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Pacific Biosciences v. Oxford Nanopore

Representative Claim(s)

1. A method of determining a nucleotide sequence of a region of interest in a polynucleotide, the method comprising:

introducing a polynucleotide comprising a region of interest to a sequence analysis system comprising a nanopore in a membrane, wherein the polynucleotide comprises a double-stranded portion comprising complementary strands of the region of interest;

applying a voltage across the membrane;

monitoring variations in ionic current through the nanopore of the sequence analysis system during enzyme chaperone-regulated passage of the polynucleotide through the nanopore;

analyzing the monitored variations in ionic current to obtain nucleotide sequence information for the polynucleotide, wherein the nucleotide sequence information comprises redundant sequence information for the region of interest, wherein the redundant sequence information comprises the nucleotide sequence of the complementary strands; and

determining a consensus sequence for the region of interest based on the redundant sequence information.

Posture:

Motion to dismiss.

Exception Category: None

“Oxford argues that the asserted claims “are simply directed to the abstract mental process of ‘comparing’ two gene sequences” and “the naturally occurring correlation between complementary DNA strands.” … Oxford contends that the asserted claims do not satisfy the step one test because their “focus” is on “determining [a] consensus sequence by comparing the two complementary strands.” … PacBio responds that Oxford is focused only on the last element of a multi-limitation claim and that “the claim as a whole is directed to a concrete technique for improved nanopore sequencing that increases accuracy through the use of novel nucleic acid templates.” …The Court agrees with PacBio.”

“The asserted claims provide “a novel method of manipulating polynucleotides to create sequencing templates that can be used to generate redundant sequencing information and improve nanopore sequencing.” …The method requires introducing the polynucleotide to a system comprising a nanopore in a membrane, whereby a voltage is applied across the membrane, the variations in current are monitored, and the information from one strand is analyzed against the information from the complementary strand for improved accuracy. (See ’929 patent, cl. 1) Oxford’s contention that the claims are merely directed to the abstract idea of comparing and the natural phenomenon of complementarity of nucleotides ignores almost all of the content of the claim, including most of its limitations.”

“The precedential decision that considered a patent most similar to the patent-in-suit is the Federal Circuit’s decision in Rapid Litigation, [citation omitted]. In that case, the inventors discovered that hepatocytes (a type of liver cell) are able to survive multiple freeze-thaw cycles and not just one such cycle. … But the inventors did not attempt to patent this discovery. Instead, ‘the inventors developed [and patented] an improved process of preserving hepatocytes’.  … Similarly, here, while the asserted claims note the natural correlation between complementary strands of DNA, the claimed process as a whole is directed not to that correlation but to an improved method of nanopore sequencing.”

Significantly More: Not Decided

“As Oxford has not met its burden at step one, it is not necessary to reach step two. However, the Court will briefly address it anyway.”

“With respect to the ’929 patent, the relevant time is around 2008–2009, when the patent applications to which the ’929 patent claims priority were filed. Oxford argues that the claim elements, both independently and as an ordered combination, contain no inventive concept, because they are each disclosed in eight prior art references cited in the ’929 patent’s specification, which together provide “a timeline of the development of sequencing with a nanopore” between 1995 and 2006. … PacBio responds that “[t]he record, including cited references, is very clear that nanopore sequencing [wa]s emerging in 2009.” … At this stage of the proceedings, on the record the Court may properly consider, the Court cannot say that Oxford has shown by clear and convincing evidence that the claims do not capture an inventive concept.”

The Court also noted assertions Oxford made in a parallel litigation that, “nanopore sequencing was not known in the 2008–2009 timeframe and/or that nanopore sequencing was not enabled to the skilled artisan.”  Taking it as true that Oxford made these statements, the Court found that it would be “difficult, if not impossible, for Oxford, at this early stage, to persuade the Court by clear and convincing evidence that the state of the pertinent art was such that the asserted claims must be found to be nothing more than well-understood, routine, and conventional.”