Paper No. 15
`Filed: February 13, 2017
`
`Trials@uspto.gov
`571.272.7822
`
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`_______________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`_______________
`
`ILLUMINA, INC.,
`Petitioner,
`
`v.
`
`THE SCRIPPS RESEARCH INSTITUTE,
`Patent Owner.
`_______________
`
`Case IPR2016-01619
`Patent 6,060,596
`_______________
`
`
`
`Before GEORGIANNA W. BRADEN, TINA E. HULSE, and MICHELLE
`N. ANKENBRAND Administrative Patent Judges.
`
`BRADEN, Administrative Patent Judge.
`
`DECISION
`Denying Institution of Inter Partes Review
`37 C.F.R. § 42.108
`
`
`
`
`
`
`
`
`Filed: February 13, 2017
`
`Trials@uspto.gov
`571.272.7822
`
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`_______________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`_______________
`
`ILLUMINA, INC.,
`Petitioner,
`
`v.
`
`THE SCRIPPS RESEARCH INSTITUTE,
`Patent Owner.
`_______________
`
`Case IPR2016-01619
`Patent 6,060,596
`_______________
`
`
`
`Before GEORGIANNA W. BRADEN, TINA E. HULSE, and MICHELLE
`N. ANKENBRAND Administrative Patent Judges.
`
`BRADEN, Administrative Patent Judge.
`
`DECISION
`Denying Institution of Inter Partes Review
`37 C.F.R. § 42.108
`
`
`
`
`
`
`
`
`
`Case IPR2016-01619
`Patent 6,060,596
`
`
`A. Background
`
`I.
`
`INTRODUCTION
`
`Illumina, Inc. (“Petitioner”) filed a Petition (Paper 2, “Pet.”) to
`
`institute an inter partes review of claims 1–6 and 10–17 of U.S. Patent No.
`
`6,060,596 (Ex. 1001, “the ’596 patent”). The Scripps Research Institute
`
`(“Patent Owner”) filed a Preliminary Response (Paper 12, “Prelim. Resp.”).
`
`We have jurisdiction under 35 U.S.C. § 314, which provides that an inter
`
`partes review may not be instituted “unless . . . there is a reasonable
`
`likelihood that the petitioner would prevail with respect to at least 1 of the
`
`claims challenged in the petition.” See also 37 C.F.R § 42.4(a) (delegating
`
`authority to the Board).
`
`Upon consideration of the Petition, Patent Owner’s Preliminary
`
`Response, and the submitted evidence, we conclude Petitioner has failed to
`
`establish a reasonable likelihood it would prevail with respect to at least one
`
`of the challenged claims. Accordingly, for the reasons that follow, we
`
`decline to institute an inter partes review.
`
`B. Related Proceedings
`
`Petitioner informs us that the ’596 patent is the subject of a co-
`
`pending district court case: The Scripps Research Institute v. Illumina, Inc.,
`
`Case No. 3:16-cv-661-JLS-BGS (S.D. Cal., filed March 17, 2016). Pet. 4.
`
`C. The ’596 Patent
`
`The ’596 patent was filed on March 3, 1998, and is titled “Encoded
`
`Combinatorial Chemical Libraries.” Ex. 1001, Title. It is directed to
`
`methods for creating encoded combinatorial chemical libraries comprised of
`
`a plurality of bifunctional molecules having both a chemical polymer and an
`
`identifier oligonucleotide sequence that defines the structure of the chemical
`
`
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`2
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`Patent 6,060,596
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`polymer. Id. at Abstract. According to the’596 patent, two alternating
`
`parallel combinatorial syntheses are performed so that a genetic tag is
`
`chemically linked to the chemical structure being synthesized. Id. at 2:55–
`
`57. The genetic tag functions as an identifier for the structure of the
`
`chemical unit. Id. at 2:61–62. Libraries then are built up by the repetition of
`
`this synthesis process following division of chemical units. Id. at 2:62–63.
`
`The ’596 patent teaches that active molecules are selected from the
`
`chemical libraries by binding to preselected biological molecules of interest.
`
`Id. at 2:64–66. The ’596 patent states that “the identity of the active
`
`molecule is determined by reading the genetic tag, i.e., the identifier
`
`oligonucleotide sequence.” Id. at 2:66–3:1.
`
`D. Illustrative Claims
`
`As noted above, Petitioner challenges claims 1–6 and 10–17, with
`
`claim 1 being the only independent claim. Claim 1 is illustrative of the
`
`challenged claims, and is reproduced below (with paragraphing added):
`
`1. A bifunctional molecule according to the formula A—B—C,
`wherein A is a polymer comprising a linear series of chemical
`units represented by the formula (Xn)a,
`wherein X is a single chemical unit in polymer A, B is a linker
`molecule operatively linked to A and C, and identifier
`oligonucleotide C is represented by the formula (Zn)a,
`wherein a unit
`identifier nucleotide sequence Z within
`oligonucleotide C identifies the chemical unit X at position n;
`and
`wherein n is a position identifier for both X in polymer A and Z
`in oligonucleotide C having the value of 1+i where i is an
`integer from 0 to 10, such that when n is 1, X or Z is located
`most proximal to the linker, and a is an integer from 4 to 50.
`
`Ex. 1001, 43:2–14.
`
`
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`3
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`Patent 6,060,596
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`E. The Evidence of Record
`
`Petitioner relies upon the following references, as well as the
`
`Declaration of Brian M. Stoltz, Ph.D. (Ex. 1007):
`
`Reference
`Dower
`
`Patent/Printed Publication
`U.S. Patent No. 6,143,497
`
`Date
`Issued Nov. 7, 2000
`
`Exhibit
`1008
`
`Juby
`
`Carl D. Juby et al., Facile
`Preparation of 3’
`Oligonucleotide Conjugates,
`32(7) TETRAHEDRON LETTERS
`879–82 (1991)
`
`Pub. Feb. 11, 1991
`
`1010
`
`Nelson
`
`U.S. Patent No. 5,141,813
`
`Issued Aug. 25, 1992
`
`1011
`
`U.S. Patent No. 5,573,905
`
`Issued Nov. 12, 1996
`
`1003
`
`The ’905
`patent
`
`
`
`F. The Asserted Grounds of Unpatentability
`
`Petitioner challenges the patentability of the ’596 patent based on the
`
`following grounds under 35 U.S.C. §§ 102(b) and 103(a) (Pet. 5):
`
`Reference(s)
`
`Dower
`Dower and Juby
`
`Dower and Nelson
`
`The ’905 patent
`
`Claims Challenged
`Basis
`§ 103(a) 1–6 and 10–17
`§ 103(a) 1–6 and 10–17
`
`§ 103(a) 1–6 and 10–17
`
`§ 102(b) 1–6 and 10–17
`
`II. DISCUSSION
`
`A. Priority of the Challenged Claims
`
`Petitioner challenges the priority date of the challenged claims of the
`
`’596 patent. Pet. 53–68.
`
`To be entitled to the benefit of a parent application, one requirement is
`
`that the invention presently claimed must have been disclosed in the parent
`
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`application in the manner provided by 35 U.S.C. § 112, first paragraph. See
`
`35 U.S.C. § 120; In re Lukach, 442 F.2d 967, 968–69 (CCPA 1971). An
`
`ipsis verbis disclosure, however, is not necessary to satisfy the written
`
`description requirement. Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563
`
`(Fed. Cir. 1991). The disclosure need only reasonably convey to persons
`
`skilled in the art that the inventor had possession of the subject matter in
`
`question, even if every nuance of the claims is not explicitly described in the
`
`specification. Id.; see Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336,
`
`1351 (Fed. Cir. 2010).
`
`The test for written description is an objective inquiry into the four
`
`corners of the specification from the perspective of a person of ordinary skill
`
`in the art. Using this test, the invention must be described in a manner
`
`sufficient to demonstrate that the inventor actually invented the claimed
`
`invention. Ariad Pharm. Inc., 598 F.3d at 1351. “One shows that one is ‘in
`
`possession’ of the invention by describing the invention, with all its claimed
`
`limitations, not that which makes it obvious.” Lockwood v. Am. Airlines,
`
`Inc., 107 F.3d 1565, 1572 (Fed. Cir. 1997) (internal citation omitted).
`
`Written description is a question of fact judged as of the relevant filing date.
`
`Falko-Gunter Falkner v. Inglis, 448 F.3d 1357, 1363 (Fed. Cir. 2006).
`
`The ’596 patent issued from U.S. Application No. 09/033,743, filed
`
`on March 3, 1998. The ’596 patent states that it is a divisional of U.S.
`
`Application No. 08/665,511 (“the ’511 application”), filed June 18, 1996
`
`(now U.S. Patent No. 5,723,598), which, in turn, is a divisional of U.S.
`
`Application No. 07/860,445 (“the ’445 application”), filed March 30, 1992
`
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`(now the ’905 patent).1 Ex. 1001, 1:4–7. Petitioner contends that the ’445
`
`application fails to provide adequate written description support for the
`
`subject matter of the challenged claims, and as such, the ’596 patent is not
`
`entitled to a priority date earlier than its March 3, 1998 application filing
`
`date. Id. at 53 (citing Exs. 1003, 1004, and 1006). Petitioner argues that the
`
`’905 patent, thus, qualifies as prior art under 35 U.S.C. § 102(a) and
`
`anticipates the subject matter of the claims. Id. at 68.
`
`Patent Owner contends the claims of the ’596 patent were included in
`
`the ’445 application, and therefore, are entitled to priority to that application.
`
`Prelim. Resp. 38 (citing Crown Packaging Tech., Inc. v. Ball Metal
`
`Beverage Container Corp., 635 F.3d 1373, 1380 (Fed. Cir. 2011) (“Original
`
`claims are part of the specification and in many cases will satisfy the written
`
`description requirement”); LizardTech, Inc. v. Earth Res. Mapping, Inc., 424
`
`F.3d 1336, 1346 (Fed. Cir. 2005) (“originally filed claim can provide the
`
`requisite written description to satisfy section 112”)). Patent Owner
`
`provides a chart showing where each claim of the ’596 patent is located in
`
`the ’445 application. Id. at 39–43.
`
`We agree with Patent Owner that the scope and the language of the
`
`claims in the ’445 application are the same or substantially similar to those
`
`
`1 As Petitioner notes, the ’511 application and the ’445 application “share
`the same specification” as each other and the ’596 patent. Pet. 53 n.2.
`Accordingly, like Petitioner and Patent Owner, we focus our analysis on the
`’445 application—the earliest priority application. See id.; Prelim.
`Resp. 38–43.
`
`
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`6
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`in the ’596 patent. Compare Ex. 1001, 43:2–44:39, with Ex. 1004, 63–67.2
`
`Additionally, the claims in the ’445 application were subject to a restriction
`
`requirement issued by the USPTO resulting in the later-filed divisional
`
`applications. See Ex. 2003, 164.
`
`Petitioner contends the ’596 patent claims are directed to a
`
`functionally defined genus. Pet 54–59. Petitioner argues, however, there is
`
`no disclosure in the’445 application of species sufficient to support the
`
`genus claims of the ’596 patent. Id. at 59–68. According to Petitioner,
`
`merely identifying that the claim language of the challenged claims is the
`
`same as that in the priority applications is insufficient to demonstrate written
`
`description support for the challenged claims. Id. at 54–55 (citing Ariad
`
`Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1350 (Fed. Cir. 2010)
`
`(en banc)). Petitioner further argues that the claims cover a multitude of
`
`molecule components, but the ’445 application fails to provide guidance on
`
`certain of those components (e.g., types of polymers). Id. at 55–59.
`
`Petitioner contends that given the limited state of the art, one of ordinary
`
`skill would not find the priority applications commensurate with the many
`
`permutations claimed in the ’596 patent. Id. at 55 (citing Ex. 1007 ¶ 132).
`
`Petitioner, therefore, concludes that the ’596 patent is not entitled to the
`
`priority date of the ’445 application.
`
`We disagree with Petitioner. The court in Ariad stated “a generic
`
`claim may define the boundaries of a vast genus of chemical compounds,
`
`and yet the questions may still remain whether the specification, including
`
`
`2 For clarity, we cite to the page numbers that Petitioner provides on Exhibit
`1004.
`
`
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`original claim language, demonstrates that the applicant has invented species
`
`sufficient to support a claim to a genus.” Ariad, 598 F.3d at 1349. The
`
`claims in Ariad, however, encompassed a broad genus defined exclusively
`
`by function. In the present case, although the claims encompass a genus of
`
`bifunctional molecules, that genus is not defined exclusively by function.
`
`Rather, we find that specification and the original claims provide sufficient
`
`information and identification of structural features common to the members
`
`of the component parts of the genus of bifunctional molecules so that one of
`
`skill in the art could have “visualize[d] or recognize[d] the members of the
`
`genus.” See id. at 1350 (quoting Regents of the Univ. of Cal. v. Eli Lilly &
`
`Co., 119 F.3d 1559, 1568–1569 (Fed. Cir. 1997). Specifically, we find the
`
`specification of the ’445 application demonstrates that the applicant was in
`
`possession of the invention at the earliest filing date, i.e., March 30, 1992.
`
`See Centocor Ortho Biotech, Inc. v. Abbott Labs., 636 F.3d 1341, 1348 (Fed.
`
`Cir. 2011) (“To satisfy the written description requirement, the
`
`[specification] must convey with reasonable clarity to those skilled in the art
`
`that, as of the filing date sought, [the inventor] was in possession of the
`
`invention, and . . . show that the inventor actually invented the invention
`
`claimed.”) (internal quotations omitted); see also Bilstad v. Wakalopulos,
`
`386 F.3d 1116, 1124 (Fed. Cir. 2004) (“[D]isclosure of a species may be
`
`sufficient written description support for a later claimed genus including that
`
`species.”).
`
`Although the ’445 application’s disclosure is limited to a few species
`
`and examples, the examples are explicit and detailed. See Ex. 1004, 50:11–
`
`61:34 (Examples 1–9, and Synthesis of a Library). Additionally, the
`
`components for A, B, and C, listed in the specification but not used in the
`
`
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`examples, were commonly used and commercially available components
`
`that likely would have exhibited predictable characteristics, even in a
`
`solution-phase screening method versus a solid-phase screening method.
`
`See, e.g., id. at 10:15–27, 25:4–26:10, Table 1, 35:30–36:19, 46:19–47:13.
`
`Moreover, as discussed below in regards to claim construction (see Section
`
`II.B.1), we find a common feature necessary for the recited linker molecule
`
`B. Therefore, based on the evidence of record, we are satisfied that the ’445
`
`application would have conveyed, with reasonable clarity, to one of ordinary
`
`skill that the inventors had invented or were in possession of bifunctional
`
`molecules according to the formula A—B—C, . . . wherein B is a linker
`
`molecule operatively linked to A and C, and that the disclosed species in the
`
`’445 application was sufficient to support claims to a genus.
`
`Accordingly, after careful review of both parties’ arguments and
`
`evidence, we find Petitioner has failed to show sufficiently that the
`
`challenged claims of the ’596 patent are not entitled to a priority date of
`
`March 30, 1992, on the basis of lack of adequate written description support
`
`for the claimed subject matter in the ’445 application.
`
`B. Claim Construction
`
`The ’596 patent expired on March 30, 2012. Pet. 19. In an inter
`
`partes review, a claim in an unexpired patent is given its broadest reasonable
`
`construction in light of the specification of the patent in which it appears. 37
`
`C.F.R. § 42.100(b). The Board’s review of the claims of an expired patent,
`
`however, is similar to that of a district court’s review. See 37 C.F.R.
`
`§ 42.5(b); see also In re Rambus, Inc., 753 F.3d 1253, 1255–56 (Fed. Cir.
`
`2014) (involving an inter partes reexamination) (“If, as is the case here, a
`
`reexamination involves claims of an expired patent, a patentee is unable to
`
`
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`make claim amendments and the PTO applies the claim construction
`
`principles outlined by this court in Phillips v. AWH Corp., 415 F.3d 1303
`
`(Fed. Cir. 2005)”); see also In re Rambus, Inc., 694 F.3d 42, 46 (Fed. Cir.
`
`2012) (involving an ex parte reexamination) (“the Board’s review of the
`
`claims of an expired patent is similar to that of a district court’s review”).
`
`Accordingly, we construe the claims of the now-expired ’596 patent
`
`under the principles set forth in Phillips, 415 F.3d at 1312–13 (words of a
`
`claim “are generally given their ordinary and customary meaning” as
`
`understood by a person of ordinary skill in the art in question at the time of
`
`the invention). We will not apply, however, a rule of construction that
`
`claims should be construed to preserve their validity.3 See also, e.g., Google
`
`Inc. v. Createads LLC, Case IPR2014-00200, slip op. at 2 (PTAB July 16,
`
`2014) (Paper 19) (“[n]o presumption of validity is applied” to interpreting
`
`claims in an expired patent).
`
`“In determining the meaning of the disputed claim limitation, we look
`
`principally to the intrinsic evidence of record, examining the claim language
`
`itself, the written description, and the prosecution history, if in evidence.”
`
`DePuy Spine, Inc. v. Medtronic Sofamor Danek, Inc., 469 F.3d 1005, 1014
`
`(Fed. Cir. 2006) (citing Phillips, 415 F.3d at 1312–17). The words of a
`
`claim generally are given their ordinary and customary meaning, which is
`
`the meaning the term would have to a person of ordinary skill at the time of
`
`the invention, in the context of the entire patent including the specification.
`
`
`3 “While we have acknowledged the maxim that claims should be construed
`to preserve their validity, we have not applied that principle broadly, and we
`have certainly not endorsed a regime in which validity analysis is a regular
`component of claim construction.” Phillips, 415 F.3d at 1327.
`
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`See Phillips, 415 F.3d at 1312–13. Although it is improper to read a
`
`limitation from the specification into the claims, the claims still must be read
`
`in view of the specification of which they are a part. See Microsoft Corp. v.
`
`Multi-Tech Sys., Inc., 357 F.3d 1340, 1347 (Fed. Cir. 2004). In certain
`
`circumstances, however, a claim term may not be given its ordinary and
`
`customary meaning. “[A] claim term will not receive its ordinary meaning if
`
`the patentee acted as his own lexicographer and clearly set forth a definition
`
`of the disputed claim term in either the specification or prosecution history.”
`
`CCS Fitness, Inc. v. Brunswick Corp., 288 F.3d 1359, 1366 (Fed. Cir. 2002).
`
`Furthermore, a claim term also will not receive its ordinary meaning where
`
`the intrinsic record contains “an intentional disclaimer, or disavowal, of
`
`claim scope by the inventor.” Phillips, 415 F.3d at 1316.
`
`We construe the challenged claims according to these principles.
`
`
`
`1. “linker molecule”
`
`The parties disagree on the construction of the term “linker molecule,”
`
`as recited by independent claim 1. Claim 1 specifically recites “a
`
`bifunctional molecule according to the formula A—B—C, . . . wherein B is
`
`a linker molecule operatively linked to A and C.” Ex. 1001, 43:2–6.
`
`Petitioner contends that the term should be given “its plain meaning of any
`
`group of atoms that operatively links polymer A and oligonucleotide C.”
`
`Pet. 20. According to Petitioner, the linkage need not take any particular
`
`form, nor must it directly link A to C. Id. Petitioner specifically cites to the
`
`specification’s disclosure that “the nature of the linkage is not considered an
`
`essential feature of this invention.” Id. (citing Ex. 1001, 8:39–41) (emphasis
`
`omitted). Therefore, Petitioner argues that the “linker molecule” merely
`
`“performs the function of bringing the polymer and oligonucleotide into
`
`
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`proximity so that the identifier units can identify the chemical units.” Id.
`
`(citing Ex. 1007 ¶ 56). Petitioner’s position appears to be that the language
`
`of claim 1 only limits the linker molecule to one that “functionally” links
`
`components A and C. Id. at 21 (citing Ex. 1029, 228).
`
`Patent Owner contests Petitioner’s construction, arguing that “linker
`
`molecule” should be given its plain meaning of a “single molecule that
`
`performs the function of operatively linking a single chemical moiety to a
`
`single identifier oligonucleotide.” Prelim. Resp. 21–22. Patent Owner bases
`
`its construction on three points. First, Patent Owner argues that the ’596
`
`patent claims distinguish between molecule and polymer/oligomer as
`
`components of the claimed bifunctional molecule. Id. at 18.
`
`Second, Patent Owner argues that the specification describes the
`
`linker molecule in both functional and structural language. Id. at 18, 20.
`
`Patent Owner cites to the specification’s description of a preferred
`
`embodiment with linker molecules that “need not exceed a length sufficient
`
`to provide the linkage function indicated. Thus, a chain length of from at
`
`least one to about 20 atoms is preferred.” Id. at 20 (citing Ex. 1001, 8:44–
`
`45). According to Patent Owner, the preferred embodiment disclosed in the
`
`’596 patent indicates that the term “linker molecule” cannot be “construed to
`
`include a large and visible polymer, composed of multiple repeating units,”
`
`especially when the claim explicitly recites the term “molecule” and not
`
`molecules. Id. (citing Ex. 2004 ¶ 3).
`
`Lastly, Patent Owner argues that Petitioner attempts to read the “to”
`
`out of “linking the chemical moiety to the identifier oligonucleotide” by
`
`arguing that the linker simply needs to “bring[] the polymer and
`
`oligonucleotide into proximity.” Id. at 21 (citing Pet. 20). Patent Owner
`
`
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`contends that the claims do not require mere proximity of the polymer and
`
`oligonucleotide, and that the “linker molecule” does not simply link polymer
`
`A and oligonucleotide C; rather, the linker molecule “performs the function
`
`of operatively linking a single the chemical moiety to a single identifier
`
`oligonucleotide.” Id. at 21–22.
`
`Although we are not persuaded by Patent Owner that the plain
`
`language of the claims and the disclosure in the specification distinguish
`
`between the recited “molecule” and oligonucleotides and polymers, we are
`
`persuaded that Petitioner’s proffered construction is too broad given the
`
`specification and the relevant prosecution history. Specifically, we do not
`
`agree with Petitioner’s interpretation of the specification’s discussion
`
`regarding “linker molecules.” See Pet. 20 (citing Ex. 1001, 8:39–41).
`
`Petitioner focuses on the language stating that “the nature of the linkage is
`
`not considered an essential feature of this invention,” but fails to consider
`
`the preceding language stating “[a]s the nature of chemical linkages is
`
`diverse, any of a variety of chemistries may be utilized to effect the
`
`indicated operative linkages to A and to C.” See Ex. 1001, 8:37–39. Taken
`
`as a whole, the sentence appears to indicate that the nature of the linkage
`
`between A to B and B to C is not an essential feature of the invention.
`
`Specifically, we understand the specification to mean that the linkage itself
`
`may be a covalent bond, a non-covalent bond, or some other form of
`
`conjugation between the individual components of the “bifunctional
`
`molecule.”
`
`The examples disclosed in the ’596 patent, while not limiting, indicate
`
`that the linker molecule must allow for alternative addition (or synthesis) of
`
`an oligonucleotide and amino acid onto the linker molecule, while separately
`
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`allowing for coupling and decoupling from a solid support. Id. at 8:30–33
`
`(“linker molecule should have the capability of reversibly attaching to a
`
`solid support”), 46–50, 25:4–7 (a linker designated (1-dimethoxytrityloxy-3-
`
`fluorenylmethoxycarbonylamino propan-2yl)-(2-cyanoethyl)-(N,N- 5
`
`diisopropyl)-phosphoramidite and referred to as 5' Branched-Modifier C3
`
`(or 5'BMC3)); see id. at 8:25–27 (“Preferably, a linker molecule has a means
`
`for attaching to a solid support, thereby facilitating synthesis of the
`
`bifunctional molecule in the solid phase”), 25:1–31 (“Coupling of Linker to
`
`Solid Support,” “Coupling of Nucleotide to Solid Support”).
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`The specification explicitly discloses that the linker molecule must be
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`capable of coupling to a solid support and then “the DMT protecting group”
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`of the linker molecule is removed “from the linker” to form a free hydroxyl
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`group. Ex. 1001, 25:25–31. This free hydroxyl group is used to bind to an
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`oligonucleotide forming a nucleotide/linker/support complex. Id. at 25:31–
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`37. Thereafter, the fluoromethoxycarbonyl (FMOC) protecting group is
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`removed from the linker in the nucleotide complex to create a free amino
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`group on the linker molecule. Id. at 24:62–64, 66–67. According to the
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`’596 patent, an amino acid then can conjugate with the linker molecule
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`creating the claimed bifunctional molecule. Id. at 26:2–10. Prior to
`
`preparation of the bifunctional molecule libraries, the amino
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`acid/nucleotide/linker conjugate can be cleaved from the solid support. Id.
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`at 27:12–34. Cleavage of the bifunctional molecule from the solid support
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`does not separate the amino acids and nucleotides from the linker molecule.
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`Id. at 27:33–34 (“The homogeneous fraction is collected to yield a solution
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`of pure bifunctional molecule.”).
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`14
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`Although separation from the solid support is not recited in the claims,
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`statements made during prosecution history make it clear that such
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`separation is a necessary attribute of the linker molecule. See Ex. 1044, 7
`
`(distinguishing the claims from the prior art on the basis that “the present
`
`[divisional] application discloses the coupling and decoupling of a linkage
`
`unit identified as 5' Branched- Modifier C3 or 5'BMC3 to a bead and the
`
`use of this linkage unit for sequentially synthesizing peptides and identifier
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`oligonucleotides”), 10 (“The cited prior art does not enable a bead based
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`alternating synthesis of a peptide linked to an identifier oligonucleotide for
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`forming a library of bifunctional molecules”); Ex. 1026, 21 (“Applicant
`
`claims [in a divisional application] a specific linker molecule B having
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`termini A' and C' according to the formula A'-B-C' that is adapted for
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`reaction with an amino acid precursor unit X' at terminus A' and with a
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`nucleotide precursor Z' at terminus C'. The working example in the
`
`specification uses 5'BMC3 as a linker molecule. This example is
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`representative of all linkers which are adapted for amino acid and nucleotide
`
`precursors.”).
`
`“[T]he prosecution history can often inform the meaning of the claim
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`language by demonstrating how the inventor understood the invention and
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`whether the inventor limited the invention in the course of prosecution,
`
`making the claim scope narrower than it would otherwise be.” Phillips, 415
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`F.3d at 1317. The Federal Circuit has “recognized that a ‘clear and
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`unmistakable’ disavowal during prosecution overcomes the ‘heavy
`
`presumption’ that claim terms carry their full ordinary and customary
`
`meaning.” Biogen Idec, Inc. v. GlaxoSmithKline LLC, 713 F.3d 1090, 1095
`
`(Fed. Cir. 2013) (quoting Omega Eng’g, Inc. v. Raytek Corp., 334 F.3d
`
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`15
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`1314, 1323, 1326 (Fed. Cir. 2003)). Specifically, “when the patentee
`
`unequivocally and unambiguously disavows a certain meaning to obtain a
`
`patent, the doctrine of prosecution history disclaimer narrows the meaning of
`
`the claim consistent with the scope of the claim surrendered.” Id.
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`Prosecution history disclaimer plays an important role in the patent
`
`system. It “promotes the public notice function of the intrinsic evidence and
`
`protects the public’s reliance on definitive statements made during
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`prosecution.” Id. (internal citation and quotation marks omitted). Such
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`statements can take the form of either amendment or argument. See Elkay
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`Mfg. Co. v. Ebco Mfg. Co., 192 F.3d 973, 979 (Fed. Cir. 1999); see also
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`Computer Docking Station Corp. v. Dell, Inc., 519 F.3d 1366, 1374 (Fed.
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`Cir. 2008) (“Statements made during prosecution may also affect the scope
`
`of the claims.”). For this reason, the entirety of a patent’s file history
`
`captures the public record of the patentee’s representations concerning the
`
`scope and meaning of the claims. Seachange Int’l, Inc. v. C–COR Inc., 413
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`F.3d 1361, 1372 (Fed. Cir. 2005) (quoting Hockerson–Halberstadt, Inc. v.
`
`Avia Grp. Int’l, Inc., 222 F.3d 951, 957 (Fed. Cir. 2000)); see also Elkay,
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`192 F.3d at 979 (“[I]t is the totality of the prosecution history that must be
`
`assessed, not the individual segments of the presentation made to the
`
`[USPTO] by the applicant . . . .”). Competitors are entitled to rely on those
`
`representations when determining a course of lawful conduct, such as
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`launching a new product or designing-around a patented invention. Id.
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`Beyond the notice function and reliance-based aspects of a patent's
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`prosecution history, it “provides evidence of how the [USPTO] and the
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`inventor understood the patent.” Edwards Lifesciences LLC v. Cook Inc.,
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`582 F.3d 1322, 1327 (Fed. Cir. 2009) (quoting Phillips, 415 F.3d at 1317)
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`(alteration in original).
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`This case requires us to determine if the inventors disclaimed claim
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`scope during prosecution of that ’596 patent by making statements in the
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`prosecution history that are sufficient to overcome the “heavy presumption”
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`that the term carries its full ordinary and customary meaning advanced by
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`Petitioner. We conclude that they have. Specifically, we find that the
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`arguments made to distinguish the prior art constitute a clear and
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`unequivocal disavowal of linker molecules that fail to allow for alternative
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`addition (or synthesis) of an oligonucleotide and amino acid onto the linker
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`molecule, while separately allowing for coupling and decoupling of the
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`linker molecule from a solid support.
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`Accordingly, based on the claim language itself, the disclosure in the
`
`specification, and the narrowing statements made during prosecution, we
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`understand the claim limitation “B is a linker molecule operatively linked to
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`A and C” to mean that linker molecule B (1) links to A and to C, (2) allows
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`for alternative addition of nucleotides and amino acids to itself, and (3) is
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`capable of coupling to and decoupling from a solid support without cleaving
`
`either the polypeptide or oligonucleotide from linker molecule B.
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`2. Other Claim Terms
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`Based on our review of the record and the dispositive issues in our
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`determination of whether to institute inter partes review on the asserted
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`grounds of unpatentability, we need not address the construction of any
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`other claim terms. See Pet. 21–25; Prelim. Resp. 22–23. See Vivid Techs.,
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`Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999) (“only
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`17
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`those terms need be construed that are in controversy, and only to the extent
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`necessary to resolve the controversy”).
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`C. Principles of Law
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`A claim is unpatentable under 35 U.S.C. § 103(a) if “the differences
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`between the subject matter sought to be patented and the prior art are such
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`that the subject matter as a whole would have been obvious at the time the
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`invention was made to a person having ordinary skill in the art to which said
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`subject matter pertains.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 406
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`(2007). The question of obviousness is resolved on the basis of underlying
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`factual determinations, including: (1) the scope and content of the prior art;
`
`(2) any differences between the claimed subject matter and the prior art;
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`(3) the level of skill in the art; and (4) objective evidence of nonobviousness,
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`i.e., secondary considerations. See Graham v. John Deere Co., 383 U.S. 1,
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`17–18 (1966).
`
`“A determination of whether a patent claim is invalid as obvious
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`under § 103 requires consideration of all four Graham factors, and it is error
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`to reach a conclusion of obviousness until all those factors are considered.”
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`Apple Inc. v. Samsung Elecs. Co., Ltd., 839 F.3d 1034, 1048 (Fed. Cir. 2016)
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`(en banc) (internal citations omitted). “This requirement is in recognition of
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`the fact that each of the Graham factors helps inform the ultimate
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`obviousness determination.” Id.
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`“In an [inter partes review], the petitioner has the burden from the
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`onset to show with particularity why the patent it challenges is
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`unpatentable.” Harmonic Inc. v. Avid Tech., Inc., 815 F.3d 1356, 1363 (Fed.
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`Cir. 2016) (citing 35 U.S.C. § 312(a)(3) (requiring inter partes review
`
`petitions to identify “with particularity . . . the evidence that supports the
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`grounds for the challenge to each claim”)). This burden never shifts to
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`Patent Owner. See Dynamic Drinkware, LLC v. Nat’l Graphics, Inc., 800
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`F.3d 1375, 1378 (Fed. Cir. 2015) (citing Tech. Licensing Corp. v. Videotek,
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`Inc., 545 F.3d 1316, 1326–27 (Fed. Cir. 2008)) (discussing the burden of
`
`proof in inter partes review). Furthermore, Petitioner cannot satisfy its
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`burden of provi
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