Oxford Nanopore Technologies, the company that pioneered a new DNA analysis technique called nanopore sequencing, has remained secretive about the microscopic channel at the heart of its products. But on the heels of a patent infringement lawsuit from sequencing behemoth Illumina, Inc., the company has revealed what will drive its newest devices—a bacterial pore that seems to circumvent Illumina’s challenge.
Nanopore sequencing, hailed as a more portable and affordable way to analyze DNA than previous methods, works by measuring changes in electrical current as single nucleotides pass through a pore not much bigger than DNA itself. In 2014, Oxford Nanopore rolled out the first commercial nanopore sequencer, a handheld device called MinION. Although researchers have praised the technology and worked to improve its accuracy, they could only speculate about how MinION had succeeded where Illumina and others had failed; the structure of the MinION’s pore has remained a trade secret. In a lawsuit filed 23 February, Illumina suggested that Oxford Nanopore used a bacteria-derived pore called Mycobacterium smegmatis porin (Msp). Illumina licenses patents on an Msp system from the University of Washington, Seattle, and the University of Alabama, Birmingham, and claimed that Oxford Nanopore’s sequencers infringed those patents.
The suit came as distressing news to some researchers, who feared they might lose access to the firm’s nanopore products, or that the battle would stifle the development of new platforms. “I would love it if Illumina had released a platform. Instead what they’re doing is releasing a lawsuit,” says Winston Timp, a biomedical engineer at Johns Hopkins University in Baltimore, Maryland, whose lab has also licensed patents to Oxford Nanopore.
A webcast presentation today for customers of the company will likely put many of those fears to rest. Oxford Nanopore’s Chief Technology Officer Clive Brown announced an upgrade to its devices—a new pore the company has been describing in presentations as R9. Brown revealed that R9 is CsgG, a membrane protein derived from Escherichia coli, but present in many bacterial species.
CsgG is a relative newcomer to the lineup of nanopore candidates. A team led by Han Remaut, a molecular biologist at the Flanders Institute for Biotechnology in Belgium, worked out the structure of CsgG and published it in 2014. The pore seemed to hold promise for sequencing because it has a very narrow and well-defined passage for a DNA strand, Remaut says. Many other pores that have been explored, including Msp, taper to their narrowest points more gradually and over a longer distance, he explains. That allows for more interactions between the pore and a DNA strand, which can degrade the electrical signals of interest for sequencing.
CsgG seems to outperform its (still unidentified) predecessor, R7, at discriminating nucleotides as they pass through, Brown said. He showed preliminary results suggesting that where the R7 system ranged from 75% to 90% accuracy (depending on the how the DNA is read through the pore), the new system that includes R9 achieved 85% to 95%. Brown didn’t reveal anything about the identity of R7, but said the company will transition all its customers to R9 this spring. A more powerful sequencer known as PromethION, set to ship to researchers at the end of March, will only contain R9. Oxford Nanopore holds an exclusive license on the use of the pore, Brown said today, and has developed more than 700 variations of it. “It’s the way forward, as far as we’re concerned.”
Oxford Nanopore also responded directly to Illumina’s suit this week. In an 8 March letter to the U.S. International Trade Commission, the company denies all charges of infringement, and claims that Illumina is acting on “unsubstantiated speculation” to block Oxford Nanopore products and maintain its own monopoly over conventional DNA sequencing. Illumina has never proved that it’s capable of making its own working nanopore sequencer, the letter alleges, and removing Oxford Nanopore technology from the market as Illumina requests could harm public health research efforts such as the tracking of Ebola and Zika viruses in the field.
*Update, 11 March, 12:35 p.m.: Oxford Nanopore's response to Illumina’s patent suite was added to the story.
*Update, 9 March, 11:00 a.m.: This article has been updated with more information on CsgG.