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Oxford Nanopore to Release New Pore, Other Updates This Month; Ship First PromethIon


NEW YORK (GenomeWeb) – Oxford Nanopore Technologies plans to release a number of updates to its sequencing technology this month, including a new pore that is unrelated to the MspA pore that is at the center of an ongoing patent dispute with Illumina, and to ship the first PromethIon instrument to a customer.

During a webinar today, Clive Brown, Oxford Nanopore's chief technology officer, provided details about the updates, which include two new kits for fast-mode sequencing on the MinIon and PromethIon, flow cells with the new nanopore, and improved base calling software. He also pointed to additional developments that will be discussed at a conference the company is holding in London in May.

Last month, Oxford Nanopore was sued by Illumina for alleged infringement of patents relating to the use of Mycobacterium smegmatis porin A (MspA). Until now, Oxford Nanopore had never disclosed the type of pore it is using in its MinIon and PromethIon devices, though much of its early development work was done on the alpha-hemolysin pore.

Putting an end to speculations about the nature of its nanopores going forward, Brown said that the R9 pore, which the company plans to release later this month for the MinIon and the upcoming PromethIon, is based on the CsgG pore from E. coli.

Oxford Nanopore has licensed the CsgG technology from VIB, a research institute in Ghent, Belgium, and has been collaborating with the lab of Han Remaut at VIB on the development of the pore for nanopore sensing. In 2014, Remaut's lab published the crystal structure of CsgG in Nature. The shape of the transmembrane protein, which has nine subunits, along with the position of its constriction make it very suitable for DNA sequencing, Brown said. Oxford Nanopore has "heavily engineered" the pore to enhance its properties, he said, generating more than 700 mutants, and there is "considerable headroom for further improvements."

Oxford Nanopore plans to start shipping MinIon flow cells containing the R9 pore in March and to discontinue the R7 flow cells once its customers have transitioned to the new one.

Using the R9 flow cells, the company has internally generated 1D reads with a mean accuracy of 85 percent and 2D reads with a mean accuracy of 95 percent, Brown said, adding that accuracy is "improving very rapidly."

This month, the company also plans to release two new nanopore sequencing kits for the R9 flow cells that will allow for fast-mode sequencing, initially with a speed of 250 to 300 bases per second. Over time, the speed will increase to 500 bases per second, Brown said. One of the kits will be based on ligation and generate 1D as well as 2D reads, using a new enzyme that allows for higher speed. The other kit, which enables sample prep within 10 minutes, will use the MuA transposase and generate 1D reads only.

In addition, the firm plans to release the source code for two base callers — ANN and HMM  — to developers this month.

In April, the company then intends to launch two local base callers — one with and one without source code — that will be integrated in the MinKnow environment, a feature that many customers had asked about.

Oxford Nanopore plans to ship the first PromethIon instrument to customers at the end of this month. As previously stated, the system will be able to run between one and 48 independent flow cells, each of which has 3,000 active channels and can take up to four samples. In total, PromethIon will have up to 144,000 channels.

The system will only ship with R9-type flow cells and chemistry, and the company is running it internally with R9.2 flow cells at the moment. Both the ligation-based and the transposase-based sequencing kits that will be released for the MinIon will also be compatible with the PromethIon, and the system can work with less than 100 nanograms of input DNA, Brown said. PromethIon also comes with a high-performance local compute cluster for real-time data analysis.

Originally, Oxford Nanopore had planned to ship the first PromethIon systems to customers by the end of 2015, but there were delays due to a manufacturing issue related to a flow cell part that have now been solved, Brown said.

Initially, the company plans to build four to six PromethIon systems per month, Brown said, but it intends to ramp up manufacturing to 10 systems per month later this year to be able to clear its backlog of orders by year end. Customers who have paid a deposit to order the system but are not willing to wait that long may be able to negotiate with the company to have their deposit returned, he added.

Oxford Nanopore plans to provide further technology updates, including on the VolTrax integrated sample prep device, RNA sequencing, and protein applications, at its London Calling conference May 26 to 27.