Filed November 12, 2020
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`On behalf of Illumina, Inc.
`By: Kerry S. Taylor
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`Nathanael R. Luman
`Michael L. Fuller
`William R. Zimmerman (admitted pro hac vice)
`KNOBBE, MARTENS, OLSON & BEAR, LLP
`2040 Main Street, 14th Floor
`Irvine, CA 92614
`Fax: (858) 707-4001
`Tel.: (858) 707-4000
`Email: BoxIllumina@knobbe.com
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`UNITED STATES PATENT AND TRADEMARK OFFICE
`__________________________________
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`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`__________________________________
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`ILLUMINA, INC.
`Petitioner,
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`v.
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`TRUSTEES OF COLUMBIA UNIVERSITY
`IN THE CITY OF NEW YORK
`Patent Owner.
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`IPR2020-01177
`Patent 10,435,742
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`PETITIONER ILLUMINA’S REPLY TO
`PATENT OWNER’S PRELIMINARY RESPONSE
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`On behalf of Illumina, Inc.
`By: Kerry S. Taylor
`
`Nathanael R. Luman
`Michael L. Fuller
`William R. Zimmerman (admitted pro hac vice)
`KNOBBE, MARTENS, OLSON & BEAR, LLP
`2040 Main Street, 14th Floor
`Irvine, CA 92614
`Fax: (858) 707-4001
`Tel.: (858) 707-4000
`Email: BoxIllumina@knobbe.com
`
`
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`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.
`
`
`
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`IPR2020-01177
`Patent 10,435,742
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`PETITIONER ILLUMINA’S REPLY TO
`PATENT OWNER’S PRELIMINARY RESPONSE
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`Illumina v. Columbia
`IPR2020-01177 – Patent 10,435,742
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`
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`The Board should reject Columbia’s procedural challenges under 35 U.S.C.
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`§§ 314(a) and 315(d) and irrelevant commentary regarding claim construction.
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`I. The Board’s §314(a) Fintiv Factors Favor Institution
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`A. Fintiv Factor #6 (Compelling circumstances and the merits)
`The Board has extensive experience with the subject matter in this third-wave
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`of IPRs. A Final Written Decision (“FWD”) here would mark nearly a decade of
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`Board adjudication between identical parties, patent specifications, and Tsien and
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`Dower prior art. The claims at issue are identical to those previously adjudicated,
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`with a single negative limitation added. Pet.: 1-4. The Board is well-situated to
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`adjudicate this matter.
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`On the merits, Columbia’s POPR concedes that the prior art meets all claim
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`limitations. Columbia merely raises a similar grab-bag of arguments on motivation
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`and expectation-of-success that the Board adjudicated against Columbia in past
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`IPRs. Columbia’s retreat to those arguments demonstrates the Petition’s strength.
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`B. Fintiv Factors #1, 2, 3 and 5 (Likelihood of stay; Proximity of trial
`to FWD; Investment in parallel proceeding; Identity of parties)
`The district court tentatively scheduled a 5-day jury trial that would conclude
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`three weeks before the statutory deadline for a FWD in closely related IPR2020-
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`00988. Ex. 1154: 18. The district court case, however, has already required seven
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`extensions. See Exs. 1146-1153. The parties recently extended document production
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`by nearly two months. Ex. 1152. This extension is evidence of the parties’ limited
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`- 1 -
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`Illumina v. Columbia
`IPR2020-01177 – Patent 10,435,742
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`investment in the case so far. To date, Columbia has produced just 10 documents
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`that are non-duplicative with prior litigations. No fact witness depositions have been
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`scheduled. Expert discovery on the merits has not yet commenced.
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`Additional district court delays are likely. Columbia extended claim
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`construction briefing by filing a motion for reconsideration of the Markman Order.
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`Ex. 1159. This motion, coupled with the two-month document production delay,
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`could have a cascading effect to delay the remaining schedule. Ex. 1154: 19-20.
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`Further, COVID-19 has caused countless Delaware jury trials to be continued and
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`a backlog of trials because “it is anticipated that the Court will conduct no more than
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`one jury trial at a time and will give priority to criminal trials.” Ex. 1155 ¶¶1, 5.
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`District court uncertainty abounds, yet the Board has adhered to the 1-year statutory
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`deadline for issuing FWDs. Illumina’s request to have unpatentability tried in this
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`forum, which continues to provide date-certainty, should be given due consideration.
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`Illumina filed this IPR approximately nine months after the district court
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`complaint. This time period spanned early lockdown phases of COVID-19, during
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`which Illumina diligently evaluated the prosecution history, prior art, and substantial
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`body of prior litigation between the parties, interacted with its expert witness, and
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`drafted a meritorious IPR petition. Columbia argues that the timing of this IPR filing
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`was delayed for tactical advantage in the pending Federal Circuit appeal. POPR: 58.
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`Not true. While Columbia cited a single portion of this IPR Petition in its Federal
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`- 2 -
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`Illumina v. Columbia
`IPR2020-01177 – Patent 10,435,742
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`Circuit appeal (Ex. 1164: 3-4), it did so in a disingenuous attempt to confuse the
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`Federal Circuit; it misleadingly conflated concepts of 3’ protecting group cleavage
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`efficiency and nucleotide polymerase incorporation efficiency. Ex. 1165: 4-6; Ex.
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`1166: 3-4. Illumina gains no advantage from the timing of this IPR, as this patent
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`expired last month. Columbia’s quibble with timing is the product of its own choice
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`to assert unpatentable claims against Illumina in disjointed, multi-wave attacks over
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`the past decade, causing inevitable overlap of any number of dates.
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`C. Fintiv Factor #4 (Overlap of issues)
`Illumina’s district court invalidity contentions include multiple preliminary
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`invalidity grounds. A few of those grounds overlap with this IPR, while most do not.
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`Ex. 2004: 5-11. Whether the IPR grounds will overlap with those actually litigated
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`in district court remains uncertain given the early stages of the Delaware action.
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`II. The Board Should Reject Columbia’s §325(d) Arguments
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`Columbia seeks to evade Hovinen’s demonstration of efficient polymerase
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`incorporation of a substituted 3’-O-MOM group under §325(d). POPR: 60.
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`Columbia relies on the false premise that the POSA would myopically limit their
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`prior art considerations to one type of nucleotide sequencing, SBS, and exclude other
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`related sequencing techniques. Id. This premise is untenable. Columbia’s witness
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`agrees with Illumina that the POSA was broadly “researching DNA polymerases,
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`and/or addressing DNA sequencing techniques” and Columbia “does not dispute”
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`- 3 -
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`Illumina v. Columbia
`IPR2020-01177 – Patent 10,435,742
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`these interests. Ex. 2048 ¶21; Pet.: 13; POPR: 6; Ex. 1024: 42. Columbia concedes
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`that Hovinen was researching polymerase incorporation of substituted 3’-O-MOM
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`nucleotides. Ex. 2048 ¶57. Under the POSA’s agreed-upon interests, Hovinen (even
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`if viewed as a Sanger reference) provides significant motivation. Indeed, Tsien,
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`Dower, and Metzker demonstrate that the POSA routinely looked to Sanger
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`sequencing methods (such as Prober) to improve SBS given that both are
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`polymerase-based sequencing methods. See Ex. 1030: 14:53-56 (“analogous”),
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`25:4-12; Ex. 1031: 29:10-14; Ex. 1039: 4262 (“analogous”), 4266 (SBS nucleotides
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`“tested in a Sanger-type DNA sequencing scheme”); Ex. 1029: 20-22; Ex. 1092: 38-
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`39 (Dr. Ju’s lab admitting Sanger and SBS are integrable). Columbia’s argument
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`that a POSA would not pursue Hovinen’s substituted 3’-O-MOM nucleotides for
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`SBS is belied by its own prior art Exhibit 2021 (“Kwiatkowski”), which is an SBS
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`reference. Ex. 2021: 7:32-8:6 (citing Tsien); 3:18-37, 1:1-7; POPR: 46-47.
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`Kwiatkowski demonstrated that substituted 3’-O-MOM nucleotides are efficiently
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`incorporated by a polymerase. Ex. 2021: 17:11-18:29, Fig. 4 (compound 16).
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`Columbia also seeks to avoid Hiatt’s disclosure of 3’-O-MOM nucleotides for
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`polymerase incorporation under §325(d) because the Board previously stated that
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`Hiatt “presents an immense number of possibilities for the blocking group.” POPR:
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`60-61. Hiatt was filed in 1994, six years before the priority date of Columbia’s
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`patent. Columbia’s POPR seeks to anchor the POSA’s understanding of Hiatt to
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`- 4 -
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`Illumina v. Columbia
`IPR2020-01177 – Patent 10,435,742
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`what was known in 1994. The Petition, however, explains that the POSA in 2000
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`would have been informed of prior art advances that would have motivated the
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`pursuit of Hiatt’s 3’-O-MOM for polymerase-based DNA synthesis. See Petition:
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`32-36, 17-18, 46, 49-51, 61-63, 8-9. Section 325(d) does not apply.
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`III. Columbia’s Focus On “Chemical Linker” Is A Red Herring
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`The district court’s claim construction order does not affect the merits of the
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`Petition. See Pet.: 12-13. Columbia’s POPR provides a lengthy, irrelevant
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`discussion as to whether “chemical linker” is a single linker or can include a double
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`linker. POPR: 6-11. In a related IPR, Columbia argued that the linker term is
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`relevant to the expectation of success in making the linker. IPR2020-00988, Paper
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`17 at 4. But, in the FWD involving a patent with an identical [Y] limitation, the
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`Board found an invalidating expectation of success whether the claims were directed
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`to a “linker or linkers.” Ex. 1028: 58-59. Notably, Columbia agrees there is no need
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`to construe this term. See POPR: 6. Columbia’s discussion reflects its
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`dissatisfaction with the district court’s Markman Order and requests a contradictory
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`advisory claim construction from the Board on an issue that does not affect this IPR.
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`Worse yet, they did so while omitting the full claim construction briefing used by
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`the court. See Exs. 1156-1163. The Board should reject this attempt. Ex. 1024: 16.
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`IV. Conclusion
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`The Board should institute trial and dismiss Columbia’s arguments.
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`Illumina v. Columbia
`IPR2020-01177 – Patent 10,435,742
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`Respectfully submitted,
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`Dated: November 12, 2020
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`By: /Kerry Taylor/
`Kerry Taylor (Reg. No. 43,947)
`Nathanael R. Luman (Reg. No. 63,160)
`Michael L. Fuller (Reg. No. 36,516)
`William R. Zimmerman (admitted pro hac vice)
`KNOBBE, MARTENS, OLSON & BEAR, LLP
`Attorneys for Petitioner
`ILLUMINA, INC.
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`- 6 -
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`Illumina v. Columbia
`IPR2020-01177 – Patent 10,435,742
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`CERTIFICATE OF SERVICE
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`I hereby certify that a true and correct copy of the foregoing PETITIONER
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`ILLUMINA REPLY TO PATENT OWNER PRELIMINARY RESPONSE is
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`being served on November 12, 2020, via email, pursuant to agreement of the parties,
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`to counsel for the Trustees of Columbia University in the City of New York, at the
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`email addresses below:
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`John P. White
`jwhite@cooperdunham.com
`Gary J. Gershik
`ggershik@cooperdunham.com
`ColumbiaIPR@cooperdunham.com
`Cooper & Dunham, LLP
`30 Rockefeller Plaza, 20th Floor
`New York, NY 10112
`
`
`John D. Murnane
`VENABLE LLP
`jmurnane@venable.com
`1290 Avenue of the Americas
`New York, NY 10104
`
`Justin J. Oliver
`VENABLE LLP
`joliver@venable.com
`600 Massachusetts Ave.
`Washington, D.C. 20001
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`Dated: November 12, 2020
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`33639677
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`Respectfully submitted,
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`
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`By: /Kerry Taylor/
`Kerry Taylor (Reg. No. 43,947)
`Nathanael R. Luman (Reg. No. 63,160)
`Michael L. Fuller (Reg. No. 36,516)
`William R. Zimmerman (admitted pro hac vice)
`KNOBBE, MARTENS, OLSON & BEAR, LLP
`Attorneys for Petitioner
`ILLUMINA, INC.
`
`
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