Sequencing rivals face off over the nature of nanopores

With over 90% of all DNA data being generated using their machines, Illumina are more or less the first and last word in sequencing. However, there are a number of potential rivals out there looking to exploit new niches in the sequencing market, looking for the technology that will deliver the next breakthrough in fast, low-cost, high-throughput DNA sequence generation.

This week the flourishing world of nanopores became the latest commercial battleground, as Illumina opened legal proceedings against British rival Oxford Nanopore, claiming that they own the patent for the protein pore at the heart of Oxford’s devices. 

Bacteria naturally contain protein pores in their cell membranes that transport nutrients in and waste products out. Oxford Nanopore’s MinION device, a hand-held long-read sequencing device, contains bacterial nanopores fused into a physical device that can read DNA. Oxford started shipping their device in 2014, which draws DNA molecules through the tiny pores and records the change in electrical current as different bases – A, G, C, T – are read.

Illumina’s concern is over which bacterial pore MinION uses. Work published in 2010 by Jens Gundlach, a physicist at the University of Washington, showed that a particular pore found in Mycobacterium smegmatis (yes, it is named for its presence in genital secretions), produces a signal ten times stronger than any previously identified. Illumina hold a license for Gundlach’s work, and it is this pore that Illumina claim is “more likely than not” powering the MinION device.

Thus far, Oxford’s devices only account for a sliver of the sequencing market, but according to Shawn Baker, cofounder of genomics consultancy AllSeq, Illumina’s lawsuit is less about direct competition than it is about “protecting their space and causing headaches to Oxford as they’re trying to go public.”

Oxford have denied that Illumina’s claims have any merit. In a statement CEO Gordon Sanghera said, “it is gratifying to have the commercial relevance of Oxford Nanopore products so publicly acknowledged by the market monopolist.”

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