Trials@uspto.gov
`571-272-7822
`
`Paper 19
`Entered: December 30, 2020
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`
`ILLUMINA, INC.,
`Petitioner,
`
`v.
`
`TRUSTEES OF COLUMBIA UNIVERSITY
`IN THE CITY OF NEW YORK,
`Patent Owner.
`
`IPR2020-01177
`Patent 10,435,742 B2
`
`
`
`
`
`
`
`
`
`Before ZHENYU YANG, JAMES A. WORTH, and
`DEVON ZASTROW NEWMAN, Administrative Patent Judges.
`
`NEWMAN, Administrative Patent Judge.
`
`DECISION
`Granting Institution of Inter Partes Review
`35 U.S.C. § 314
`
`
`
`
`
`
`
`
`571-272-7822
`
`Paper 19
`Entered: December 30, 2020
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`
`ILLUMINA, INC.,
`Petitioner,
`
`v.
`
`TRUSTEES OF COLUMBIA UNIVERSITY
`IN THE CITY OF NEW YORK,
`Patent Owner.
`
`IPR2020-01177
`Patent 10,435,742 B2
`
`
`
`
`
`
`
`
`
`Before ZHENYU YANG, JAMES A. WORTH, and
`DEVON ZASTROW NEWMAN, Administrative Patent Judges.
`
`NEWMAN, Administrative Patent Judge.
`
`DECISION
`Granting Institution of Inter Partes Review
`35 U.S.C. § 314
`
`
`
`
`
`
`
`
`
`IPR2020-01177
`Patent 10,435,742 B2
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`I.
`
`INTRODUCTION
`
`a. BACKGROUND
`
`On June 26, 2020, Illumina, Inc., (“Petitioner”) filed a Petition
`
`(Paper 1, “Pet.”) requesting an inter partes review of claims 1 and 2 (the
`
`“challenged claims”) of U.S. Patent No. 10,435,742 B2 (Ex. 1004, “the ’742
`
`patent”). See 35 U.S.C. §§ 311–319. On October 16, 2020, Trustees of
`
`Columbia University in the City of New York (“Patent Owner”) filed a
`
`Preliminary Response to the Petition. Paper 12 (“Prelim. Resp.”). On
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`November 12, 2020, Petitioner filed an authorized Reply addressing
`
`discretion to institute under 35 U.S.C. §§ 314(a) and 325(d) and claim
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`construction of the term “chemical linker.” Papers 13, 14. On November
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`19, 2020, Patent Owner filed an authorized Sur-Reply responding to
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`Petitioner’s statements concerning discretion to institute and claim
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`construction. Papers 13, 16.
`
`We have the authority and discretion to determine whether to institute
`
`an inter partes review. 35 U.S.C. § 314; 37 C.F.R. § 42.4. We may not
`
`institute an inter partes review “unless . . . there is a reasonable likelihood
`
`that the petitioner would prevail with respect to at least 1 of the claims
`
`challenged in the petition.” 35 U.S.C. § 314(a). For the reasons provided
`
`below, we determine that Petitioner has satisfied the threshold requirement
`
`set forth in 35 U.S.C. § 314(a). Therefore, we institute an inter partes
`
`review of the challenged claims.
`
`b. REAL PARTIES-IN-INTEREST
`
`Petitioner identifies itself as the real party-in-interest for Petitioner.
`
`Pet. 70. Patent Owner identifies itself as the real party-in-interest for Patent
`
`Owner. Paper 4, 1.
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`
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`2
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`c. RELATED PROCEEDINGS
`
`This Petition is part of a third set of petitions Illumina filed
`
`challenging claims of several of Patent Owner’s patents. The remaining
`
`petitions in this set involve the following four patents: U.S. Patent Nos.
`
`10,407,458, 10,407,459; 10,457,984; and 10,428,380. The petitions
`
`involving each of these patents are as follows: IPR2020-00988; IPR2020-
`
`01065; IPR2020-01125; and IPR2020-01323, respectively. Patent Owner
`
`asserted these patents in the parallel district court litigation, The Trustees of
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`Columbia Univ. in the City of New York v. Illumina, Inc., 19-1681-CFC
`
`(D. Del.) (“the Delaware litigation”).
`
`The first set of petitions between the parties involved three of Patent
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`Owner’s patents, U.S. Patent Nos. 7,790,869; 7,713,698; and 8,088,575
`
`(“the ’869, ’698, and ’575 patents.” respectively). Pet. 72–73; Paper 4, 2.
`
`The Board held all challenged claims of these patents unpatentable, and the
`
`United States Court of Appeals for the Federal Circuit (“Federal Circuit”)
`
`affirmed that judgment. See Illumina, Inc. v. Trustees of the University of
`
`Columbia in the City of New York, IPR2012-00007, Paper 140 (PTAB 2014)
`
`(Ex. 1021); Illumina, Inc. v. Trustees of the University of Columbia in the
`
`City of New York, IPR2012-00006, Paper 128 (PTAB 2014) (Ex. 1022);
`
`Illumina, Inc. v. Trustees of the University of Columbia in the City of New
`
`York, IPR2013-00011, Paper 130 (PTAB 2014) (Ex. 1023); Trustees of
`
`Columbia Univ. in the City of New York v. Illumina, Inc., 620 F. App’x. 916
`
`(Fed. Cir. 2015) (Ex. 1029); Pet. 72–73; Paper 4, 2.
`
`Petitioner asserts that the challenged claims held unpatentable in the
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`’869, ’698, and ’575 patents in the first set of petitions “were nearly identical
`
`to claim 1 of the ’480 patent [U.S. Patent No. 9,725,480 (Ex. 1019)].” Pet.
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`72–73. The Board held claim 1 of the ’480 patent unpatentable over much
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`of the same art asserted here in the second set of petitions Illumina filed
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`against five patents including the ’742 patent. See Pet. 70–72; Ex. 1024, 76.
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`Petitioner also asserts that claim 1 of the ’480 patent is “nearly identical to
`
`claims 1 and 2 of the ’742 patent” at issue here. Pet. 71. More specifically,
`
`Petitioner asserts that the only difference between the unpatentable claims of
`
`the ’480 patent and the ’742 patent “is that this latest set [of claims] excludes
`
`an allyl capping group (which the Board determined was unpatentable in the
`
`last round of IPRs).” Id. at 72.
`
`In addition to the ’480 patent, the remaining four patents of Patent
`
`Owner that Illumina challenged in this second set of petitions are as follows:
`
`U.S. Patent 9,718,852; 9,719,139; 9,708,358; and 9,868,985. Pet. 70–72;
`
`Paper 4, 1. Illumina challenged these patents in IPR2018-00291; IPR2018-
`
`00318; IPR2018-00322; IPR2018-00797, respectively; and IPR2018-00385
`
`challenged the ’480 patent. The Board held all challenged claims of these
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`patents unpatentable. See Exs. 1024, 1028. Patent Owner has appealed
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`these judgments. See Pet. 72; Paper 4, 1.
`
`Petitioner also identifies its own patents that it has asserted against
`
`Patent Owner and that Patent Owner has challenged before the Board.
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`Pet. 73–74; Paper 4, 2. The Board upheld the patentability of the challenged
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`claims of one of Petitioner’s patents, U.S. Patent No. 7,566,537. Pet. 74;
`
`Paper 4, 2; Ex. 1068 (IPR2013-00517); Intelligent Bio-Sys., Inc. v. Illumina
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`Cambridge Ltd., 821 F.3d 1359 (Fed. Cir. 2016) (affirming the Board’s
`
`determination that unpatentability had not been established). See Ex. 1069,
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`17–18.
`
`d. THE ’742 PATENT (EX. 1004)
`
`The ’742 patent issued from a series of continuation applications, two
`
`of which issued as the ’575 and ’869 patents that were challenged in the first
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`4
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`set of petitions Illumina filed. Ex. 1004, code (60) (stating the only two
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`applications in the priority chain that were not continuations were the
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`earliest application and the second earliest application, neither of which
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`matured into patents at issue in the series of inter partes reviews between
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`Petitioner and Patent Owner). The ’742 patent issued October 8, 2019,
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`subject to a terminal disclaimer, and is titled “Massive Parallel Method for
`
`Decoding DNA and RNA.” Id. at codes (45), (54). The named inventors
`
`are Jingyue Ju, Zengmin Li, John Robert Edwards, and Yasuhiro Itagaki. Id.
`
`at code (72).
`
`The subject matter of the ’742 patent involves “methods for attaching
`
`a nucleic acid to a solid surface and for sequencing nucleic acid by detecting
`
`the identity of each nucleotide analog after the nucleotide analog is
`
`incorporated into a growing strand of DNA in a polymerase reaction.”
`
`Ex. 1004, Abst. The nucleotide analogs described in the ’742 patent are
`
`made by
`
`linking a unique label such as a fluorescent dye or a mass tag
`through a cleavable linker to the nucleotide base or an analogue
`of the nucleotide base, such as to the 5-position of the
`pyrimidines (T and C) and to the 7-position of the purines (G
`and A), to use a small cleavable chemical moiety to cap the
`3’-OH group of the deoxyribose to make it nonreactive, and to
`incorporate the nucleotide analogues into the growing DNA
`strand as terminators. Detection of the unique label will yield
`the sequence identity of the nucleotide. Upon removing the
`label and the 3’-OH capping group, the polymerase reaction
`will proceed to incorporate the next nucleotide analogue and
`detect the next base.
`
`Id. at 3:4–17. This method is generally referred to as the “DNA sequencing
`
`by synthesis” approach or “SBS,” because the sequence of the DNA is
`
`determined by identifying the successive additions of labeled nucleotides to
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`5
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`a strand of DNA as it is synthesized using a complimentary DNA strand as a
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`template. Id. at 3:44–54, 4:25–32.
`
`
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`In describing the 3’-OH capping moiety, the Specification of the ’742
`
`patent provides that using small chemical moieties that can be easily cleaved
`
`chemically with high yield is desirable because nucleotide analogues that
`
`incorporate such moieties “should also be recognized as substrates for DNA
`
`polymerase.” Id. at 3:22–26. The Specification of the ’742 patent provides
`
`that “[i]t is known that MOM (–CH2OCH3) and allyl (–CH2CH==CH2)
`
`groups can be used to cap an –OH group, and can be cleaved chemically
`
`with high yield.” Id. at 3:41–44 (citations omitted).
`
`e. CHALLENGED CLAIMS
`
`Petitioner challenges the two claims of the ’742 patent, both of which
`
`are independent and are directed to thymine deoxyribonucleotide analogues.
`
`Pet. 11. Claim 1 is illustrative and recites:
`
`1.
`
`A thymine deoxyribonucleotide analogue having the
`structure:
`
`
`
`
``
`
`
`
`
`
`
`
`
`
`
`
`wherein R (a) represents a small, chemically cleavable, chemical
`group capping the oxygen at the 3’ position of the deoxyribose
`of the deoxyribonucleotide analogue, (b) does not interfere with
`recognition of the analogue as a substrate by DNA polymerase,
`(c) is stable during a DNA polymerase reaction, (d) does not
`contain a ketone group, and (e) is not a –CH2CH==CH2 group;
`
`wherein OR is not a methoxy group or an ester group;
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`Patent 10,435,742 B2
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`wherein the covalent bond between the 3’-oxygen and R is stable
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`during a DNA polymerase reaction;
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`wherein tag represents a detectable fluorescent moiety;
`
`wherein Y represents a chemically cleavable, chemical linker which
`(a) does not interfere with recognition of the analogue as a
`substrate by a DNA polymerase and (b) is stable during a DNA
`polymerase reaction; and
`
`wherein the thymine deoxyribonucleotide analogue:
`
`
`
`
`
`
`(i) is recognized as a substrate by a DNA polymerase,
`
`(ii) is incorporated at the end of a growing strand of DNA
` during a DNA polymerase reaction,
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`(iii) produces a 3’–OH group on the deoxyribose upon cleavage of R,
`
`(iv) no longer includes a tag on the base upon cleavage of Y, and
`
`(v) is capable of forming hydrogen bonds with adenine or an adenine
`nucleotide analogue.
`
`Ex. 1004, 33:21–63.
`
`f. PRIOR ART AND ASSERTED GROUNDS OF
`UNPATENTABILITY
`
`Petitioner argues that claims 1 and 2 of the ’742 patent are
`
`unpatentable based on the following grounds:
`
`Claims Challenged
`1, 2
`
`35 U.S.C. §
`103(a)1
`
`Reference(s)
`Tsien,2 Hiatt3
`
`
`1 The Leahy-Smith America Invents Act (“AIA”), Pub. L. No. 112-29, 125
`Stat. 284, 287–88 (2011), amended 35 U.S.C. §§ 102, 103, and 112,
`effective March 16, 2013. Because the ’742 patent issued from a series of
`continuation applications, the earliest of which was filed prior to the
`effective date of the AIA, we apply the pre-AIA version of 35 U.S.C. § 103.
`2 Tsien, WO 91/06678, published May 16, 1991 (Ex. 1031, “Tsien”).
`3 Hiatt et al., U.S. Patent No. 5,763,594, issued June 9, 1998 (Ex. 1043,
`“Hiatt”).
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`IPR2020-01177
`Patent 10,435,742 B2
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`Claims Challenged
`1, 2
`1, 2
`1, 2
`
`35 U.S.C. §
`103(a)
`103(a)
`103(a)
`
`Reference(s)
`Dower,4 Prober,5 Hiatt
`Tsien
`Dower, Prober, Metzker6
`
`
`
`Petitioner submits the Declaration of Floyd Romesberg, Ph.D., in
`
`support of its Petition. See Ex. 1131 (“the Romesberg Declaration”). Patent
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`Owner submits the Declaration of Kenneth A. Johnson, Ph.D., in support of
`
`its arguments in the Preliminary Response. See Ex. 2048.
`
`II. ANALYSIS
`
`a. DISCRETIONARY DENIAL UNDER 35 U.S.C. § 325(D)
`
`Patent Owner, relying on arguments Petitioner made in related Board
`
`proceedings, argues that we should exercise our discretion under 35 U.S.C.
`
`§ 325(d) to deny institution for two reasons pertaining to Petitioner’s
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`reliance in this proceeding on teachings from references Hovinen7 and Hiatt.
`
`See Prelim Resp. 60–61. First, Patent Owner argues that Petitioner’s
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`contention in this case that a skilled artisan would have pursued use of the
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`MOM capping group in an SBS method based on Hovinen’s teachings
`
`“ignores that the Board[8] declined [in a prior set of cases] to adopt
`
`
`4 Dower et al., U.S. Patent 5,547,839, issued Aug. 20, 1996 (Ex. 1030,
`“Dower”).
`5 Prober et al., A System for Rapid DNA Sequencing with Fluorescent Chain-
`Terminating Dideoxynucleotides, 238 SCIENCE 336–41 (1987) (Ex. 1041,
`“Prober”).
`6 Metzker et al., Termination of DNA Synthesis by Novel 8’-modified-
`deoxyribonucleoside 5’-triphosphates, 22 NUCLEIC ACIDS RES. 4259–67
`(1994) (Ex. 1039, “Metzker”).
`7 Hovinen et al., Synthesis of 3´-O-(ω-Aminoalkoxymethyl)thymidine 5´-
`Triphosphates, Terminators of DNA Synthesis that Enable 3’-Labeling,” 1 J.
`CHEM. SOC. PERKIN TRANS. 211–217 (1994) (Ex. 1060, “Hovinen”).
`8 Patent Owner refers to the Board’s per curiam Final Written Decision in
`Illumina, Inc. v. Trustees of Columbia Univ., IPR2018-00291, IPR2018-
`
`8
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`Illumina’s prior contention that disclosure of a capping group for use in
`
`Sanger sequencing would motivate a POSA to use said capping group for
`
`SBS,” a characterization with which we disagree. Id. at 60; see infra Section
`
`II.e.ii. Patent Owner cites a statement from the Board’s Allyl Claim IPR
`
`Decision that Illumina’s expert “concede[d] that Sanger sequencing requires
`
`low termination rates (in contrast to the high termination rates SBS
`
`requires).” Prelim. Resp. 60 (quoting Ex. 1024, 32). Patent Owner argues
`
`that the Board’s rejection of the stated reasoning in the prior cases similarly
`
`justifies the exercise of discretion to deny the Petition here, where Petitioner
`
`relies on the teachings of Hovinen, a Sanger sequencing reference. Id.
`
`Second, Patent Owner argues that the Board’s statements in the Allyl
`
`Claim IPR Decision concerning Hiatt are “relevant here, where Illumina
`
`now uses Hiatt in the asserted grounds.” Id. at 60–61. Patent Owner notes
`
`that “Illumina previously argued that Hiatt provided motivation for a POSA
`
`to select a particular capping group, specifically the allyl capping group,”
`
`but the Board found that Hiatt “presents an immense number of possibilities
`
`for the blocking group.” Id. (citing Ex. 1024, 27). Patent Owner concedes
`
`that the Board’s finding was “ultimately not dispositive in the prior case,”
`
`but argues that “Illumina should not be permitted to ignore the Board’s prior
`
`finding” and cites Becton, Dickinson & Co. v. B. Braun Melsungen AG,
`
`IPR2017-01586, Paper 8 at 16–28 (Dec. 15, 2017) (precedential as to section
`
`III.C.5, first paragraph) (“Becton, Dickinson”) as “applying § 325(d) to deny
`
`institution of ground raising same arguments based on similar prior art.”
`
`Prelim Resp. 60–61.
`
`
`00318, IPR2018-00322, IPR2018-00385 Paper 67 at 32, (PTAB June 21,
`2018) (Ex. 1024) (“Allyl Claim IPR Decision” or “Allyl Claim IPR”).
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`9
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`Analysis
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`If “another proceeding or matter involving the patent is before the
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`Office,” we have discretion to deny review where “the same or substantially
`
`the same prior art or arguments previously were presented to the Office.”
`
`35 U.S.C. § 325(d). In that respect, § 325(d) provides that the Director may
`
`elect not to institute a proceeding if the challenge to the patent is based on
`
`matters previously presented to the Office.9 See also Advanced Bionics,
`
`LLC v. Med-El Elektromedizinische Geräte GmbH, IPR2019-01469, Paper 6
`
`at 7 (PTAB Feb. 13, 2020) (precedential) (“Advanced Bionics”) (setting
`
`forth the two-part framework under which the Board analyzes § 325(d)).
`
`In evaluating matters under § 325(d), the Board uses the following
`
`two-part framework: (1) determining whether the same or substantially the
`
`same art previously was presented to the Office or whether the same or
`
`substantially the same arguments previously were presented to the Office;
`
`and, (2) if either condition of the first part of the framework is satisfied,
`
`determining whether the petitioner has demonstrated that the Office erred in
`
`a manner material to the patentability of challenged claims. Advanced
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`Bionics, Paper 6 at 8.
`
`In applying the two-part framework, we consider several nonexclusive
`
`factors, including:
`
`the similarities and material differences between the asserted
`art and the prior art involved during examination;
`
`the cumulative nature of the asserted art and the prior art
`evaluated during examination;
`
`(a)
`
`
`(b)
`
`
`
`
`9 The Board institutes trial on behalf of the Director. 37 C.F.R. § 42.4(a);
`Advanced Bionics, Paper 6 at 7 n.7.
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`10
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`(c)
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`
`(d)
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`the extent to which the asserted art was evaluated during
`examination, including whether the prior art was the basis for
`rejection;
`
`the extent of the overlap between the arguments made
`during examination and the manner in which petitioner relies on
`the prior art or patent owner distinguishes the prior art;
`
`
`(e) whether petitioner has pointed out sufficiently how the
`examiner erred in its evaluation of the asserted prior art; and
`
`
`(f)
`
`the extent to which additional evidence and facts presented
`in the petition warrant reconsideration of the prior art or
`arguments.
`
`Becton, Dickinson, Paper 8 at 17–18.
`
`Factors (a), (b), and (d) of the Becton, Dickinson factors relate to
`
`whether the art or arguments presented in the Petition are the same or
`
`substantially the same as those previously presented to the Office. Advanced
`
`Bionics, Paper 6 at 10 (“. . . although Becton, Dickinson factor (d) pertains
`
`to arguments made ‘during examination,’ this factor more broadly provides
`
`guidance as to whether the arguments presented in the petition are ‘the same
`
`or substantially the same’ as the arguments previously presented to the
`
`Office during any proceeding” and referencing AIA proceedings as an
`
`example proceeding before the Office). Factors (c), (e), and (f) “relate to
`
`whether the petitioner has demonstrated a material error by the Office” in its
`
`prior consideration of that art or arguments. Id. Only if the same or
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`substantially the same art or arguments were previously presented to the
`
`Office do we then consider whether petitioner has demonstrated a material
`
`error by the Office. Id.
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`Same or Substantially the Same Art or Arguments Previously
`Presented to the Office
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`We first consider whether Petitioner asserts the same or substantially
`
`the same art or arguments that previously were presented to the Office.
`
`Advanced Bionics, Paper 6 at 8. Patent Owner raises no argument under
`
`§ 325(d) regarding Petitioner’s asserted grounds 3 and 4. See Prelim. Resp.
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`60–61. Patent Owner’s arguments under § 325(d) focus on asserted grounds
`
`1 and 2, which include Hiatt. Id. Hovinen is not included in any of
`
`Petitioner’s asserted grounds and also was not included in the asserted
`
`grounds the Board addressed in the Allyl Claim IPR. See Pet. 11 (listing
`
`asserted grounds); Ex. 1024, 2–3 (Allyl Claim IPR Decision’s table of
`
`asserted grounds). Rather, as we explain below, Petitioner cites to Hovinen
`
`only as further evidence that 3’-O-MOM capped nucleotides were
`
`recognized as a substrate and incorporated by a polymerase. See infra
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`section II.e.ii.(3)a). Thus, we do not agree with Patent Owner that the Board
`
`previously considered Hovinen’s teachings in determining that the
`
`challenged claims in the Allyl Claim IPR were unpatentable. Accordingly,
`
`we are not persuaded that Hovinen was previously presented to the Office
`
`within the meaning of § 325(d). See Advanced Bionics, Paper 6 at 7–8.
`
`With regard to Hiatt, there is no dispute that both grounds 1 and 2 of
`
`the Petition rely on Hiatt’s disclosure of a 3’-O-MOM capping group as
`
`teaching or suggesting the “R group” of claims 1 and 2, a capping group for
`
`reversibly blocking a nucleotide’s 3’-OH moiety during enzymatic DNA
`
`synthesis. See, e.g., Pet. 16–30. In the Allyl Claim IPR Decision, however,
`
`none of Petitioner’s asserted grounds relied upon Hiatt. See Ex. 1024 at 2–3
`
`(listing grounds). Further, as Patent Owner acknowledges (Prelim.
`
`Resp. 61), the Board’s statement regarding the scope of Hiatt’s disclosure
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`was not dispositive to the decision to find the claims in the Allyl Claim IPR
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`unpatentable. Nor did this statement form the foundation of the Board’s
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`reasoning in doing so. See Ex. 1024 at 35–67 (explaining reasoning
`
`regarding unpatentability). Accordingly, we are not persuaded that the
`
`arguments at issue regarding Hiatt were previously presented to the Office
`
`within the meaning of § 325(d). See Advanced Bionics, Paper 6 at 7–8.
`
`Therefore, weighing factors (a), (b), and (d) with regard to all four
`
`grounds at issue in this proceeding, we find that the statements Patent Owner
`
`cites, while pertinent to the teachings of Hovinen and Hiatt, do not
`
`sufficiently bear on the patentability determination of the claims at issue in
`
`the Allyl Claim IPR to be considered the “same or similar arguments” under
`
`Advanced Bionics. That these statements do not relate to half of the grounds
`
`at issue in this proceeding bolsters our conclusion. See SAS Q&A’s, Part D,
`
`Effect of SAS on Future Challenges that Could Be Denied for Statutory
`
`Reasons, D1 (June 5, 2018) (“SAS Q&A’s, Part D”), available at
`
`https://www.uspto.gov/sites/default/files/documents/sas_qas_20180605.pdf
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`(the Board “evaluate[s] the challenges and determine whether § 325(d) is
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`sufficiently implicated that its statutory purpose would be undermined by
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`instituting on all challenges”). Accordingly, we decline to exercise our
`
`discretion to deny institution.
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`b. LEVEL OF ORDINARY SKILL IN THE ART
`
`We consider the asserted grounds of unpatentability in view of the
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`understanding of a person of ordinary skill in the art. KSR Int’l Co. v.
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`Teleflex Inc., 550 U.S. 398, 399 (2007) (stating that obviousness is
`
`determined against the backdrop of the scope and content of the prior art, the
`
`differences between the prior art and the claims at issue, and the level of
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`ordinary skill in the art). Factual indicators of the level of ordinary skill in
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`13
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`the art include “the various prior art approaches employed, the types of
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`problems encountered in the art, the rapidity with which innovations are
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`made, the sophistication of the technology involved, and the educational
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`background of those actively working in the field.” Jacobson Bros., Inc. v.
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`U.S., 512 F.2d 1065, 1071 (Ct. Cl. 1975); see also Orthopedic Equip. Co. v.
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`U.S., 702 F.2d 1005, 1011 (Fed. Cir. 1983) (quoting with approval Jacobson
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`Bros.).
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`Petitioner contends that a person of ordinary skill in the art would
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`have “have been a member of a team of scientists developing nucleotide
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`analogues, researching DNA polymerases, and/or addressing DNA
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`sequencing techniques. Such a person would have held a doctoral degree in
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`chemistry, molecular biology, or a closely related discipline, and had at least
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`five years of practical academic or industrial laboratory experience.”
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`Pet. 13. Patent Owner does not dispute this definition for purposes of this
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`inter partes review. Prelim. Resp. 6.
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`In the second set of inter partes reviews, we adopted Petitioner’s
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`definition as set forth above. See Ex. 1024, 15. We see no reason to deviate
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`from that definition here. We have considered the contentions of the parties,
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`and for purposes of this decision on this record, we apply Petitioner’s
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`definition of a person of ordinary skill in the art.
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`c. CLAIM CONSTRUCTION
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`We construe claims using the same claim construction standard that
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`would be used to construe the claim in a civil action under 35 U.S.C.
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`§ 282(b). 37 C.F.R. § 42.100 (2019). Therefore, we construe the challenged
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`claims under the framework set forth in Phillips v. AWH Corp., 415 F.3d
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`1303, 1312–19 (Fed. Cir. 2005) (en banc). Under this framework, claim
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`terms are given their ordinary and customary meaning, as would be
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`understood by a person of ordinary skill in the art (“POSA”), at the time of
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`the invention, in light of the language of the claims, the specification, and
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`the prosecution history of record. Id. Only those terms that are in
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`controversy need be construed and only to the extent necessary to resolve
`
`the controversy. See Nidec Motor Corp. v. Zhongshan Broad Ocean Motor
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`Co. Matal, 868 F.3d 1013, 1017 (Fed. Cir. 2017) (citing Vivid Techs., Inc. v.
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`Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999)).
`
`Petitioner offers a construction of the term “allyl ether” as set forth in
`
`claim 2 of the ’742 patent (“wherein OR is not a methoxy group, an ester
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`group, or an allyl ether group”), see Pet. 12, and Patent Owner offers a
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`construction of the term “small” and assigns a “plain and ordinary meaning”
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`to the term “chemical linker,” see Prelim. Resp. 6–8. Petitioner asserts that
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`we should construe the term “allyl ether” to mean “—CH2CH==CH2,”
`
`which Petitioner asserts “does not exclude the known 2-methylallyl (–
`
`CH2C(Me)==CH2) and 3-methylallyl (—CH2CH=CH-CH3) ethers.” Pet. 12.
`
`We determine that it is not necessary to construe this term to decide whether
`
`to institute an inter partes review. There is no dispute on this record at this
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`stage of the proceeding that a methoxymethyl or “MOM” capping group,
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`i.e., -CH2OCH3 that Petitioner asserts meets the claim limitation for a 3’OH
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`capping moiety, is not an allyl ether. See Pet. 21; Prelim. Resp. 9; Reply 1
`
`(“On the merits, Columbia’s [Preliminary Response] concedes that the prior
`
`art meets all claim limitations.”); Ex. 1136, 5.
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`Patent Owner construes a “small” capping group to mean “a capping
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`group that is less than 3.7A in diameter.” Prelim. Resp. 6. Patent Owner
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`does not appear to challenge that a MOM capping group is “small.” Prelim.
`
`Resp. 9; Reply 1. In fact, the Specification of the ’742 patent identifies
`
`MOM as an appropriate capping group, along with allyl, that “can be used to
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`cap an —OH group, and can be cleaved chemically with high yield.”
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`Ex. 1004, 3:41–44 (citations omitted). Therefore, we determine that it is not
`
`necessary to construe this term to decide whether to institute an inter partes
`
`review.
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`Finally, although Patent Owner asserts that we need not construe the
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`claim phrase “chemical linker,” see Prelim. Resp. 6, Patent Owner offers a
`
`construction as the plain and ordinary meaning of the term as “the chemical
`
`structure, made up of one or more chemical groups, that links the base to the
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`tag.” Id. This construction contravenes the District Court’s construction in
`
`the parallel Delaware litigation that the chemical linker “Y” is “a single
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`linker that directly connects the base to the label.” Id. at 10. We find that
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`we need not expressly construe “chemical linker” here, as Patent Owner
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`does not dispute at this time that the asserted prior art teaches a chemical
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`linker as recited in the claims. See Prelim. Resp. 9–10; Reply 1.
`
`d. PATENTABILITY ANALYSIS
`
`i. Principles of Law
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`A patent claim is unpatentable under 35 U.S.C. § 103(a) if the
`
`differences between the claimed subject matter and the prior art are such 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, 550 U.S. at 406. The question of obviousness
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`is resolved on the basis of underlying factual determinations including:
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`(1) the scope and content of the prior art; (2) any differences between the
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`claimed subject matter and the prior art; (3) the level of ordinary skill in the
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`art; and (4) objective evidence of nonobviousness. Graham v. John Deere
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`Co., 383 U.S. 1, 17–18 (1966). “Both the suggestion and the expectation of
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`success must be founded in the prior art, not in the applicant’s disclosure.”
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`In re Dow Chemical Co., 837 F.2d 469, 473 (Fed. Cir. 1988).
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`In that regard, an obviousness analysis “need not seek out precise
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`teachings directed to the specific subject matter of the challenged claim, for
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`a court can take account of the inferences and creative steps that a person of
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`ordinary skill in the art would employ.” KSR, 550 U.S. at 418; see In re
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`Translogic Tech, Inc., 504 F.3d 1249, 1259 (Fed. Cir. 2007). In KSR, the
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`Supreme Court also stated that an invention may be found obvious if trying a
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`course of conduct would have been obvious to a POSA:
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`When there is a design need or market pressure to solve a
`problem and there are a finite number of identified, predictable
`solutions, a person of ordinary skill has good reason to pursue
`the known options within his or her technical grasp. If this leads
`to the anticipated success, it is likely the product not of
`innovation but of ordinary skill and common sense. In that
`instance the fact that a combination was obvious to try might
`show that it was obvious under § 103.
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`550 U.S. at 421. “KSR affirmed the logical inverse of this statement by
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`stating that § 103 bars patentability unless ‘the improvement is more than
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`the predictable use of prior art elements according to their established
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`functions.’” In re Kubin, 561 F.3d 1351, 1359–60 (Fed. Cir. 2009) (citing
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`KSR, 550 U.S. at 417).
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`We analyze the asserted grounds of unpatentability in accordance with
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`the above-stated principles. In making such an analysis, we find that
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`Petitioner has shown a reasonable likelihood of prevailing in establishing
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`that claims 1 and 2 of the ’742 patent are unpatentable.
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`ii. The Tsien Grounds
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`Petitioner asserts that claims 1 and 2 of the ’742 patent are
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`unpatentable over Tsien and Hiatt, or Tsien alone. Pet. 11. Petitioner
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`17
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`provides an analysis of how each claim limitation is taught by Tsien and
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`Hiatt and how a POSA would have reason to combine the teachings with a
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`reasonable expectation of success. Pet. 13–39. Petitioner relies on the
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`declaration of Dr. Romesberg in support of its positions. See Ex. 1131.
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`Patent Owner responds that one of skill in the art would not have had
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`a reason to choose the MOM capping group based on what was known about
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`SBS at the relevant time, and would have had no reasonable expectation of
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`success of efficient incorporation of the MOM capping group, as Tsien
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`requires. Prelim. Resp. 13–26. Patent Owner also asserts that one of skill in
`
`the art would have had no motivation “to combine Hiatt’s non-SBS methods
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`with Tsien’s or Dowers’ SBS methods to achieve the claimed nucleotides for
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`SBS.” Prelim. Resp. 26–44.
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`For the following reasons, we find that Petitioner has shown a
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`reasonable likelihood of success in establishing that claims 1 and 2 of the
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`’742 patent would have been obvious in light of the Tsien combinations.
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`We begin our analysis of Petitioner’s challenges with a description of the
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`pertinent teachings of the asserted art.
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`(1)
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`Tsien (Ex. 1031)
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`Tsien is titled “DNA Sequencing” and “relates to an instrument and a
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`method to determine the nucleotide sequence in a DNA molecule without
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`the use of a gel electrophoresis step.” Ex. 1031, at [54], [57]. Tsien
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`published on May 16, 1991, has an October 26, 1990, international filing
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`date and claims priority to an October 26, 1989, United States patent
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`application. Id. at [43], [22], [30].
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`Tsien describes an SBS method. Ex. 1131 ¶ 45; Ex. 2020 ¶ 25. In
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`particular, Tsien describes determining the sequence of a single stranded
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`DNA molecule by synthesizing the complementary DNA molecule.
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`Ex. 1031, 6:28–7:14. Tsien explains that deoxyribonucleotide triphosphates
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`(dNTP) are used to build up numerous copies of the complementary
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`molecule and that, as each dNTP is added, it is identified by a label. Id.
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