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Pacific Biosciences of California, Inc. v. Oxford Nanopore Technologies, Inc.

United States District Court, D. Delaware

March 6, 2019

PACIFIC BIOSCIENCES OF CALIFORNIA, INC., Plaintiff,
v.
OXFORD NANOPORE TECHNOLOGIES, INC. and OXFORD NANOPORE TECHNOLOGIES, LTD., Defendants.

          Brian E. Farnan and Michael J. Farnan, FARNAN LLP, Wilmington, DE Edward R. Reines and Derek C. Walter, WEIL, GOTSHAL & MANGES LLP, Redwood Shores, CA Attorneys for Plaintiff

          Jack B. Blumenfeld, Jennifer Ying, and Jeffrey J. Lyons, MORRIS, NICHOLS, ARSHT & TUNNELL LLP, Wilmington, DE Stephen M. Hash, Puneet Kohli, and Samoneh Kadivar, BAKER BOTTS L.L.P., Austin, TX David G. Wille and Johnson K. Kuncheria, BAKER BOTTS L.L.P., Dallas, TX Attorneys for Defendants

          MEMORANDUM OPINION

          STARK U.S. DISTRICT JUDGE.

         Plaintiff Pacific Biosciences of California, Inc. ("PacBio" or "Plaintiff) has brought two patent infringement suits against Defendants Oxford Nanopore Technologies, Inc. ("Oxford" or "Defendant") and Oxford Nanopore Technologies, Ltd. ("ONT LTD") asserting U.S. Patent Nos. 9, 546, 400 (the '"400 patent"), 9, 772, 323 (the '"323 patent"), 9, 678, 056 (the '"056 patent"), and 9, 738, 929 (the '"929 patent"). The four patents-in-suit generally relate to nanopore sequencing.

         Presently before the Court is the issue of claim construction. PacBio and Oxford[1]submitted two technology tutorials (see D.I. 98, 99), objections to one of the technology tutorials (see D.I. 126), claim construction briefs (see D.I. 91, 92, 124, 127), exhibits (see D.I. 80, 91, 94, 125, 128), and expert declarations (see D.I. 95, 96, 97).[2] The Court held a claim construction hearing on December 17, 2018, at which both sides presented oral argument. (See D.I. 135 ("Tr."))

         I. LEGAL STANDARDS

         The ultimate question of the proper construction of a patent is a question of law. See Teva Pharm. USA, Inc. v. Sandoz, Inc., 135 S.Ct. 831, 837 (2015) (citing Markman v. Westview Instruments, Inc., 517 U.S. 370, 388-91 (1996)). "It is a bedrock principle of patent law that the claims of a patent define the invention to which the patentee is entitled the right to exclude." Phillips v. AWH Corp., 415 F.3d 1303, 1312 (Fed. Cir. 2005) (internal quotation marks omitted).

         "[T]here is no magic formula or catechism for conducting claim construction." Id. at 1324. Instead, the Court is free to attach the appropriate weight to appropriate sources "in light of the statutes and policies that inform patent law." Id.

         "[T]he words of a claim are generally given their ordinary and customary meaning ... [which is] the meaning that the term would have to a person of ordinary skill in the art in question at the time of the invention, i.e., as of the effective filing date of the patent application." Id. at 1312-13 (internal citations and quotation marks omitted). "[T]he ordinary meaning of a claim term is its meaning to the ordinary artisan after reading the entire patent." Id. at 1321 (internal quotation marks omitted). The patent specification "is always highly relevant to the claim construction analysis. Usually, it is dispositive; it is the single best guide to the meaning of a disputed term." Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed. Cir. 1996).

         While "the claims themselves provide substantial guidance as to the meaning of particular claim terms," the context of the surrounding words of the claim also must be considered. Phillips, 415 F.3d at 1314. Furthermore, "[o]ther claims of the patent in question, both asserted and unasserted, can also be valuable sources of enlightenment. . . [b]ecause claim terms are normally used consistently throughout the patent." Id. (internal citation omitted).

         It is likewise true that "[differences among claims can also be a useful guide. . . . For example, the presence of a dependent claim that adds a particular limitation gives rise to a presumption that the limitation in question is not present in the independent claim." Id. at 1314-15 (internal citation omitted). This "presumption is especially strong when the limitation in dispute is the only meaningful difference between an independent and dependent claim, and one party is urging that the limitation in the dependent claim should be read into the independent claim." SunRace Roots Enter. Co., Ltd. v. SRAM Corp., 336 F.3d 1298, 1303 (Fed. Cir. 2003).

         It is also possible that "the specification may reveal a special definition given to a claim term by the patentee that differs from the meaning it would otherwise possess. In such cases, the inventor's lexicography governs." Phillips, 415 F.3d at 1316. It bears emphasis that "[e]ven when the specification describes only a single embodiment, the claims of the patent will not be read restrictively unless the patentee has demonstrated a clear intention to limit the claim scope using words or expressions of manifest exclusion or restriction." Hill-Rom Servs., Inc. v. Stryker Corp., 755 F.3d 1367, 1372 (Fed. Cir. 2014) (quoting Liebel-Flarsheim Co. v. Medrad, Inc., 358 F.3d 898, 906 (Fed. Cir. 2004)) (internal quotation marks omitted).

         In addition to the specification, a court "should also consider the patent's prosecution history, if it is in evidence." Markman v. Westview Instruments, Inc., 52 F.3d 967, 980 (Fed. Cir. 1995), aff'd, 517 U.S. 370 (1996). The prosecution history, which is "intrinsic evidence," "consists of the complete record of the proceedings before the PTO [Patent and Trademark Office] and includes the prior art cited during the examination of the patent." Phillips, 415 F.3d at 1317. "[T]he prosecution history can often inform the meaning of the claim language by demonstrating how the inventor understood the invention and whether the inventor limited the invention in the course of prosecution, making the claim scope narrower than it would otherwise be."Id.

         In some cases, "the district court will need to look beyond the patent's intrinsic evidence and to consult extrinsic evidence in order to understand, for example, the background science or the meaning of a term in the relevant art during the relevant time period." Teva, 135 S.Ct. at 841. Extrinsic evidence "consists of all evidence external to the patent and prosecution history, including expert and inventor testimony, dictionaries, and learned treatises." Markman, 52 F.3d at 980. For instance, technical dictionaries can assist the court in determining the meaning of a term to those of skill in the relevant art because such dictionaries "endeavor to collect the accepted meanings of terms used in various fields of science and technology." Phillips, 415 F.3d at 1318. In addition, expert testimony can be useful "to ensure that the court's understanding of the technical aspects of the patent is consistent with that of a person of skill in the art, or to establish that a particular term in the patent or the prior art has a particular meaning in the pertinent field." Id. Nonetheless, courts must not lose sight of the fact that "expert reports and testimony [are] generated at the time of and for the purpose of litigation and thus can suffer from bias that is not present in intrinsic evidence." Id. Furthermore, "statements made by a patent owner during an IPR [inter partes review] proceeding . . . can be considered for claim construction." Aylus Networks, Inc. v. Apple Inc., 856 F.3d 1353, 1362 (Fed. Cir. 2017). Overall, while extrinsic evidence "may be useful" to the court, it is "less reliable" than intrinsic evidence, and its consideration "is unlikely to result in a reliable interpretation of patent claim scope unless considered in the context of the intrinsic evidence." Id. at 1318-19. Where the intrinsic record unambiguously describes the scope of the patented invention, reliance on any extrinsic evidence is improper. See Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1308 (Fed. Cir. 1999) (citing Vitronics, 90 F.3d at 1583).

         Finally, "[t]he construction that stays true to the claim language and most naturally aligns with the patent's description of the invention will be, in the end, the correct construction." Renishaw PLC v. Marposs Societa' per Azioni, 158 F.3d 1243, 1250 (Fed. Cir. 1998). It follows that "a claim interpretation that would exclude the inventor's device is rarely the correct interpretation." Osram GmbH v. Int'l Trade Comm'n, 505 F.3d 1351, 1358 (Fed. Cir. 2007) (quoting Modine Mfg. Co. v. U.S. Int'l Trade Comm 'n, 75 F.3d 1545, 1550 (Fed. Cir. 1996)).

         II. CONSTRUCTION OF DISPUTED TERMS[3]

         A. '929 Patent

         1."Monitoring variations in ionic current"[4]

PacBio

No construction necessary

Oxford

"intermittently monitoring variations in ionic current"

Court

No construction necessary

         The Court agrees with PacBio that the claims are not limited to intermittent monitoring. Although the word "intermittent" appears repeatedly in the specification, it is not contained in the claims. Oxford argues that the specification "consistently requires intermittent detection" so adding "intermittent" to the claims is not an improper importation of a limitation. (D.I. 92 at 16; see also Tr. at 12, 14) Oxford is not arguing that its construction is required due to express lexicography, disclaimer, or disavowal. (See Tr. at 16)

         While many (possibly all) embodiments of the invention discussed in the specification involve intermittent detection, nothing in the patent (including the use of "present invention" and "invention" language) excludes the possibility of consistent, non-intermittent methods of "monitoring variations in ionic current."[5] "Absent a clear disavowal or contrary definition in the specification or the prosecution history, the patentee is entitled to the full scope of its claim language." Home Diagnostics, Inc. v. LifeScan, Inc., 381 F.3d 1352, 1358 (Fed. Cir. 2004). The Court is not persuaded that the specification disavows or disparages consistent, non-intermittent monitoring.

         2."Polynucleotide"[6]

PacBio

"a molecule having multiple nucleotides"

Oxford

"a double-stranded nucleic acid molecule comprising a first terminal portion, an intermediate portion, and a second terminal portion wherein at least a first linker ligated to the first terminal portion of the nucleic acid molecule connects a 3' terminus at the first terminal portion with a 5' terminus at the first terminal portion"

Court

"a molecule having multiple nucleotides"

         Oxford does not dispute that PacBio's proposed construction provides the plain meaning of "polynucleotide." (See Tr. at 33) Rather, Oxford argues that PacBio should be held to its previous representations to the Court when successfully opposing Oxford's motion to dismiss pursuant to 35 U.S.C. § 101 in the 17-1353 action, because claim constructions must be applied consistently for purposes of both invalidity and infringement. (See D.I. 127 at 15-16)

         In its brief opposing Oxford's motion to dismiss, PacBio discussed the claims' "novel method of manipulating polynucleotides" by using "novel nucleic acid templates." (C.A. No. 17- 1353 D.I. 24 at 1-2, 12) In the Court's opinion denying the motion to dismiss, the Court relied on these representations - but the Court was discussing the asserted claims as a whole, particularly the novelty of the methods, rather than this particular claim term.[7] Moreover, the parties had not asked the Court to construe any claim terms in connection with the § 101 motion, and the Court did not adopt any definition of "polynucleotide" or limit it to the invention's novel concept.

         PacBio has consistently asserted that the claimed invention manipulates polynucleotides to create novel templates, but does not begin with novel templates of polynucleotides. Nothing stated by PacBio in connection with the motion to dismiss, nor by the Court in denying that motion, alters that fact. Here, then, the Court is persuaded that a person of ordinary skill in the art ("POSA") would understand that the term "polynucleotide" is intended to be broad and have its (undisputed) plain and ordinary meaning.

         3."nucleotide sequence"[8]

PacBio

"information reflecting the identity and order of each of the bases"

Oxford

"the identity and order of each of the bases"

Court

"the identity and order of each of the bases"

         There are two issues pertaining to this term: PacBio's concern regarding error rates and Oxford's concern regarding raw data. With respect to error rates, the parties agree that the term must account for the fact that nucleotide sequencing in the real world is not perfect, so the determined identity and order of bases must account for some degree of error. (See Tr. at 40-45) Oxford's representation that its construction is not intended to exclude errors made in determining a nucleotide sequence (see Id. at 43-45) resolves PacBio's concern.

         Oxford contends that PacBio's proposed construction would allow Plaintiff to argue that the term refers to the underlying raw data that reflects the actual base calls rather than the base calls themselves. (See Id. at 44-45, 48) At oral argument, PacBio did not persuasively disclaim such an argument. The Court agrees with Oxford that the "nucleotide sequence" must be the base calls themselves (i.e., A, C, G, or T), not the underlying data that reflects the identity of the base calls. This conclusion is supported by the patent's specification, which distinguishes "sequence read data," which is "representative of the nucleotide sequence," from "the actual sequence of the template nucleic acid molecule," noting the two "may not be identical." ('929 patent at 61:38-42) (emphasis added) PacBio's construction would improperly expand the term to include irrelevant "information." (See D.I. 92 at 18-19) Accordingly, the Court will adopt Oxford's proposed construction.

         4. "The sequence of the template nucleic ...


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