Case 1:17-cv-00275-RGA Document 1 Filed 03/15/17 Page 1 of 12 PageID #: 1
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
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`PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
`Plaintiff,
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`vs.
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` OXFORD NANOPORE TECHNOLOGIES, INC.
`Defendant.
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`Civil Action No. _______________
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` JURY TRIAL DEMANDED
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`COMPLAINT FOR PATENT INFRINGEMENT
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`Plaintiff Pacific Biosciences of California, Inc. (“Plaintiff” or “PacBio”) for its complaint
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`against Defendant Oxford Nanopore Technologies, Inc. (“Oxford”) alleges and states the
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`following:
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`NATURE OF THE ACTION
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`1.
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`This is an action for patent infringement arising under the United States Patent
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`Act, 35 U.S.C. §§1, et seq., including 35 U.S.C. § 271.
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`2.
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`PacBio brings this action to halt Oxford’s infringement of PacBio’s rights under
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`the Patent Laws of the United States 35 U.S.C. § 1, et seq., which arise under U.S. Patent No.
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`9,546,400 (“the ’400 patent”) (attached as Exhibit 1).
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`THE PARTIES
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`3.
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`PacBio is a corporation organized and existing under the laws of the State of
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`Delaware, having a principal place of business at 1305 O’Brien Drive, Menlo Park, California
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`94025.
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`4.
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`PacBio was founded in the year 2000 and develops, manufactures, and sells a
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`novel DNA sequencing platform that helps researchers resolve genetically complex problems.
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`PACBIO Ex. 2002 p.1
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`Case 1:17-cv-00275-RGA Document 1 Filed 03/15/17 Page 2 of 12 PageID #: 2
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`PacBio’s DNA sequencing technology is based on real-time detection of the incorporation of
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`nucleotides into a single strand of DNA. That technology goes by the name “SMRT®”
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`sequencing, which is short for “Single Molecule, Real-Time” sequencing. PacBio’s SMRT®
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`sequencing platform encompasses not just DNA sequencing instruments, but also novel
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`sequencing chips and chemical reagents for use with PacBio’s DNA sequencing instrument and
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`sophisticated software for analyzing the data that emerges from PacBio’s sequencing
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`instruments.
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`5.
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`PacBio’s SMRT® Sequencing Platform and technology allows researchers to
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`carry out numerous applications, including at least (1) de novo genome assembly to finish
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`genomes in order to more fully identify, annotate, and decipher genomic structures; (2) targeted
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`sequencing to more comprehensively characterize genetic variations; and (3) identification of
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`DNA base modifications to help characterize epigenetic regulation and DNA damage. PacBio’s
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`SMRT® Sequencing Platform and technology provides high accuracy, ultra-long reads, uniform
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`coverage, and is believed to be the only DNA sequencing technology that provides the ability to
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`simultaneously detect epigenetic changes.
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`6.
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`In addition to the commercialization of its flagship SMRT® sequencing platform,
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`PacBio has broad expertise in single-molecule sequencing and is engaged in exploratory work
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`related to single-molecule sequencing, including techniques related to single-molecule
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`sequencing based on detection platforms such as nanopores. Collectively, PacBio’s research and
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`development efforts have resulted in a patent portfolio that includes over 330 issued U.S. patents
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`and pending applications related to single-molecule sequencing techniques.
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`7.
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`Defendant Oxford is a corporation organized under the laws of Delaware with its
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`principal place of business at 1 Kendall Square, Bldg. 200, Cambridge, Massachusetts 02139.
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`PACBIO Ex. 2002 p.2
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`On information and belief, Oxford is engaged in the commercialization throughout the United
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`States of nanopore-based single-molecule sequencing products, including at least the MinION
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`and PromethION sequencing instruments and reagents and kits for use with these instruments.
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`JURISDICTION AND VENUE
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`8.
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`This action arises under the Patent Laws of the United States, Title 35, United
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`States Code, §§ 1 et seq., including 35 U.S.C. §§ 271 and 281.
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`9.
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`This Court has jurisdiction over the subject matter of this action pursuant to 28
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`U.S.C. §§ 1331 and 1338(a).
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`10.
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`This Court has personal jurisdiction over defendant Oxford. Oxford has
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`substantial contacts with the forum as a consequence of conducting business in Delaware, and
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`has purposefully availed itself of the benefits and protections of Delaware state law by
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`incorporating under Delaware law.
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`11.
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`Venue is proper in this District under 28 U.S.C. §§ 1391(b) and (c), and 1400(b)
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`because Oxford is a Delaware corporation and Delaware is a convenient forum for resolution of
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`the parties’ disputes set forth herein.
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`BACKGROUND
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`12.
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`On information and belief, in the 2015 timeframe Oxford began commercializing
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`single-molecule sequencing products based on the use of protein nanopores. Oxford purports to
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`offer a single-molecule sequencing product that, like PacBio’s products, are capable of
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`determining the sequence of long stretches of DNA in a single pass. The ability to generate such
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`“long reads” is an area where PacBio has and continues to be widely recognized as the technical
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`and commercial leader. PacBio and Oxford compete in the single-molecule sequencing market.
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`3
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`PACBIO Ex. 2002 p.3
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`13.
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`Oxforrd’s single-mmolecule seqquencing prooducts incluude at least
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`the MinIONN and
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`PromethIION sequenccing instrumments and reaagents, consuumables, andd software fofor use with ssame.
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`Two viewws of a repreesentative MMinION devicce are shownn below:
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`Exhibit 33; Exhibit 4
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`at 292. Thhe top imagee shows a wworking MinnION devicee, and the boottom
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`view shoows the interior of the deevice. The pportion labeleed “C” in th
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`flow celll with an arrray of indivvidual nanopores. Nannopores are
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`e above phootograph deppicts a
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`tiny holes eembedded i
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`membranne and are foormed by insserting proteeins that havve a hollow ttube throughh their centerr into
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`a polymeer membranee, as shown iin the imagee below:
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`PACBIO Ex. 2002 p.4
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`Case 1:17-cv-00275-RGA Document 1 Filed 03/15/17 Page 5 of 12 PageID #: 5
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`See Exhiibit 5. Thee Accused PProducts eaach include
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`one or morre flow cellls that incluude a
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`“nanoporre array.”
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`144. Whilee the MinIOON instrument includess a single
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`instrumennt includes
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`48 flow ccells and haas been deescribed as
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`flow cell, tthe PromethhION
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`a “whole bbox of MinnION
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`sequenceers.” Exhibitt 6. A representative ProomethION innstrument wwith its 48 floow cells is shhown
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`below:
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`5
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`PACBIO Ex. 2002 p.5
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`Case 1:17-cv-00275-RGA Document 1 Filed 03/15/17 Page 6 of 12 PageID #: 6
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`15.
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`To seqquence DNAA using Oxfford’s produccts, one firstt applies a vvoltage acrosss the
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`membranne such that an electricall current flowws through tthe hole. A
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`strand of DNNA is then ddrawn
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`through tthe hole:
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`Exhibit 77. As the DNNA passes thhrough the hole, it disruppts the electrrical current
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`that is passiing
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`relate empt to corr, one can attehe sequence,o evaluate ththrough tthe hole, thuus producing a signal. To
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`this signaal with the DDNA bases thhat are passiing through tthe hole.
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`16. More
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`particularlyy, in nanopoore-based DDNA sequenccing systemms, such as
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`es not anopore ariserough the nahe DNA thrpassage of thesults from psignal that resold by OOxford, the s
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`just fromm a single DNNA base, buut from a conntiguous grooup of DNAA bases that iinteracts witth the
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`nanoporee at a given
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`time. Therrefore, to deetermine thee DNA sequuence, Oxforrd nanoporee uses
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`calibratioon informatiion producedd by measuring the siggnals from thhe different
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`combinatioons of
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`e. bases thaat may interaact with the nnanopore at a given time
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`17.
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`Oxforrd infringes,, literally orr under the
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`doctrine off equivalentss, PacBio’s
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`patent thhrough its
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`activities cconnected too at least
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`the MinIO
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`N and/or tthe PromethhION
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`instrumennts. For insttance, repressentative claaim 1 of the ’’400 patent iis listed beloow:
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`6
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`PACBIO Ex. 2002 p.6
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`Case 1:17-cv-00275-RGA Document 1 Filed 03/15/17 Page 7 of 12 PageID #: 7
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`1. A method for sequencing a nucleic acid template comprising:
`a) providing a substrate comprising a nanopore in contact with a solution, the
`solution comprising a template nucleic acid above the nanopore;
`b) providing a voltage across the nanopore;
`c) measuring a property which has a value that varies for N monomeric units of the
`template nucleic acid in the pore, wherein the measuring is performed as a
`function of time, while the template nucleic acid is translocating through the
`nanopore, wherein N is three or greater; and
`d) determining the sequence of the template nucleic acid using the measured
`property from step (c) by performing a process including comparing the
`measured property from step (c) to calibration information produced by
`measuring such property for 4 to the N sequence combinations.
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`18.
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`Use of Oxford’s sequencing products leads to direct infringement of this claim in
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`the following way. First, Oxford’s products include nucleic acid sequencing instrument having a
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`nanopore-containing membrane that is in contact with a solution (step a). A voltage is then
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`applied across the membrane to drive a current across the membrane (step b). A nucleic acid
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`molecule to be sequenced is then drawn through the nanopore, and, as a result, the current is
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`disrupted in a time-dependent manner that varies based on the N (wherein N is three or greater)
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`monomeric nucleic acid bases that are interacting with the pore at a given time (step c). An
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`artificial neural network is then used to compare the signal obtained from drawing the nucleic
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`acid through the nanopore to calibration information obtained from measuring such a signal from
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`the 4 to the N combinations of bases, thus allowing one to determine the sequence of the nucleic
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`acid (step d).
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`19.
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`As an example, attached hereto as Exhibit 2 is a preliminary and exemplary claim
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`chart detailing Oxford’s infringement of multiple claims of the ’400 patent. This chart is not
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`intended to limit PacBio’s right to modify the chart or allege that other activities of Oxford
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`infringe the identified claims or any other claims of the ’400 patent or any other patents. Exhibit
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`2 is hereby incorporated by reference in its entirety. Each claim element in Exhibit 2 that is
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`7
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`PACBIO Ex. 2002 p.7
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`mapped to Oxford’s MinION and/or PromethION instruments shall be considered an allegation
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`within the meaning of the Federal Rules of Civil Procedure and therefore a response to each
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`allegation is required.
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`COUNT I
`(Infringement of U.S. Patent No. 9,546,400)
`Plaintiff repeats and re-alleges each and every allegation contained in the
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`20.
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`preceding paragraphs of this Complaint as if stated in their entirety herein, and incorporates them
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`herein by reference.
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`21.
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`The ’400 patent, entitled “Nanopore Sequencing Using N-mers,” issued on
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`January 17, 2017, to inventors Steven Turner and Benjamin Flusberg. The ’400 patent is
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`assigned on its face to Plaintiff PacBio. PacBio is the owner of all rights, title to and interest in
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`the ’400 patent.
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`22.
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`On information and belief, Oxford has infringed and continues to infringe at least
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`claims 1-8, 10, and 14-15 of the ’400 patent pursuant to 35 U.S.C. § 271(a), literally or under the
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`doctrine of equivalents, by using within the United States without authority the MinION and/or
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`the PromethION instruments. As an example, attached as Exhibit 3 is a preliminary and
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`exemplary claim chart detailing Oxford’s infringement of these claims of the ’400 patent. This
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`chart is not intended to limit PacBio’s right to modify the chart or allege that other activities of
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`Oxford infringe the identified claims or any other claims of the ’400 patent or any other patents.
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`Exhibit 3 is hereby incorporated by reference in its entirety. Each claim element in Exhibit 2 that
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`is mapped to Oxford’s MinION and/or PromethION instruments shall be considered an
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`allegation within the meaning of the Federal Rules of Civil Procedure and therefore a response to
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`each allegation is required.
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`8
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`PACBIO Ex. 2002 p.8
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`23.
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`Oxford has had knowledge of and notice of the ’400 patent and its infringement
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`long before the filing of this complaint. For instance, on March 21, 2016, Oxford cited PacBio’s
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`U.S. Patent Application Publication No. 2010/0331194 in an information disclosure statement
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`during prosecution of Oxford’s U.S. Patent Application No. 13/147,159. See Ex. 12 at 5. The
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`application that published as PacBio’s Publication No. 2010/0331194 is the parent of the
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`application that issued as the ’400 patent, and as such shares the same specification as the ’400
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`patent. On information and belief, Oxford has monitored PacBio’s patent filings and has been
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`aware of the ’400 patent since its issuance on January 17, 2017. At a minimum, Oxford has had
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`knowledge of and notice of the ’400 patent and its infringement since at least, and through, the
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`filing and service of PacBio’s complaint in this action and despite this knowledge continues to
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`commit the aforementioned infringing acts.
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`24.
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`Oxford actively, knowingly, and intentionally has induced, or has threatened to
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`induce, infringement of at least claims 1-8, 10, and 14-15 of the ’400 patent through a range of
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`activities. First, on information and belief, Oxford has induced infringement by controlling the
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`design and manufacture of, offering for sale, and selling the MinIon and/or PromethION
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`instruments with the knowledge and specific intent that its customers will use these instruments
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`to infringe, literally or under the doctrine of equivalents, by performing the claimed method for
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`sequencing a nucleic acid template. For instance, Oxford has admitted in an ongoing
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`International Trade Commission investigation that it imports, sold for importation, and or/sells
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`its MinION product and PromethION product within the United States. See Ex. 8 ¶ 53.
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`25.
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`Second, on information and belief, Oxford has induced infringement by its
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`customers through the dissemination of promotional and marketing materials relating to the
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`MinION and/or PromethION instruments with the knowledge and specific intent that its
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`PACBIO Ex. 2002 p.9
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`Case 1:17-cv-00275-RGA Document 1 Filed 03/15/17 Page 10 of 12 PageID #: 10
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`customers will use these instruments to infringe, literally or under the doctrine of equivalents, by
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`performing the claimed method for sequencing a nucleic acid template. For instance, Oxford
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`promotes the MinION and/or PromethION instruments on its website, stating that its products
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`offer numerous benefits such as real-time DNA/RNA sequencing, no capital cost, long reads,
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`scalability, high-fidelity, and rapid library preparation time. See Ex. 9.
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`26.
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`Third, on information and belief, Oxford has induced infringement by its
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`customers through the creation of distribution channels for the MinION and/or PromethION
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`instruments in the United States with the knowledge and specific intent that its customers will
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`use these instruments to infringe, literally or under the doctrine of equivalents, by performing the
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`claimed method for sequencing a nucleic acid template. For instance, Oxford’s website allows
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`customers in the United States to purchase starter packs for Oxford’s MinION instruments that,
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`when used, will lead to infringement of the ’400 patent. As Oxford’s website states, “[b]uy a
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`Starter Pack to join the growing numbers in the Nanopore Community.” See Ex. 10. As another
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`example, Oxford has created an early access program for its PromethION instrument that
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`provides access to a PromethION device, site installation support, flow cells and reagents, and
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`further information and support. See Ex. 11.
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`27.
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`Fourth, on information and belief, Oxford has induced infringement through the
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`distribution of other instructional materials, product manuals, and technical materials with the
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`knowledge and the specific intent to encourage and facilitate its customer’s infringing (either
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`literally or under the doctrine of equivalents) use of MinION and/or PromethION instruments.
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`Oxford is liable for its induced infringement of the ’400 patent pursuant to 35 U.S.C. § 271 (b).
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`28.
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`Oxford has contributed to, or has threatened to contribute to, the infringement by
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`its customers of the ’400 patent by, without authority, selling and offering to sell within the
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`10
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`PACBIO Ex. 2002 p.10
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`United States materials and apparatuses for practicing the claimed invention of the ’400 patent,
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`including at least the MinION and PromethION instruments. When, for example, either of these
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`instruments is used by Oxford’s customers for nucleic acid sequencing, the claimed method of
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`the ’400 patent for sequencing a nucleic acid template is performed, thereby infringing, literally
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`or under the doctrine of equivalents, at least claims 1-8, 10, and 14-15 of the ’400 patent.
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`29.
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`On information and belief, Oxford knows that the MinION and PromethION
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`instruments constitute a material part of the inventions of the ’400 patent and that they are not a
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`staple article or commodity of commerce suitable for substantial noninfringing use. As
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`documented above, the MinION and PromethION instruments consist of specialized substrates
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`containing protein nanopores that are used in conjunction with specialized reagents for the
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`purpose of sequencing nucleic acid templates. See supra ¶¶ 12 - 19. As such, neither the
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`MinION nor PromethION instruments nor any of the reagent kits for use with these instruments
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`is a staple article of commerce suitable for substantial non-infringing use. Oxford knows that
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`these instruments are not staple articles or commodities of commerce suitable for substantial
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`non-infringing use because they have no use apart from infringing the ’400 patent. Oxford is
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`liable for its contributory infringement of the ’400 patent pursuant to 35 U.S.C. § 271(c).
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`30.
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`Oxford’s infringement of the ’400 patent has injured PacBio in its business and
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`property rights. PacBio is entitled to recover monetary damages for such injuries pursuant to 35
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`U.S.C. § 284 in an amount to be determined at trial. Oxford’s infringement of the ’400 patent has
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`caused irreparable harm to Plaintiffs and will continue to cause such harm unless and until
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`Oxford’s infringing activities are enjoined by this Court.
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`PRAYER FOR RELIEF
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`WHEREFORE, prays for relief as follows:
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`PACBIO Ex. 2002 p.11
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`Case 1:17-cv-00275-RGA Document 1 Filed 03/15/17 Page 12 of 12 PageID #: 12
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`A.
`B.
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`patent;
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`Judgment that Oxford has infringed the ’400 patent;
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`An order permanently enjoining Oxford from further infringement of the ’400
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`An award of damages pursuant to 35 U.S.C. § 284 plus pre-judgment and post-
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`judgment interest;
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`An award to PacBio of its costs and reasonable expenses to the fullest extent
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`permitted by law;
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`A declaration that this case is exceptional pursuant to 35 U.S.C. § 285, and an
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`award of attorneys’ fees and costs; and
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`An award of such other and further relief as the Court may deem just and proper.
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`DEMAND FOR JURY TRIAL
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`Pursuant to Federal Rule of Civil Procedure 38(b), PacBio hereby demands a trial by jury
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`on all issues so triable.
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`Dated: March 15, 2017
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`Of Counsel:
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`Edward R. Reines
`Derek C. Walter
`WEIL, GOTSHAL & MANGES LLP
`201 Redwood Shores Parkway
`Redwood Shores, CA 94065
`(650) 802-3000
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`Respectfully submitted,
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`FARNAN LLP
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`/s/ Brian E. Farnan
`Brian E. Farnan (Bar No. 4089)
`Michael J. Farnan (Bar No. 5165)
`919 N. Market St., 12th Floor
`Wilmington, DE 19801
`(302) 777-0300
`(302) 777-0301 (Fax)
`bfarnan@farnanlaw.com
`mfarnan@farnanlaw.com
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`Attorneys for Plaintiff
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`PACBIO Ex. 2002 p.12
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