said. In addition, she had to make sure the computers had the right connections and all necessary drivers installed.

Another consideration was to ensure that students were able to download the sequence data onto their own machines once the MinIon runs were completed. The files are large — on the order of gigabytes per experiment — Zaaijer said, and she found that the BitTorrent software worked well for synching student computers with the MinIon workstations, though it required the software to be installed in advance.

"These are all things you need to prepare in advance before the hackathon starts," she said.

On the day of the event, students received an explanation of the nanopore sequencing technology, pipetted their samples into the MinIons, started the sequencing runs, and were able to observe the data being generated on the computer in real time. When the runs were completed — depending on how much data is needed, the MinIon can run up to 48 hours — the data were transferred to the students' computers, so they were able to proceed with the analysis at home.

Students initially used the Poretools software to assess their run as a whole, for example, the number and quality of the reads, and to convert the FAST5 files that come off the MinIon into FASTQ files.

This files format allowed them to perform downstream analyses, such as Blast searches, to identify what species the reads came from. To create these analysis pipelines, the students wrote their own code, which has been published on GitHub. By the end of the month, Zaaijer also plans to submit a manuscript to eLife describing the hackathons and the results.

Students also developed their own approaches for determining how long they would have to sequence to find out what species are present, or in what ratios. "Because they are very computationally educated, they were very good about writing those programs," she said.

Overall, the experiments and analyses went fairly well, though there were a few glitches. One run during the first hackathon, for example, failed due to a connection problem between the MinIon and the computer. Also, flowcells varied in yield, and three flowcells had fewer than 50 active nanopores, not enough to obtain sufficient sequence data.

Three out of the four student groups in the "Snacks to Sequence" project were able to identify the ingredients of their food sample correctly, or at least they came close — one group, for example, received a database hit for the bighorn sheep, a non-domesticated species that is in the same family as cattle, for their beef sample. The fourth group had problems parsing the large data file through the Blast database.

The "CSI Columbia" project turned out to be a little trickier: only one out of the five groups was able to correctly identify their person, Craig Venter. Remarkably, this group had the lowest flowcell yield, suggesting that "if you are creative, and you have a good solution, you can work with any number of reads, apparently," Zaaijer said.

Before and after the hackathons, students answered questionnaires about how they envisioned mobile sequencing in the future, for example, for identifying persons at borders or to diagnose health problems at home. Interestingly, some students became a little less optimistic after conducting their own project. "After using the MinIon, the students realized that although the sequencing technology has a lot of potential, there are still challenges that we have to solve in order to really implement this in society for consumer usage," Zaaijer said.

She and Erlich would like to offer the course again in the next semester but do not know yet whether it will continue to be funded by Oxford Nanopore. "We thought it was an excellent way to teach students genomics," she said.

And while courses at other research institutions have given students the opportunity to analyze genomic data — in 2012 Mount Sinai School of Medicine had students interpret their own genome data — Zaaijer said the hands-on experience with the actual sequencing process added another dimension. Seeing the data a couple of minutes after starting the run "provoked such enthusiasm and curiosity — we definitely think that's an addition to educating students in genomics," she said.

The experience could probably be extended to students who are less computer-savvy than the Columbia class, she said, requiring "a little bit more preparation, guidance, and pipeline preparation" from the educator. "We are thinking about how we can implement this in high schools to make future students more familiar with genomics," she said, an important goal given the growing importance of genomics in society.

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