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`Paper No. _
`Filed: November 19, 2020
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`UNITED STATES PATENT AND TRADEMARK OFFICE
`_______________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`_______________
`
` ILLUMINA, INC.,
`Petitioner,
`
`v.
`
` THE TRUSTEES OF COLUMBIA UNIVERSITY
`IN THE CITY OF NEW YORK
`Patent Owner.
`_______________
`
`IPR2020-01177 (Patent 10,435,742)
`
`PATENT OWNER’S SUR-REPLY TO PETITIONER’S REPLY
`
`
`
`
`
`Case IPR2020-01177
`Patent No. 10,435,742
`
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`The Board should deny the Petition and confirm that Columbia’s claimed
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`“linker” can consist of multiple chemical groups stitched together.
`
`I.
`
`THE BOARD’S § 314(a) FINTIV FACTORS FAVOR DENYING INSTITUTION
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`All six Fintiv factors favor denying institution. Illumina’s Reply does not
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`address Fintiv factors 1 and 5 (likelihood of stay, identity of parties), which support
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`denying institution as previously explained. See Paper 12 at 54-56, 59. Regarding
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`Fintiv factor 2, Illumina admits that the Delaware trial date is earlier than the
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`projected statutory deadline for the relevant Final Written Decisions, but
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`characterizes the trial date as merely “tentatively scheduled[.]” That is wrong. The
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`Scheduling Order states that “[t]his matter is scheduled for a 5-day jury trial
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`beginning at 9:30 a.m. on November 15, 2021, with the subsequent trial days
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`beginning at 9:00 am.” Ex. 1154 at ¶ 25. Prior to Illumina’s Reply, neither the Court,
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`Columbia, nor Illumina has ever expressed doubt regarding the trial date.
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`Illumina’s COVID-19 conjecture should likewise be rejected. Illumina quotes
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`the current District of Delaware guidelines (“no more than one jury trial at a time”)
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`to speculate that the trial, which is scheduled to begin in 12 months, will be delayed.
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`Illumina also makes far too much of the “seven extensions” in the litigation. One
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`extended Illumina’s deadline to file its Answer, five extended claim construction
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`briefing deadlines, and the last extended the document production deadline. Exs.
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`1146-1152. Such extensions are routine in complex patent litigations, and they rarely
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`Patent No. 10,435,742
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`affect trial dates. Notably, here, the Markman hearing occurred as originally
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`scheduled despite the aforementioned extensions.
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`Further downplaying Fintiv factor 2, Illumina characterizes the trial date as
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`being only “three weeks” prior to the projected statutory deadline “in closely related
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`IPR2020-00988.” However, Illumina ignores the four related IPR proceedings
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`(IPR2020-01065, IPR2020-01125, IPR2020-01177, and IPR2020-01323), and that
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`the Delaware trial date is over two and a half months prior to the projected deadline
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`for the Final Written Decision in counterpart IPR2020-01323. See Paper 12 at 57.
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`Regarding Fintiv factor 3, Columbia’s Preliminary Response detailed the
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`significant resources already expended in the Delaware litigation. Illumina’s Reply
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`merely notes that “fact witness depositions” and “[e]xpert discovery” have yet to
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`occur, but the fact that additional discovery costs will be incurred says nothing about
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`whether significant resources have already been expended. They have, as Columbia
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`explained and Illumina failed to address. Illumina also belittles the number of
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`documents that Columbia has produced, but in fact Columbia has produced over
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`89,000 pages of documents, which were first produced in a related litigation and are
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`considered re-produced in the present litigation by agreement of the parties. Ex. 2046
`
`at ¶ 18.
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`Regarding Fintiv factor 4, Illumina admits that the obviousness grounds raised
`
`in its Petition have also been asserted in the Delaware litigation. While Illumina
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`Patent No. 10,435,742
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`hypothesizes that it could drop those obviousness grounds in the litigation, it has not
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`yet done so, and thus this factor favors denying institution. Regarding Fintiv factor
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`6, Illumina’s obviousness grounds are particularly weak, as previously explained.
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`Paper 12 at 59. Moreover, Illumina’s assertion that the claims are essentially the
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`same as those previously adjudicated in prior Illumina v. Columbia IPRs is belied
`
`by Illumina’s admission that it took almost eight months of “diligent[]” efforts for
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`Illumina to formulate the arguments in its current Petition.
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`II.
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`ILLUMINA’S PETITION SHOULD BE DENIED UNDER 35 U.S.C. § 325(d)
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`Notably, Illumina’s Reply does not dispute that its Petition re-raises
`
`arguments that the Board has previously declined to adopt concerning Sanger
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`sequencing and Hiatt, as set forth in Columbia’s Preliminary Response. Paper 12 at
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`60-61. In fact, Illumina’s Reply does not even address the Board’s prior findings or
`
`the 35 U.S.C. § 325(d) standard. Having no rebuttal to § 325(d), Illumina instead
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`improperly uses its Reply to raise new theories regarding the prior art in an attempt
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`to fix its deficient Petition. See, e.g., Paper 14 at 4 (raising new (and incorrect)
`
`argument regarding Kwiatkowski). Such tactics should be rejected.
`
`III. COLUMBIA’S “LINKER” COVERS MULTIPLE
`CHEMICAL GROUPS STITCHED TOGETHER
`
`Contrary to Illumina’s contention, Columbia is not seeking an “advisory claim
`
`construction,” but is merely confirming what (i) the Board previously found in this
`
`patent family and (ii) Illumina again confirmed in its Petition. Under § 103,
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`Case IPR2020-01177
`Patent No. 10,435,742
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`Illumina’s Petition must show that there was a reasonable expectation of success in
`
`making the claimed nucleotides. To meet that standard, Illumina contends in its
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`Petition that a POSA would synthesize the linker of the claimed nucleotides by
`
`stitching together an “alkynylamino group” and “a cleavable linker” group. Petition
`
`at 36-39. Illumina’s expert provides additional detail, explaining that a POSA would
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`synthesize the claimed linker by stitching together a “propargylamine group”
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`(another term for an alkynylamino group) and an “allyl linker” group. Ex. 1131 at ¶
`
`162. Illumina has previously depicted such a structure in its Petitions:
`
`
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`Ex. 2034 at 49 (Illumina’s IPR2018-00291 Petition, colored annotations added).
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`Thus, there can be no dispute that Illumina’s current Petition depends on the claimed
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`“linker” (as depicted in the green box above) covering a structure consisting of
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`multiple chemical groups, e.g., a propargylamine group (as depicted in the blue box
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`above) and an “allyl linker” group (as depicted in the red box above). See also Ex.
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`1131 at ¶ 200 (Dr. Romesberg explaining that a POSA would make the claimed
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`Case IPR2020-01177
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`linker via “the initial instalment of a propargyl amine [to the nucleotide base], with
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`the amine then used to attach the remainder of the linker”).
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`Thus, Columbia has simply repeated the meaning of linker previously
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`accepted in the prosecution history by the Board and by Illumina’s own expert.
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`Illumina, however, appears to be arguing that the meaning of linker is not a relevant
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`claim construction issue by asserting that “the Board found [that the claims are
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`invalid] whether the claims were directed to a ‘linker or linkers’.” Illumina’s attempt
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`to hide from its past and present arguments regarding the previously accepted
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`meaning of linker should not prevent this Panel from confirming that meaning. The
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`Board’s prior linker construction is clear.
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`Columbia requests that if the Board institutes trial, which for the reasons
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`explained in Columbia’s Preliminary Response, Dr. Johnson’s Declaration, and this
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`Sur-Reply it should not, the Board confirm that the claimed “linker” covers multiple
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`chemical groups stitched together. Illumina’s Petition depends on that plain and
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`ordinary construction, as explained above, and such a construction is consistent with
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`the Board’s and Federal Circuit’s prior findings. See Paper 12 at 6-11.
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`IV. CONCLUSION
`
`The Board should deny the Petition and confirm that Columbia’s claimed
`
`“linker” can consist of multiple chemical groups stitched together.
`
`
`
`Respectfully submitted,
`
`5
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`Case IPR2020-01177
`Patent No. 10,435,742
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`Dated: November 19, 2020
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`
`
`/ John P. White /
`By:
`John P. White, Reg. No. 28,678
`Lead Attorney for Patent Owner
`Cooper & Dunham LLP
`30 Rockefeller Plaza, 20th Floor
`New York, NY 10112
`Telephone: (212) 278-0400
`Fax: (212) 391-0525
`
`Gary J. Gershik, Reg. No. 39,992
`Cooper & Dunham LLP
`30 Rockefeller Plaza, 20th Floor
`New York, NY 10112
`Telephone: (212) 278-0400
`Fax: (212) 391-0525
`
`John D. Murnane, Reg. No. 29,836
`VENABLE LLP
`JDMurnane@Venable.com
`1290 Avenue of the Americas
`New York, NY 10104
`Telephone: (212) 218-2100
`Fax: (212) 218-2200
`
`Justin J. Oliver, Reg. No. 44,986
`VENABLE LLP
`JOliver@Venable.com
`600 Massachusetts Ave.
`Washington, D.C. 20001
`Tel: (202) 721-5423
`Fax: (212) 218-2200
`
`
`6
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`Case IPR2020-01177
`Patent No. 10,435,742
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`
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`CERTIFICATE OF SERVICE
`
`I hereby certify that a true and correct copy of the foregoing PATENT
`
`OWNER’S SUR-REPLY is being served on November 19, 2020, via email to
`
`Counsel for Petitioner at the email addresses below:
`
`
`
`Kerry S. Taylor
`Nathanael R. Luman
`Michael L. Fuller
`KNOBBE, MARTENS, OLSON
`& BEAR, LLP
`2040 Main Street, 14th Floor
`Irvine, CA 92614
`Email: BoxIllumina@knobbe.com
`
`
`Dated: November 19, 2020
`
`
`
`
`
`
`
`
`/ John P. White /
`By:
`John P. White, Reg. No. 28,678
`Lead Attorney for Patent Owner
`Cooper & Dunham LLP
`30 Rockefeller Plaza, 20th Floor
`New York, NY 10112
`Telephone: (212) 278-0400
`Fax: (212) 391-0525
`
`
`
`
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