Illumina sues Oxford Nanopore over patent infringement

Illumina has announced it is to sue Oxford Nanopore (ONT) for allegedly infringing on two of its patents in the development of its handheld MinIoN DNA sequencer. The disputed patents cover a protein nanopore sequencing system, the very core of ONT's technology, and were exclusively licensed by Illumina from the University of Alabama, Birmingham Research Foundation and the University of Washington. 
ONT and Illumina formed a strategic alliance to commercialise next generation sequencing technologies in 2009, buying however this ended however the relationship soured as ONT shifted focus from BASE (exonuclease) to strand sequencing technology, and subsequent arbitration. ONT announced in late 2013 that Illumina has divested its 13.5% shareholding in the company via a "cut price" secondary placing for £56.4m, cutting the startup's implied valuation by over £100m. Commenting on the patent lawsuit, Gordon Sanghera, ONT's CEO said "It is gratifying to have the commercial relevance of Oxford Nanopore products so publicly acknowledged by the market monopolist for NGS.", adding that ONT expexts no disruption to its commerical progress. The lawsuits were filed concurrently with US International Trade Commission and the US District Court for the Southern District of California. 

This article has been updated to include additional details from the lawsuit and a comment from Oxford Nanopore Technologies.

NEW YORK (GenomeWeb) – Illumina said today that it has sued Oxford Nanopore Technologies for allegedly infringing two patents related to nanopore sequencing.

The lawsuits, filed concurrently with the US International Trade Commission and the US District Court for the Southern District of California, concern US Patent No. 8,673,550 and No. 9,170,230, both of which are entitled "MSP Nanopores and Related Methods." Illumina exclusively licensed those patents from the University of Alabama, Birmingham Research Foundation and the University of Washington.

The patents relate to the use of Mycobacterium smegmatis porinA, MspA, as the basis for a protein nanopore sequencing system. University of Washington's Jens Gundlach first demonstrated that MspA could serve as a protein nanopore for sequencing DNA in 2010, and has since made advances in the technology, collaborating with UAB microbiologist Michael Niederweis to demonstrate that the MspA pore coupled with a "ratcheting system" could read short DNA sequences.

In a statement, Illumina said that the lawsuits focus on Oxford's MinIon and PromethIon devices.

Oxford's MinIon is a handheld nanopore sequencing device that is commercially available, while the PromethIon is a higher-throughput version that has not yet been commercialized.

Oxford has not disclosed details of the protein nanopore it is using in its instruments. Prior to Gundlach's work on the MspA pore, the majority of protein nanopore technology had involved the use of alpha-hemolysin protein.

Illumina declined to comment on the case, but in the complaint filed with the US District Court for the Southern District of California, Illumina alleged that Oxford Nanopore is using the MspA pore in its devices and that the use of the MspA pore infringes its patents.

In the suit, Illumina cited as evidence comments by Oxford Nanopore's management and technology advisory board as well as a study published by researchers from Harvard University in which the authors noted that Oxford Nanopore provided them with MspA pores. It also pointed to patent applications that Oxford Nanopore filed after the '550 patent had been issued that "use Msp nanopores covered by the patents-in-suit." Illumina alleged that "all the Msp nanopores in that [Oxford Nanopore] application are derived from one of the mutant Msp nanopores disclosed in the patents-in-suit."

In addition, Illumina said that Oxford Nanopore knew of the '550 and '230 patents because it filed for an inter partes review of the '550 patent in 2014. Last year, the US Patent and Trademark Office's Patent Trial and Appeal Board granted an inter partes review of one claim of the '550 patent, which describes the characterization of a heterogeneous mixture, but denied to review the claims in the patent that describe the use of a mutant MspA pore.

Oxford Nanopore declined to comment on the suit but posted a statement on its website saying that it believes Illumina's suit is "without merit." The company does not "anticipate any disruption to our ongoing commercial progress."

Furthermore, Oxford Nanopore's CEO Gordon Sanghera said, "It is gratifying to have the commercial relevance of Oxford Nanopore products so publicly acknowledged by the market monopolist for NGS."

Illumina claims in the suit that Oxford Nanopore knowingly infringed and continues to infringe on its patents and as such requested damages "adequate to compensate it for the injuries." It did not specify an amount, but said that damages should at least be a "reasonable royalty."

The recent suit isn't the first legal tussle between Illumina and Oxford Nanopore. The two firms had struck a commercialization deal in 2009 for an exonuclease nanopore sequencing strategy Oxford Nanopore was developing. Oxford ended up abandoning that technique for the strand sequencing method used in the MinIon and PromethIon, leading to arbitration between the companies and the termination of the commercialization agreement.