This article has been updated with additonal information from Oxford Nanopore's presentation.
NEW YORK (GenomeWeb) – Oxford Nanopore Technologies is developing a new smartphone-powered nanopore sensing device for DNA sequencing and other applications. The company has also founded a spinoff, called Genome Foundry, that will use proprietary chemistry and focus on synthetic biology applications.
The new nanopore device — called SmidgIon — is in early development and is expected to be available in late 2017, according to Chief Technology Officer Clive Brown, who reported on this and other new products in development at the company's user meeting in London this week. It will use the same core nanopore sensing technology as the company's MinIon and PromethIon devices, but it will be smaller than the MinIon, with 256 channels per flow cell, and attach to a smartphone or other low-power device, and it can be adapted to DNA, RNA, or protein sensing.
According to the company, the SmidgIon is designed for a broad range of field applications, including monitoring of pathogens in a disease breakout, analysis of environmental or agricultural samples, and real-time species identification of timber or wildlife.
Another product in early development — dubbed Project Zumbador — aims to combine nucleic acid extraction and library preparation into one device, starting from a biological sample, and is expected to be released in the third quarter, Brown said.
The company is also working on kits for direct RNA sequencing on the MinIon and PromethIon, which it plans to make available to developers within the next few months. According to the firm, one method for preparing RNA for direct sequencing involves ligation of an adapter that is preloaded with the motor protein that controls translocation and allows the RNA to be threaded into the nanopore. Oxford has used the approach to sequence RNA from human rhinovirus, and has shown that direct RNA sequencing can detect RNA methylation.
Brown said the first PromethIon was recently shipped to a customer, and he showed some in-house data from the platform, which uses up to 48 modular flow cells with up to 3,000 channels each. Using the R9 chemistry at 250 bases per second and pore, accuracy and pore utilization are consistent with that of the MinIon, he said. The system's capacity is currently up to 6.2 terabases per 48-hour run, which will increase to 12.4 terabases in the future, he said. The company is working on debugging software for managing live basecalling of large datasets, optimizing chip surface chemistry and wet production processes, and developing a fast base caller, according to his presentation.
Another product, the VolTrax sample preparation device, will go out this fall to early access customers who currently use Oxford's nanopore platforms. For the first release, the consumable VolTrax cartridge attaches to a small USB-powered device and later to the MinIon or PromethIon, the company said.
Further, Oxford Nanopore is no longer selling flow cells with the R7 nanopore, Brown said. It has replaced them with flow cells using the R9 nanopore, the company's name for the CsgG nanopore it recently licensed from VIB in Belgium and University College London. The new flow cells also incorporate sturdier membranes and an updated helicase motor protein, Brown added. The longest read the company has obtained with the new flow cells is 500 kilobases, and it is now focusing on improving throughput and homopolymer detection, he said.
The company said in a statement that R9 offers improved accuracy, in particular for 1D reads that only read one strand of DNA. New basecalling software, based on neural networks instead of a hidden Markov model, further enhances accuracy. The R9 flow cells sequence DNA at a speed of 250 bases per second and nanopore, up from 70 bases per second for R7, which the company said will result in "much larger yields of data" on the MinIon. Current accuracy is almost 90 percent for 1D reads and on the order of 95 percent for 2D reads, according to Brown.
Along with the R9 flow cells, the company is introducing a rapid sequencing kit. Library preparation with this kit only takes 10 minutes and requires fewer consumables than before, and data is analyzed immediately after starting a MinIon run. The rapid sequencing kit is currently being tested by a number of early access customers and "will be fully released imminently," according to the statement.
Oxford Nanopore is also planning to make local basecalling software available through the MinKnow platform in the near future.
Finally, Brown mentioned a new Oxford Nanopore spinoff company, called Genome Foundry, that aims to develop a "MinIon of synthetic biology," using proprietary, non-phosphoramidite-based DNA synthesis chemistry. The goal is to develop long DNA molecules in parallel, using VolTrax-like devices, according to the presentation.