Paper 20
`Trials@uspto.gov
`Entered: December 8, 2020
`571-272-7822
`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.
`
`IPR2020-00988
`Patent 10,407,458 B2
`
`
`
`
`
`
`
`
`
`Before SUSAN L. C. MITCHELL, JAMES A. WORTH, and
`MICHELLE N. ANKENBRAND, Administrative Patent Judges.
`MITCHELL, Administrative Patent Judge.
`
`DECISION
`Granting Institution of Inter Partes Review
`35 U.S.C. § 314
`
`
`
`
`
`
`
`
`Trials@uspto.gov
`Entered: December 8, 2020
`571-272-7822
`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.
`
`IPR2020-00988
`Patent 10,407,458 B2
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`
`
`
`
`
`
`
`
`Before SUSAN L. C. MITCHELL, JAMES A. WORTH, and
`MICHELLE N. ANKENBRAND, Administrative Patent Judges.
`MITCHELL, Administrative Patent Judge.
`
`DECISION
`Granting Institution of Inter Partes Review
`35 U.S.C. § 314
`
`
`
`
`
`
`
`
`
`IPR2020-00988
`Patent 10,407,458 B2
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`INTRODUCTION
`
`I.
`a. BACKGROUND
`On May 29, 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. 10,407,458 B2 (Ex. 1001, “the ’458
`patent”). See 35 U.S.C. §§ 311–319. On September 9, 2020, Trustees of
`Columbia University in the City of New York (“Patent Owner”) filed a
`Preliminary Response to the Petition. Paper 11 (“Prelim. Resp.”). On
`October 8, 2020, Petitioner filed an authorized Reply addressing discretion
`to institute under 35 U.S.C. §§ 314(a) and 325(d) and claim construction of
`the term “chemical linker.” Papers 13, 15 (“Reply”). On October 15, 2020,
`Patent Owner filed an authorized Sur-Reply responding to Petitioner’s
`statements concerning discretion to institute and claim construction. Papers
`13, 17 (“Sur-Reply”).
`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 the Petitioners have 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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`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.
`10,407,459; 10,457,984; 10,435,742; and 10,428,380. The petitions
`involving each of these patents are as follows: IPR2020-01065; IPR2020-
`01125; IPR2020-01177; and IPR2020-01323, respectively. Patent Owner
`asserted these patents in the parallel district court litigation, The Trustees of
`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
`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
`March 6, 2014) (Ex. 1021); Illumina, Inc. v. Trustees of the University of
`Columbia in the City of New York, IPR2012-00006, Paper 128 (PTAB
`March 6, 2014) (Ex. 1022); Illumina, Inc. v. Trustees of the University of
`Columbia in the City of New York, IPR2013-00011, Paper 130 (PTAB
`March 6, 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
`’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.
`
`3
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`Patent 10,407,458 B2
`72–73. The Board held claim 1 of the ’480 patent unpatentable over much
`of the same art asserted here in the second set of petitions Illumina filed
`against five patents including the ’480 patent. See Pet. 70–72; Ex. 1024, 76.
`Petitioner also asserts that claim 1 of the ’480 patent is “nearly identical to
`claims 1 and 2 of the ’458 patent” at issue here. Pet. 71. More specifically,
`Petitioner asserts that the only difference between the unpatentable claims of
`the ’480 patent and the ’458 patent “is that this latest set 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
`patents unpatentable. See Exs. 1024, 1028. Patent Owner has appealed
`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.
`Pet. 73–74; Paper 4, 2. The Board upheld the patentability of the challenged
`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
`Cambridge Ltd., 821 F.3d 1359 (Fed. Cir. 2016).
`d. THE ’458 PATENT (EX. 1001)
`The ’458 patent issued from a series of continuation applications, two
`of which issued as the ’575 and ’869 patents that were challenged in the first
`set of petitions Illumina filed. Ex. 1001, code (60) (stating the only two
`
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`applications in the priority chain that were not continuations were the
`earliest application and the second earliest application, neither of which
`matured into patents at issue in the series of inter partes reviews between
`Petitioner and Patent Owner). The ’458 patent issued September 10, 2019,
`subject to a terminal disclaimer, and is titled “Massive Parallel Method for
`Decoding DNA and RNA.” Id. (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 ’458 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. 1001, Abst. The nucleotide analogs described in the ’458 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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`Patent 10,407,458 B2
`a strand of DNA as it is synthesized using a complimentary DNA strand as a
`template. Id. at 3:44–54, 4:25–32.
`
`In describing the 3’-OH capping moiety, the Specification of the ’458
`patent provides that using small chemical moieties that can be easily cleaved
`chemically with high yield is desired because such nucleotide analogues
`incorporating such moieties “should also be recognized as substrates for
`DNA polymerase.” Id. at 3:22–26. The Specification of the ’458 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 ’458 patent, both of which
`are independent and are directed to a guanine deoxyribonucleotide
`analogues. Pet. Claim 1 is illustrative and recites:
`1.
`A guanine 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;
`wherein the covalent bond between the 3’-oxygen and R is stable
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`during a DNA polymerase reaction;
`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 guanine 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,
`(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 cytosine or a cytosine
` nucleotide analogue.
`Id. at 33:28–34:29.
`f. PRIOR ART AND ASSERTED GROUNDS OF
`UNPATENTABILITY
`Petitioner argues that claims 1 and 2 of the ’458 patent are
`unpatentable based on the following grounds:
`Claims Challenged
`35 U.S.C. §
`1, 2
`103(a)1
`
`References
`Tsien, 2 Prober,3 Hiatt4
`
`
`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 ’458 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 Prober et al., A System for Rapid DNA Sequencing with Fluorescent Chain-
`Terminating Dideoxynucleotides, 238 SCIENCE 336–41 (1987) (Ex. 1041,
`“Prober”).
`4 Hiatt et al., U.S. Patent No. 5,763,594, issued June 9, 1998 (Ex. 1043,
`“Hiatt”).
`
`7
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`References
`35 U.S.C. §
`Claims Challenged
`Dower, 5 Prober, Hiatt
`103(a)
`1, 2
`Tsien, Prober
`103(a)
`1, 2
`Dower, Prober, Metzker6
`103(a)
`1, 2
`Petitioner submits the Declaration of Floyd Romesberg, Ph.D., in
`
`support of its Petition. See Ex. 1038 (“the Romesberg Declaration”). Patent
`Owner submits the Declaration of Kenneth A. Johnson, Ph.D, in support of
`its arguments in the Preliminary Response. See Ex. 2020.
`II. ANALYSIS
`a. APPLICATION OF 35 U.S.C. § 314(A) – PATENT OWNER’S
`REQUEST FOR DISCRETIONARY DENIAL
`Institution of an inter partes review under 35 U.S.C. § 314(a) is
`discretionary. See 35 U.S.C. § 314(a) (stating “[t]he Director may not
`authorize an inter partes review to be instituted unless the Director
`determines that the information presented in the petition . . . shows that there
`is a reasonable likelihood that the petitioner would prevail with respect to at
`least 1 of the claims challenged in the petition” (emphasis added)); Cuozzo
`Speed Techs., LLC v. Lee, 136 S. Ct. 2131, 2140 (2016) (“[T]he agency’s
`decision to deny a petition is a matter committed to the Patent Office’s
`discretion.”); SAS Inst. Inc. v. Iancu, 138 S. Ct. 1348, 1356 (2018)
`(“[Section] 314(a) invests the Director with discretion on the question
`whether to institute review . . . .” (emphasis omitted)); Harmonic Inc. v. Avid
`
`
`5 Dower et al., U.S. Patent 5,547,839, issued Aug. 20, 1996 (Ex. 1030,
`“Dower”).
`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”).
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`Tech., Inc., 815 F.3d 1356, 1367 (Fed. Cir. 2016) (“[T]he PTO is
`permitted, but never compelled, to institute an IPR proceeding.”).
`Patent Owner asserts that we should exercise our discretion under
`section 314(a) because it “would be inefficient use of Board resources in
`light of a parallel district court litigation involving the same parties, the
`same claims, the same prior art, and the same invalidity arguments.”
`Prelim Resp. 50 (citing the Delaware litigation). Petitioner responds that:
`The Board has extensive experience with the subject
`matter in this third-wave of IPRs. A Final Written Decision
`(“FWD”) here would mark nearly a decade of Board
`adjudication between identical parties, patent specifications,
`and Tsien and Dower prior art. The claims at issue are
`identical to those previously adjudicated, with a single
`negative limitation added. Pet. 1–4. The instant panel retains
`two judges from the second-wave of IPRs and is well-situated
`to adjudicate this matter.
`Reply 1. Both parties provide a more detailed analysis applying the
`factors set forth in Apple Inc. v. Fintiv, Inc., IPR2020-00019, Paper 11
`(PTAB March 20, 2020) (precedential) (“Fintiv”), for determining
`whether we should exercise our discretion to deny the Petition. See
`Prelim. Resp. 50–55; Reply 1–5; Sur-Reply 1–3.
`
`Fintiv identifies the following factors that we should consider and
`weigh when a patent owner raises an argument for discretionary denial due
`to an earlier trial date in a parallel proceeding:
`1. whether the court granted a stay or evidence exists that
`one may be granted if a proceeding is instituted;
`2. proximity of the court’s trial date to the Board’s projected
`statutory deadline for a final written decision;
`3. investment in the parallel proceeding by the court and the
`parties;
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`4. overlap between issues raised in the petition and in the parallel
`proceeding;
`5. whether the petitioner and the defendant in the parallel
`proceeding are the same party; and
`6. other circumstances that impact the Board’s exercise of
`discretion, including the merits.
`Fintiv, Paper 11 at 5–6. According to Fintiv, these factors relate to
`“efficiency, fairness, and the merits” and require the Board to take “a
`holistic view of whether efficiency and integrity of the system are best
`served by denying or instituting review.” Id. at 6. Our analysis of the
`Fintiv factors is set forth below.
`Factor 1: Likelihood of a Stay
`i.
`Patent Owner notes that the district court in the Delaware litigation
`has not issued a stay, but does not indicate whether any party has sought
`such a stay or plans to seek such a stay should we institute an inter partes
`review. See Prelim. Resp. 51. Thus, this factor is neutral.
`Patent Owner touts that the Delaware litigation was filed over a year
`ago in September 2019, has a trial date earlier than the projected statutory
`deadline for the Final Written Decision in this case, and that the parties and
`the district court have expended significant resources in the parallel
`Delaware litigation. Id. at 51–52 (citing Ex. 2027; Ex. 2028). Patent
`Owner, however, does not explain how these facts are relevant to a stay in
`the Delaware litigation. We find these facts more relevant to the next two
`Fintiv factors and discuss them below.
`Factor 2: Proximity of Trial Date to the Board’s Projected
`ii.
`Statutory Deadline
`Patent Owner asserts that trial is scheduled to begin in the Delaware
`litigation on November 15, 2021, which is about three weeks prior to the
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`projected statutory deadline for our final written decision in this case. See
`Prelim. Resp. 52–53. Patent Owner asserts that the Board generally weighs
`this factor in favor of denying institution when the trial date of the parallel
`litigation is set before the projected statutory deadline for a final written
`decision. Id. at 53.
`Petitioner counters that the trial date may slip as the district court
`already has granted many extensions in the Delaware litigation and asserts
`that additional district court delays are likely. Reply 1–2 (citing Ex. 1154,
`18; Exs. 1146–1153). Specifically, Petitioner asserts that the parties have
`extended the deadline for completing document production by nearly two
`months, see Ex. 1152, and Patent Owner has filed a motion for
`reconsideration of the District Court’s Markman Order, causing further
`extension. Reply 1–2. Patent Owner responds that such extensions are
`routine in patent litigations and posits that they rarely affect trial dates. Sur-
`Reply 1–2.
`Because the trial date and the date of our final written decision are
`around the same time, our decision to institute implicates other factors, such
`as the investment factor. See Fintiv, Paper 11 at 9. Accordingly, we find
`that the close proximity of the trial date to our projected final written
`decision statutory deadline in this case weighs only marginally in favor of
`exercising our discretion to deny institution.
`Factor 3: Investment in Proceedings
`iii.
`Patent Owner asserts that the parties and the district court have
`expended significant resources in the Delaware litigation. Prelim. Resp. 51–
`52. Patent Owner details these efforts, indicating that Markman briefing is
`complete, the Markman hearing has been held, and the district court has
`issued a decision construing the claims. Id. at 52.
`
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`Petitioner counters that the district court extended the document
`production deadline by almost two months, indicating limited investment in
`the Delaware litigation, Patent Owner has produced just ten documents that
`are non-duplicative with prior litigations, no fact witness depositions have
`been scheduled, and no expert discovery on the merits has begun. Reply 1–
`2. Patent Owner responds that it has produced over 89,000 pages of
`documents, albeit documents previously produced in a related litigation and
`considered re-produced in the Delaware litigation by agreement of the
`parties. Sur-Reply 2.
`Petitioner also asserts that it promptly filed this request for an inter
`partes review about eight months after the Delaware litigation began, time
`which encompassed lockdown phases under the current pandemic. Reply 2.
`Patent Owner considers this eight-month delay in filing a petition for an
`inter partes review an attempt to gain a tactical advantage to avoid any
`opportunity for Patent Owner to evaluate the consistency of positions taken
`in the Petition at issue here as compared to Petitioner’s positions taken in the
`pending appeal of the immediately previous set of petitions. Prelim.
`Resp. 54.
`Fintiv provides the following guidance with respect to factor 3:
`[I]f, at the time of the institution decision, the district court has
`issued substantive orders related to the patent at issue in the
`petition, this fact favors denial. Likewise, district court claim
`construction orders may indicate that the court and parties
`have invested sufficient time in the parallel proceeding to
`favor denial. If, at the time of the institution decision, the
`district court has not issued orders related to the patent at issue
`in the petition, this fact weighs against exercising discretion to
`deny institution under NHK.
`Fintiv, Paper 11 at 9–10. Fintiv explains that “[t]his investment factor is
`related to the trial date factor, in that more work completed by the parties and
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`the court in the parallel proceeding tends to support the arguments that the
`parallel proceeding is more advanced, a stay may be less likely, and
`instituting would lead to duplicative costs.” Id. at 10.
`
`Although the Markman phase of the Delaware litigation is
`substantially complete, fact discovery appears to be in its early stages, and
`the parties have not yet begun expert discovery on the merits. As a result,
`we find that this factor weighs slightly in favor exercising our discretion
`to deny institution of a trial here. We do not consider the timing of the
`filing of the Petition here to weigh in favor of or against exercising our
`discretion to deny institution because we are not aware of any evidence
`that the Delaware litigation had progressed significantly at the time
`Petitioner filed the Petition. See Fintiv, Paper 11 at 11 (explaining how
`the timing of a petition’s filing may weigh in favor of or against
`exercising discretion to deny institution). In fact, Patent Owner’s
`summary of the Delaware litigation and the docket it submitted from the
`litigation indicate that the parties had served contentions, discovery
`requests, and responses to discovery requests, and that Markman briefing
`had not yet begun. See Prelim. Resp. 51–52; Ex. 2028, D.I. 25, 27, 28, 30
`(notice of service entries reflecting contentions, discovery requests, and
`responses to discovery requests), 47, 52, 53 (notice of service entries
`reflecting Markman briefing). Finally, we take no position concerning
`Patent Owner’s argument that Petitioner was seeking a tactical advantage
`through the timing of the Petition’s filing.
`Factor 4: Overlap of Issues
`iv.
`Patent Owner asserts that this Petition and the Delaware litigation
`“include identical patent claims, identical prior art, and substantially
`identical invalidity arguments.” Prelim. Resp. 54; compare Pet., with
`
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`Ex. 2004. Petitioner asserts that some grounds in the Delaware litigation
`“overlap with this IPR, while most do not.” Reply 3 (citing Ex. 2004, 5–11).
`Although the Delaware litigation appears to have far more invalidity
`contentions involving more art and combinations of that art than presented in
`the unpatentability grounds here, the grounds presented in the Petition here
`appear to overlap with those contentions. Compare Pet. 10–11, with
`Ex. 2004, 5–11. Thus, we find that this factor weighs in favor of exercising
`our discretion to deny institution.
`Factor 5: Whether the Petitioner and the Defendant in the
`v.
`Parallel Proceeding are the Same Party
`Petitioner is a party in the Delaware litigation. Prelim. Resp. 55.
`Therefore, this factor weighs in favor of exercising our discretion to deny
`institution.
`Factor 6: Other Circumstances, Including the Merits
`vi.
`Patent Owner asserts that the merits of this Petition “are particularly
`weak.” Prelim. Resp. 55. Patent Owner further states that:
`The Columbia inventors were the first to conceive the use of
`the MOM capping group for SBS, and Illumina has not
`argued otherwise. Thus, the present situation is unlike the
`Allyl Claim IPRs, where the prior art allegedly suggested the
`use of the allyl capping group (which Columbia continues to
`dispute on appeal). Here, despite a decade of efforts to
`practice SBS, it is undisputed that not a single researcher
`proposed the use of the MOM capping group for SBS.
`
`Id.
`
`Petitioner responds:
`The Board has extensive experience with the subject
`matter in this third-wave of IPRs. A Final Written Decision
`(“FWD”) here would mark nearly a decade of Board
`adjudication between identical parties, patent specifications,
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`and Tsien and Dower prior art. The claims at issue are
`identical to those previously adjudicated, with a single
`negative limitation added. Pet. 1–4. The instant panel retains
`two judges from the second-wave of IPRs and is well-situated
`to adjudicate this matter.
`Reply 1. Petitioner also asserts that Patent Owner presents arguments
`previously presented and adjudicated in past inter partes reviews, a
`position with which we agree. Id.; see supra Section I.c. (setting forth the
`relatedness of the ’458 patent to Patent Owner’s other patents that the
`Board previously adjudicated in several inter partes review proceedings
`between these same parties).
`
`Based on our review of the arguments and evidence presented on
`the preliminary record, as discussed below in Section II.e, we find that the
`strong merits weigh against exercising discretion to deny institution.
`Balancing the Fintiv Factors
`vii.
`We decline to exercise our discretion to deny the Petition under
`§ 314(a). We determine that the strength of the merits and history of IPR
`proceedings between Petitioner and Patent Owner involving substantially
`similar claims and prior art outweigh the other Fintiv factors. We agree with
`Petitioner that “[t]he claims deemed unpatentable in the second wave of
`IPRs are identical to the claims challenged in this IPR, with the exception
`that a single species of allyl capping group was removed from the claim
`genus.” Pet. 3; compare Ex. 1009, 34:2–35:4, with Ex. 1001, 33:29–35:4
`(adding the allyl proviso: “is not a –CH2CH==CH2 group” (claim 1) and “is
`not . . . an allyl ether group” (claim 2)). In evaluating the Fintiv factors with
`a holistic view, we are not persuaded to exercise discretion to deny
`institution of inter partes review.
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`b. APPLICATION OF 35 U.S.C. § 325(D) – PATENT OWNER’S
`REQUEST FOR DISCRETIONARY DENIAL
`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
`reliance in this proceeding on teachings from references Hovinen7 and Hiatt.
`See Prelim Resp. 55–57. First, Patent Owner argues that Petitioner’s
`contention in this case that a skilled artisan would have pursued use of the
`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
`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 55–56; 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. 56 (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.
`
`
`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-
`00318, IPR2018-00322, IPR2018-00385 Paper 67 at 32, (PTAB June 21,
`2018) (Ex. 1024) (“Allyl Claim IPR Decision” or “Allyl Claim IPR”).
`
`16
`
`
`
`IPR2020-00988
`Patent 10,407,458 B2
`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. 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. 56–57.
`
`Analysis
`If “another proceeding or matter involving the patent is before the
`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)).
`
`
`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.
`
`17
`
`
`
`IPR2020-00988
`Patent 10,407,458 B2
`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
`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;
`
`the extent to which the asserted art was evaluated during
`examination, including whether the prior art was the basis for
`rejection;
`
`(a)
`
`
`(b)
`
`
`(c)
`
`
`(d)
`
`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.
`
`18
`
`
`
`IPR2020-00988
`Patent 10,407,458 B2
`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
`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.
`
`Same or Substantially the Same Art or Arguments
`Previously Presented to the Office
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