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With Patent Suit, Illumina Looks to Tame Emerging British Rival Oxford Nanopore

DNA sequencing companies to face off over nanopore technology.
February 24, 2016

Gene-sequencing giant Illumina is like the Standard Oil of the genome age. Except instead of oil it pumps DNA.  

More than 90 percent of all DNA data is generated by machines Illumina sells, and the San Diego company wants to keep it that way.

That explains why Illumina said today it would try to block commercial sales of a disruptive new DNA sequencing instrument developed by a high-flying British rival, Oxford Nanopore.

In a patent lawsuit and a separate complaint with the U.S. International Trade Commission, Illumina said the British company’s cutting-edge DNA sequencing devices contain stolen ideas and should be stopped at the docks. 

Starting in 2014, Oxford began shipping a new type of “nanopore” DNA sequencer that analyzes DNA by drawing the molecules through a tiny, delicate pore (see “Radical New DNA Sequencer Finally Gets into Researchers’ Hands”). Each combination of the genetic letters A, G, C, T produces a change in electrical current as it moves through, allowing the molecule to be read. 

Illumina says it controls the patent on the pore that Oxford uses, something Oxford denies. But the bigger battle is about technology platforms and whether or not nanopore sequencing can displace Illumina’s machines.

Illumina’s refrigerator-sized instruments are fast and accurate (see “Why Illumina Is Number One”). But because it works differently, Oxford’s MinION, as the device is called, is small enough to be portable (it's about the size of a cell phone) and reads out very long stretches of DNA.

A “nanopore” DNA sequencer sold by Oxford Nanopore is powered by a USB connection.

Although it’s slower and less accurate than Illumina’s instruments, nanopore technology threatens to become a competitor as scientists find entirely new applications for it like sequencing Ebola viruses and diagnosing patients from a makeshift lab in Guinea.

On his blog, Mick Watson, a gene researcher at the University of Edinburgh who uses both technologies, called the lawsuits “incredibly disappointing” and said for researchers it was “like having two of your friends fighting.”

In fact, the two companies have been sparring since 2012 after breaking off plans to jointly develop a nanopore instrument and becoming rivals.

In a statement, Oxford Nanopore CEO Gordon Sanghera said the lawsuits were without merit. He quipped that “it is gratifying to have the commercial relevance of Oxford Nanopore products so publicly acknowledged by the market monopolist.”

Oxford hasn’t reported any sales figures but the company has said “more than 1,000” scientific teams are using the MinION.

Oxford is rated Britain’s most exciting—and most valuable—fast-growth technology company. It’s already worth about 970 million pounds, or $1.4 billion, and is planning an IPO, according to the Sunday Times

So far, Oxford’s devices account for a sliver of the market for fast sequencing machines, chemicals, and software, which is worth $3 billion to $4 billion a year, according to Shawn Baker, cofounder of AllSeq, a genomics consultancy.

Because Oxford is not yet much of a commercial presence, Baker says, Illumina’s lawsuit is about “protecting their space and causing headaches to Oxford as they’re trying to go public.”

Illumina has aggressively defended its turf, adeptly using price cuts, lawsuits, and acquisitions to maintain its market position. In 2012 it even opened fire on one of its biggest customers, the Chinese research operation BGI, after that organization acquired a competing technology.

Bacteria naturally use protein pores to move nutrients into their cell bodies. But the pores are very delicate, and it took Oxford 10 years to learn how to fuse a them into a physical device that could read DNA.

Oxford has never publicly revealed exactly what pore is inside its machines—the company says that’s a trade secret. But according to Illumina’s lawsuits, the MinION is “more likely than not” using a pore developed by Jens Gundlach, a physicist at the University of Washington and collaborators at the University of Alabama.

Until Gundlach’s work, published starting in 2010 and later licensed by Illumina, nanopore sequencing was held up by technical problems. But Gundlach found that a funnel-shaped pore from the bacteria Mycobacterium smegmatis (so named because it’s found in genital secretions) produced a signal about 10 times stronger than previous pores, according to Illumina’s patent suit, which was joined by both universities.

In its suit, Illumina says many lines of evidence suggest Oxford is using improved versions of that pore in the MinION.

In asking U.S. trade officials to investigate Oxford and possibly bar imports of the MinION to the U.S., Illumina could anger researchers, since no comparable technology is available. Illumina has never announced plans to sell a nanopore product of its own.

Illumina’s lawyers—Fish & Richardson in Washington, D.C.—noted that the wider public wouldn’t be harmed if the MinION were stopped at customs and prohibited from entering the U.S. Illumina can “fill any void” with its own products, they say.  

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