NEW YORK (GenomeWeb) – Oxford Nanopore Technologies and several of its customers are starting to explore using the MinIon sequencer in education and citizen science research, a potential future market for the company that remains largely untapped by others.
Several customers, including a team affiliated with the New York Genome Center and Columbia University and a researcher at Mount Desert Island Biological Laboratory in Maine, have already incorporated parts of the MinIon workflow into undergraduate and graduate courses. But a number of challenges remain to make the MinIon suitable for educators who don't have access to the infrastructure of a molecular biology laboratory or lack expertise in bioinformatics.
"We are starting to explore how we can support educators wishing to use the MinIon in schools, universities or even in citizen science," Oxford Nanopore posted on its website last month, adding that it is enabling MinIon users "to share and discuss educational project plans or examples of how they used MinIon for education purposes" on its site, so the company can "learn more from these projects about tailoring products and services for the educational community."
In the meantime, customers have started to publish reports of their use of the MinIon in education. Last month, for example, Yaniv Erlich at the NYGC and his postdoc Sophie Zaaijer posted a paper on the BioRxiv preprint server about their experience with the MinIon in a genomics course at Columbia University last fall.
On its website, Oxford Nanopore also links to a survey for individuals mulling the use of the MinIon in an educational setting, conducted by Karen James, an early-access MinIon customer and a staff scientist at the MDI Biological Laboratory in Maine, in collaboration with the company.
James has been working on DNA-based species identification as part of citizen science projects and has been collaborating with researchers at Acadia National Park on a project called BioTrails that plans to engage park visitors in scientific studies. "My ultimate goal is to have citizen scientists collecting samples in Acadia National Park, or other national parks … and using DNA sequencing, perhaps the MinIon, to identify the samples that they are collecting," James told GenomeWeb.
"The survey is meant to try and begin to capture the different kinds of educators and learners out there, and how they might wish to use the MinIon in their educational programs or projects," she said. The questions address a variety of potential users, including high school teachers, instructors at colleges and grad schools, citizen science project directors, science communicators, and biohackers, and ask about participants' ongoing educational activities related to DNA sequencing, equipment already in place, and how they imagine using the MinIon in educational projects, such as the types of organisms they would like to sequence and what application — ranging from whole-genome sequencing to amplicon sequencing — they are most interested in. James said the survey will be open for at least another month, and she plans to present the results sometime this year, possibly at Oxford Nanopore's next user meeting in London in May.
In her own work, James has been using the MinIon since 2014, when she was among the first group of scientists to join the MinIon Access Program. That year, she had two high school summer students prepare MinIon sequencing libraries from DNA extracted from the gut contents of invasive green crabs to investigate whether the crabs were potentially harming eelgrass meadows by eating the grass. Unfortunately, the sequence data they obtained using MinIon's early flow cells and basecalling software had high error rates and was not useful, but the project "gave us the experience that we needed in terms of library preparation and using the device," she said.
Last summer, one of the interns returned to prepare more MinIon sequencing libraries, using both DNA extracted from environmental samples such as green crab gut, seawater, marine sediment, and bird fecal material, and from individual plant and animal species. Those samples are currently being analyzed on the MinIon with the latest generation of flow cells and reagents.
In addition, as part of a week-long intensive short course James teaches at the MDI Biological Laboratory, she had undergraduate students prepare MinIon sequencing libraries. The course ended before the students had a chance to run the samples, and the sequence data James generated subsequently did not turn out to be great because the amount of DNA was too low. But the course was still a worthwhile experience: "The students were excited [about participating] whether or not they got good data in the end," she said. "In a course, it's not just about the data, it's about learning science. So creating a MinIon sequencing library and all the things that go with that is actually a useful thing for undergraduates to do."
James said for her own research, she is mainly interested in two potential applications of the MinIon: as a DNA barcode reader to identify individual species, and for metabarcoding, which is similar to 16S rRNA gene sequencing but for higher organisms and aims to identify species in a mixed sample. "If the consumables got inexpensive and reusable and robust enough, we could maybe use this as a handheld species identifier," she said.
James has not used other next-generation sequencing platform besides the MinIon, largely for lack of funding, but said she would like to compare her metabarcoding results with those of others using Illumina's MiSeq or HiSeq, or Roche's 454.
The low entry costs — Oxford Nanopore customers pay $1,000 to receive their first MinIon starter pack, and $900 for individual flow cells after that, plus more for reagent kits, instead of tens of thousands of dollars for the least expensive Illumina or Ion Torrent platforms — is arguably the main attraction of the MinIon for users like James who engage in both research and education. "I have a small lab, I am at a small nonprofit research institution, and I have not really had access to [other] kinds of sequencers before," James said. "And that's the reason that I'm interested in [the MinIon] — the cost and infrastructure that you need are lower, both in terms of human resources and also in terms of the physical infrastructure."
"Many ecologists are professors at small liberal arts colleges, and they might not have huge budgets, so this represents a really exciting opportunity to expand the access to next-generation sequencing far beyond those who have well-resourced laboratories with big instruments like Illumina sequencers," she said.
But other barriers still exist that prevent the MinIon from becoming a widespread tool for educational — or recreational — sequencing. For example, sample and library preparation currently require a long list of equipment and consumables that are not easy to come by without access to a molecular biology laboratory, including a PCR machine, a microcentrifuge, and a set of micropipettes. Also, "making the MinIon sequencing libraries is not trivial; you need a well-resourced lab, you need good hands at the laboratory bench, you need consumables," James said. "That would be really difficult for, say, a high school teacher to do in their classroom or teaching laboratory."
To make sample preparation more user friendly, Oxford Nanopore is working on a microfluidic device, called VolTrax, for automated sample and library preparation. The company has not said when VolTrax will become commercially available, and the device will initially still require users to extract DNA from their samples first, though in the future, it is supposed to take raw samples. "I really think that the VolTrax is going to be a huge part of making MinIon sequencing accessible to more educators," James said.
On the data analysis side, Oxford Nanopore's Metrichor group is working on software that will allow customers to obtain results without having to interact directly with the primary sequence data, which requires some knowledge of bioinformatics. This includes the already-released "What's In My Pot," or WIMP, application, which can identify and taxonomically classify bacteria, viruses, and fungi present in a sample from MinIon sequence data in real time. "If they expand WIMP to include the sorts of things I'm interested in, like plants and animals, that will represent a really exciting analytical workflow that's accessible to educators and not just people with bioinformatics expertise," James said.
During a presentation at Oxford Nanopore's user meeting in New York last month, Dan Turner, head of the company's applications group, said that tools for 16S rRNA gene sequence analysis and barcode-based plant and animal identification will be "one of the next things to release" for the company, though it may not be part of the WIMP workflow.