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