After announcing an early-access program for its MinIon sequencer at the American Society of Human Genetics annual meeting in Boston last week, Oxford Nanopore Technologies showed off the device at its booth and gave a live demonstration of runs to a select group of potential customers at its research laboratory in Cambridge, Mass.
While researchers welcome the prospect of getting their hands on Oxford Nanopore's technology in the near future, their enthusiasm is somewhat guarded, given the absence of actual sequence data, which the company does not plan to put out on its own and which attendees of last week's demo event did not get to see. Instead, the firm wants to let customers' data speak for itself once it becomes available.
With the early access program, "we're trying to understand how the technology works in the hands of our customers and where potential applications are that we could support early," a company spokesperson told In Sequence. "Rather than us put out a spec, we want to work with our customers and see how it performs in their hands."
Also, because MinIon runs are so versatile – run times, for example, are user-defined − it is impossible to provide a fixed set of specs, Oxford Nanopore's CEO Gordon Sanghera said.
In the meantime, Oxford Nanopore has not changed its guidance from 2012 for the expected performance of both the MinIon and the GridIon at launch. At that time, it said the systems will deliver reads up to 100 kilobases, with raw read error rates of about 1 percent. A MinIon run could last up to six hours, limited by the lifetime of the electrodes, and generate several hundred megabases of data per hour (IS 2/21/2012).
A flow cell's total available lifetime can be utilized over time. "It's like a light bulb, you can switch it on and off," Sanghera explained. In addition, it can be used with multiple samples. "You can run an experiment, wash it out, and then run another experiment," he said.
Flow cells are shipped with nanopores already embedded in a membrane, one of the main changes the company has made since 2012. However, the main issue that delayed commercialization was related to the sensor chip, a problem that has been solved.
The MinIon consists of a small box that contains the data transfer system and a USB connection; a flow cell that is inserted into the box, with a sensor chip and an application-specific integrated circuit, or an ASIC; and a lid.
While the data transfer box is reusable and the flow cells are disposable, the company plans to replace the box with newer models on a regular basis, possibly more than once a year. "Ultimately, we do not want these in the field for too long," Sanghera said. "The rate at which electronics develops, we want to be able to iterate fast."
"That's where the [idea of] 'disposable' comes from – we don't want legacy hardware systems left in the field," he explained.
About 40 individuals, most of them based in the US, attended a pilot demonstration of multiple MinIon sequencers at the firm's R&D lab in Cambridge last week. Following the event, the company invited them to sign up for the early access program, which will open in late November.
While participants were prohibited from sharing details about the technology that are not yet public, Oxford Nanopore granted them permission to talk about the event and their impressions in general terms, and several posted information and photos on their websites.
A number of participants told In Sequence that they received a company-prepared DNA sample – transposon-generated fragments of bacteriophage lambda DNA, which has a 48.5-kilobase genome – which they pipetted into a flow cell.
The nanopores became "immediately active," they said, as revealed by the "squiggle lines" that appeared on the screen.
The MinIon device, which is about the size of a pencil case, is surprisingly robust, they noted – picking it up and turning it upside down during the run had no obvious effect on data collection.
However, no base calls were made, so researchers did not have a chance to assess the quality of the data. One reason, participants suggested, is that the company still needs to calibrate its base-calling software with more data from test samples.
Nevertheless, several attendees were happy to see that nanopore sequencing appears to be working in principle. "The technology had a long gestation period, and we've been waiting for the birth," said Chris Mason, an assistant professor at Weill Cornell Medical College who took part in the pilot demonstrations. "It's finally happened."
However, he said, the pilot event had "four notable absences – A, T, G, and C."
The instrument apparently will not take raw samples, such as blood, as input initially, instead requiring prepared DNA. However, the fact that it only requires a USB connection means that "you could use it in extremely remote areas" for on-the-fly sequencing, Mason said, such as pathogen detection.
George Grills, director of operations of core facilities at the Cornell University Life Sciences Core Laboratories Center, who also attended the demo event, said what he saw was "extremely promising for the stage of development that it's at," though he does not expect the technology to replace so-called second-generation sequencing anytime soon.
Provided Oxford Nano meets its stated goals for read length and accuracy, the system will "enable research that is not feasible, economically or technically, with any currently available platform," he said.
And while there will likely be some overlap in applications with Pacific Biosciences' long-read technology, Oxford's MinIon will probably have a "different sweet spot."
The "biggest challenge" for Oxford Nanopore will likely be the downstream informatics, he said, in particular making sure its software lives up to the standards for ease of use of software used for current sequencing platforms.
Grills said he plans to talk to the Cornell research community about its interest in becoming an early-access site for the MinIon. Like any type of beta-testing program, he said, this will incur costs, such as laboratory and informatics staff time.
Early access
Starting in late November, life science researchers will be able to enroll in the MinIon Access Program (GWDN 10/23/2013).
The company is not saying yet when it will ship out the first devices, which countries it plans to include in the program, or how many instruments it plans to place initially, but the goal is to ship " hundreds" of MinIons in total, according to the spokesperson.
While any researcher will be eligible for the program, the company will give "strong preference" to those working in the field of applied next-gen sequencing "where long reads, simple workflow, low costs, and real-time analysis can be shown to make a key difference," as well as to those adopting several MinIon systems, according to the firm's website.
But Oxford Nanopore also wants to attract a diversity of potential users, including those "outside traditional sequencing," Sanghera said. "We're not saying the only people who should do this are high-end DNA sequencing key opinion leaders. We would be delighted if they come in, and set expectations, and opine about the platform, but that's not the only thing we want to do with this program."
For a refundable deposit of $1,000, participants will receive at least one MinIon system, flow cells, and software tools. They will also obtain a "regular baseline supply" of flow cells "sufficient to allow frequent usage of the system" – the company is not saying yet how many that will be – and can purchase additional flow cells for about $1,000 apiece, Sanghera said. Oxford Nano will also supply sample preparation kits, although participants may develop their own sample prep and analysis methods.
Program members will need to sign an end-user license agreement, which states that they need to return all used flow cells to the Oxford Nanopore.
They will also need to go through a "burn-in" period, during which they will run test samples and share their data with the company. "We do want to make sure what we send them works," Sanghera said.
Only "after consistent and satisfactory performance has been achieved under pre-agreed criteria" will they be allowed to run their own samples and publish results. Details about the "burn-in" process will be provided in November.
The company stressed that participants will be "the first to publish data from their own samples." Also, "successful" participants will get preference for the early-access program of the GridIon, the company's larger sequencing platform, a timeline for which it has not yet disclosed.
The reason for starting with a large number of early-access MinIon users, rather than a small traditional beta-testing program, is that "this platform absolutely lends itself to doing that," Sanghera said, noting that it has few moving parts and does not cost users much to acquire.
"It's a mass-market product, so to do the testing in the hands of a small number of expert people would not represent the ultimate market to us," the spokesperson said.
Sanghera said the firm chose to start with early access for the MinIon before the GridIon because "it's an easier footprint to rapidly iterate, based on customer feedback, and the elements in there are identical in the GridIon."
"We can cut our teeth with MinIon, and those learnings are directly transferable to GridIon and will help us shape the GridIon access plan as well," he said.