In Nanapore Sequencing, Progress and Lawsuits

In Nanapore Sequencing, Progress and Lawsuits

Companies have been working for several years to develop sequencing platforms based on nanopore technology.  Sceptics have noted limitations such as data quality and have questioned whether or not this new technology will reach the market as a diagnostic platform.  Significant progress towards this goal has been made recently, together with lawsuits over patent rights to this technology.  Kalorama Information covers sequencing markets in our report, Next Generation Sequencing Markets.

DNA sequencing is already used in clinical laboratories for oncology and genetic tests, and also certain infectious disease applications.  However, at this time, sequencing based tests are require several days to complete the library preparation and PCR amplification, DNA sequencing, and data analysis steps.  While sequencing costs have dropped dramatically since the first human genome was sequenced, DNA sequencing is still expensive.  Most sequencing based diagnostic tests performed today are laboratory developed tests (LDTs), and all sequencing based tests today must be performed in centralized laboratories by highly trained personnel.

The most recent company to enter the field of nanopore sequencing is Two Pore Guys, which previewed their device in January 2017 ahead of the J.P. Morgan conference.  Two Pore Guys has developed a hand-held device that the company claims (on its web site) is “accurate as medical lab equipment, but is as inexpensive and easy to use as a blood glucose monitor.”  Also in January 2017, Two Pore Guys reported that the company was collaborating with oncologists at the University of California, San Francisco to develop a liquid biopsy assay.

Two Pore Guys has entered a competitive field.  In 2014, Roche acquired Genia Technologies for $125 million in cash plus up to $225 million in in contingent payments depending on the achievement of certain milestones.  Genia is developing a nanopore technology based sequencing platform.  A proof-of-principle article was published in the May 2016 issue of the Proceedings of the National Academy of Sciences.  For a while, Roche did not commit to a single emerging sequencing technology.  In September 2013, Pacific Biosciences and Roche Diagnostics had entered into an agreement to develop diagnostic products, based on Pacific Biosciences' Single Molecule, Real-Time (SMRT®) technology.    However, in December 2016, Roche terminated its agreement with Pacific Biosciences.  Roche is moving ahead with development of Genia’s nanopore based technology and platform.

In December 2016, Oxford Nanopore Technologies announced that it had raised £100 million ($126 million) in new funding through a private placement of ordinary shares.  Oxford Nanopore has developed and launched the MinION, the first nanopore DNA sequencer.  This pocket-sized device is the only portable DNA/RNA sequencer available today.  It is currently available for research use.  In addition, Oxford Nanopore Technologies is developing two additional devices: PromethION (a benchtop system) and SmidgION (for use with mobile devices such as smart phones).  Researchers using the MinION have published a growing portfolio of articles.

Meanwhile, patent fights have started for rights to nanopore sequencing technology.  In late 2016, the Regents of the University of California filed a lawsuit against Roger Chen and Genia Technologies.  Roger Chen is Chief Technical Officer at Genia. He has a M.S. from the University of California, Santa Cruz.  The lawsuit alleges that four patents plus a patent application were assigned to Genia Technologies but should have been assigned to the University of California.  These patents and patent application are all related to nanopore sequencing.

The month before, in November 2016, Pacific Biosciences filed a lawsuit against Oxford Nanopore Technologies.  This complaint alleges that Oxford Nanopore’s MinION and PromethION devices (plus associated consumables, reagents, and software) infringe on U.S. patent No. 9,404,146.  This patent is owned by Pacific Biosciences.

One patent lawsuit has been settled, solved by research and development progress on the part of the defendant.  In February 2016, Illumina had sued Oxford Nanopore Technologies for patent infringement.  In 2013, Illumina had licensed rights to a nanopore DNA sequencing technology developed by a University of Alabama at Birmingham microbiologist and a University of Washington physicist.   This technology included use the biological nanopore, Mycobacterium smegmatis porinA (MspA), for sequencing systems.  In August 2016, the two companies settled their lawsuit.  This settlement included a final judgment and permanent injunction against defendant Oxford Nanopore.  However, in March 2016, Oxford Nanopore announced the release of a new nanopore.  In May 2016, Oxford Nanopore reported that its new nanopore made possible faster and more accurate sequencing.  As part of the August 2016 settlement, Oxford Nanopore asserted that it had stopped using the MspA nanopore.