Nanopore Sequencing Improvements Generate Enthusiasm

In February 2014, Oxford Nanopore Technologies (United Kingdom) rolled out the MinION nanopore-based sequencer. Initial user descriptions indicated that the device failed to live up to the company’s promises—it was slower than expected and made “a worrying number” of errors. But Oxford Nanopore has made improvements and pilot users are excitedly publishing results and testing the use cases for the palm-sized sequencer. Recent publications by pilot users have shown that a MinION can reliably sequence small genomes, such as bacteria. It can discriminate between closely related bacteria and viruses, read complex portions of the human genome, and differentiate between the genetic variants. Field trials have included Ebola sequencing in West Africa, biodiversity sequencing in forests and rain forests, and reportedly even upcoming trials in space. Researchers are hopeful that if the MinION can be modified to run on a smartphone instead of a computer, there could be endless field applications. Early users say the MinION’s benefits are its real-time, portable nature and its “super-long” reads. The palm-sized device plugs into a laptop’s USB port and data is displayed on the screen as generated, rather than at the end of a run. Oxford Nanopore recently held its first user conference dubbed London Calling (London; May 14-15). Among the highlights of the early users were:

• Nick Loman, Ph.D. (University of Birmingham, United Kingdom) presented his experience using the MinION to identify Salmonella as the source of food poisoning in just 100 minutes of sequencing (30 minutes for species identification; 50 minutes for serotype; 100 minutes for full characterization).

• Jared Simpson, Ph.D. (Ontario Institute for Cancer Research, Canada) produced a complete Escherichia coli genome assembly with 98.4 percent nucleotide identity, compared to the reference genome.

One of the most talked-about presentations at London Calling was Oxford Nanopore’s Chief Technology Officer Clive Brown’s company update. It outlined improvements and specs for the company’s next round of sequencers. In response, industry watchers called the company’s announcements “game-changing,” “revolutionary” and possibly heralding the arrival of field or at-home sequencing.

• Sample Prep - Brown announced the company’s goal is to get sample prep down to 10 minutes. The company unveiled Voltrax, a fully integrated, nanoliter volume, automated sample prep solution, that will be available later this year. It is portable, programmable, and disposable, with between six and 12 sample input ports. It automates the entire sample prep process and loads directly onto the MinION and PromethION. It was reported that this significant improvement in sample preparation should allow direct sequencing from blood, with a time to results (for targeted sequencing or species identification) of about 30 minutes from sample collection.

• High Performance Circuits - The company announced upgrades to the ASIC (Application Specific Integrated Circuit), the core of the PromethION and MinION sequencers, which controls and measures the ionic current flow. The current ASIC chip has 512 channels, but the new chip will have 3,000. Oxford Nanopore announced that they are separating the nanopore sensing membrane from the ASIC, which will permit better manufacturing control of the two and allow for reuse of the ASIC, which will lower consumable costs.

• Throughput - “Fast mode” will improve pore speed. “Normal mode” reads at 30 bases per second, but the new “fast mode,” which will be released within a few months, will read at 500 bases per second, with no decrease in base-calling quality. Experts say that “fast mode” makes the MinION comparable in throughput and cost to HiSeq.

• PromethION - A prototype of the PromethION was unveiled at the conference. The device will be launched in a restricted, early-access program later this year. The PromethION is essentially 48 MkII flow cell units, providing 144,000 sequencing channels that can work in unison on the same sample, individually, or multiplexed. The laptop-sized device can accommodate one to 192 samples.

• Pricing - Brown also announced “pay-as-you-go” sequencing with a “zero-hour” flow cell (although “full flow cells” are still available). It was released that for the MinION MkI flow cell, the first three-hour block is to be priced at $270, but for the MkII, available next year with the new 3,000-channel ASIC, pricing will begin at $20 for the first hour of sequencing. The cost will then drop for additional sequencing hours on the same flow cell.

Takeaway: Advancements in Oxford Nanopore’s MinION are making real-time, field and bedside testing a seeming possibility in the not too distant future.