Case: 19-2302 Document: 53 Page: 1 Filed: 09/25/2020
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`Appeal Nos. 2019-2302, -2303, -2304, -2305, -2452
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`IN THE UNITED STATES COURT OF APPEALS
`FOR THE FEDERAL CIRCUIT
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`THE TRUSTEES OF COLUMBIA UNIVERSITY
` IN THE CITY OF NEW YORK,
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`v.
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`ILLUMINA, INC.,
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`Appellant,
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`Appellee.
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`Appeals from the United States Patent and Trademark Office, Patent Trial and
`Appeal Board in Nos. IPR2018-00291, IPR2018-00318, IPR2018-00322,
`IPR2018-00385, and IPR2018-00797
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`OPPOSITION TO APPELLANT’S MOTION FOR JUDICIAL NOTICE
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`Edward R. Reines
`Derek C. Walter
`WEIL, GOTSHAL & MANGES LLP
`201 Redwood Shores Parkway
`Redwood Shores, CA 94065
`(650) 802-3000
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`Brian G. Liegel
`WEIL, GOTSHAL & MANGES LLP
`1395 Brickell Avenue, Suite 1200
`Miami, FL 33131
`(305) 577-3100
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`Counsel for Appellee Illumina, Inc.
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`September 25, 2020
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`Illumina Ex. 1165
`Illumina v. Columbia
`IPR2020-01177
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`Case: 19-2302 Document: 53 Page: 2 Filed: 09/25/2020
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`CERTIFICATE OF INTEREST
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`Counsel for Appellee Illumina, Inc., certifies the following:
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`1.
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`The full name of every party or amicus represented by us is:
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` Illumina, Inc.
`The name of the real party in interest represented by us is:
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`2.
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` Illumina, Inc.
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`All parent corporations and any public companies that own 10 percent
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`3.
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`or more of the stock of the parties represented by us are:
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` None
`The names of all law firms and the partners or associates that
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`4.
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`appeared for the parties now represented by us in the trial court or are expected to
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`appear in this Court are:
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` WEIL, GOTSHAL & MANGES, LLP: Edward R. Reines, Derek C.
`Walter, Brian G. Liegel
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` KNOBBE, MARTENS, OLSON & BEAR, LLP: Kerry S. Taylor,
`Michael L. Fuller, William R. Zimmerman, Nathanael R. Luman
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`The title and number of any case known to counsel to be pending in
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`5.
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`this or any other court or agency that will directly affect or be directly affected by
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`this Court’s decision in the pending appeal:
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`i
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`Case: 19-2302 Document: 53 Page: 3 Filed: 09/25/2020
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` The Trustees of Columbia University in the City of New York et al. v.
`Illumina, Inc., No. 17-cv-00973 (D. Del.).
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` The Trustees of Columbia University in the City of New York et al. v.
`Illumina, Inc., No. 1:19-cv-01681 (D. Del.)
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` Illumina, Inc. v. The Trustees of Columbia University in the City of
`New York, PTAB-IPR2020-01323
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` Illumina, Inc. v. The Trustees of Columbia University in the City of
`New York, PTAB-IPR2020-01177
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` Illumina, Inc. v. The Trustees of Columbia University in the City of
`New York, PTAB-IPR2020-01125
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` Illumina, Inc. v. The Trustees of Columbia University in the City of
`New York, PTAB-IPR2020-01065
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` Illumina, Inc. v. The Trustees of Columbia University in the City of
`New York, PTAB-IPR2020-00988
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`Dated: September 25, 2020
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`/s/ Edward R. Reines
`Edward R. Reines
`WEIL GOTSHAL & MANGES LLP
`201 Redwood Shores Parkway
`Redwood Shores, CA 94065
`Telephone: (650) 802-3000
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`Counsel for Appellee
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`ii
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`Case: 19-2302 Document: 53 Page: 4 Filed: 09/25/2020
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`Illumina, Inc. (“Illumina”) respectfully submits this Opposition to Appellant
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`The Trustees of Columbia University in the City of New York’s (“Columbia”)
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`Motion for Judicial Notice. (D.I. 51 in 19-2302) (the “Motion”).
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`ARGUMENT
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`I.
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`COLUMBIA’S REQUEST FOR JUDICIAL NOTICE IS IMPROPER
`“[A]ppellate review in § 141 proceedings is confined to the record before the
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`PTO.” Nantkwest, Inc. v. Iancu, 898 F.3d 1177, 1180 (Fed. Cir. 2018); see also 35
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`U.S.C. § 144. Columbia nevertheless asks this Court to consider the merits of new
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`“evidence” on appeal. But this Court’s “review of the Board’s decision is confined
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`to the four corners of the record.” Novartis AG v. Torrent Pharm. Ltd., 853 F.3d
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`1316, 1329 (Fed. Cir. 2017) (internal quotations and citations omitted).
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`Courts have long rejected attempts to use judicial notice to circumvent these
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`foundational principles. See Holmes v. Kelly, 586 F.2d 234, 237 (C.C.P.A. 1978)
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`(“Since this court is bound by 35 U.S.C. § 144 to determine appeals ‘on the evidence
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`produced before the Patent and Trademark Office,’ we decline to take judicial notice
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`of the patents submitted by Holmes in his reply brief.”) (internal citation omitted);
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`Application of Lemin, 408 F.2d 1045, 1049 (C.C.P.A. 1969) (rejecting request to
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`“judicially notice and consider the technical publications presented with the request
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`for reconsideration” because it is the “established practice of this court not to
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`1
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`Case: 19-2302 Document: 53 Page: 5 Filed: 09/25/2020
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`consider evidence not considered by the tribunals below since we do not have the
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`benefit of their views thereon”).
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`Columbia’s motion relies on authority that establishes only that the Court may
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`take judicial notice of the fact of agency filings at any stage of the proceeding. See
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`Motion at 4 (“the fact of their filing cannot be reasonably questioned”) (emphasis
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`added). Yet, Columbia’s request goes far beyond this. Columbia improperly asks
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`this Court to evaluate new materials and make factual determinations about the
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`substance of those materials.
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`Rule 201 does not permit that. In Ultratec, Inc. v. CaptionCall, LLC, 872 F.3d
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`1267, 1274 n.6 (Fed. Cir. 2017), this Court rejected an indistinguishable attempt to
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`misuse judicial notice. There, also in an appeal from a PTAB decision, the appellee
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`asked this Court to consider trial testimony from a parallel district court proceeding
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`by taking judicial notice of it. Id. Like Columbia, the appellee encouraged this
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`Court to “take judicial notice of the testimony and determine in the first instance
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`whether it was consistent with [the declarant’s] IPR declarations.” Id. This Court
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`squarely rejected the judicial notice request because it “does not have authority . . .
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`to review evidence not considered by the agency and make factual determinations
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`about the substance of that evidence.” Id.
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`This Court has previously confirmed the importance of the “limits imposed
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`by Rule 201(b)(2)” which permit it to consider “only the fact” that a filing was made,
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`2
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`Case: 19-2302 Document: 53 Page: 6 Filed: 09/25/2020
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`not the substance of the argument. See VirtualAgility Inc. v. Salesforce.com, Inc.,
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`759 F.3d 1307, 1312 (Fed. Cir. 2014) (“We consider only the fact that a Motion to
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`Amend was filed – not the impact of the proposed amendments on the parties’ claim
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`construction and infringement arguments. The latter cannot be ‘accurately and
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`readily determined from sources whose accuracy cannot reasonably be
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`questioned.’”) (quoting Fed. R. Evid. 201(b)(2)) (emphasis in original).1 Columbia
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`elides this important distinction. Indeed, the Motion confesses that the entire
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`purpose is to demonstrate that the substance of the statements purportedly “are
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`incompatible with, and therefore undercut, Illumina’s arguments in the present
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`appeals.” Motion at 1. This argument is wrong as a matter of fact, as discussed
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`below. But, importantly, it is also wrong as a matter of procedure. This improper
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`request should be denied.
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`1  Columbia’s cases confirm this. For example, the complete quotation in Old
`Reliable Wholesale, Inc. v. Cornell Corp., 635 F.3d 539, 549 (Fed. Cir. 2011) reads:
`“Although the results of the PTO reexamination proceedings were not available to
`the district court, this court can take judicial notice of the fact that the PTO, after
`assessing the relevant prior art, issued a notice of intent to issue a reexamination
`certificate confirming the patentability of all claims of the ’950 patent.” Id.
`(emphasis added). And, like Old Reliable, Function Media and Los Angeles
`Biomedical each consider only undisputed legal acts established by docket filings.
`See Function Media, L.L.C. v. Google, Inc., 708 F.3d 1310, 1316 n.4 (Fed. Cir. 2013)
`(judicial notice of fact of examiners decision and Board’s affirmance); Los Angeles
`Biomedical Res. Inst. at Harbor-UCLA Med. Ctr. v. Eli Lilly & Co., 849 F.3d 1049,
`1061 n.6 (Fed. Cir. 2017) (judicial notice of infringement contentions in district
`court). And, in Uniloc USA, Inc. v. ADP, LLC, 772 F. App’x 890, 898, n.3 (Fed.
`Cir. 2019), this Court was clear that the prosecution history was part of the record. 
`3
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`Case: 19-2302 Document: 53 Page: 7 Filed: 09/25/2020
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`II. THE “NEW” MATERIALS ARE MEANINGLESS TO THE ISSUES IN
`THIS APPEAL AND THUS THE MOTION SHOULD BE DENIED
`The materials that are the subject of this judicial notice request are
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`meaningless to this appeal. This is an independent reason to deny Columbia’s
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`motion.
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`The PTAB correctly found Metzker teaches that “increasing concentration can
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`resolve certain incorporation issues,” and, accordingly a skilled artisan following
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`Metzker’s instruction to increase nucleotide concentrations would reasonably have
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`expected to achieve complete termination and efficient incorporation. See Appx44,
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`Illumina’s Response Brief D.I. 30 in 19-2302 (April 13, 2020) at 25-26. Beyond
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`Metzker, the PTAB also relied on Canard – a paper cited by Columbia – as support
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`for this proposition. See Appx113 (“Canard . . . indicates that higher concentration
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`levels can reach high incorporation levels where a chain terminator is inefficient.”).
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`Columbia’s own expert conceded this fact as well. Appx6812 at 6-11. So despite
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`whatever Columbia now alleges about Metzker, Canard and Columbia’s own expert
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`admission constitute ample evidence to support the IPR decision under review.
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`But even on its own terms, Columbia’s attack on the teaching of Metzker is
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`misleading because Columbia obfuscates incorporation and cleavage. Throughout
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`this proceeding, Columbia has consistently (and correctly) recognized that
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`incorporating a chemical group into a molecule fundamentally differs from cleaving
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`4
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`Case: 19-2302 Document: 53 Page: 8 Filed: 09/25/2020
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`it off. See Appx2153; Appx2168. Yet, its Motion wrongly conflates these distinct
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`concepts.
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`First, Columbia relies on a statement Illumina made in IPR2020-00988, but
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`via selective quotation, portrays it as relating to incorporation when it actually relates
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`to cleavage. Illumina states in that IPR that the methoxy group in Metzker could not
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`be effectively cleaved “under DNA-compatible conditions” as required for the
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`cleavage step of sequencing-by-synthesis (SBS) method at issue. Appellants’
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`ExhibitA_00068-ExhibitA_00069 (“cleavability concerns would have given a
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`POSA a reason to avoid a methoxy group as a reversible 3’-capping group for SBS”).
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`But Illumina never suggested that increasing the concentration of blocking groups
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`such as methoxy (as Metzker encourages) would be unsuccessful to increase
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`incorporation.
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`Likewise, the portion of Dr. Romesberg’s opinion relied upon by Columbia
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`was similarly discussing the inadequacy of a methoxy group for the cleavability
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`required for SBS; he did not challenge that increasing the concentration of a blocking
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`group would improve incorporation of that group. See Appellants’ ExhibitB_00112
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`(discussing that another blocking group “would be more easily cleaved than a methyl
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`ether”). Although Metzker suggests that methoxy is unsuitable for SBS because it
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`is not cleavable, that has nothing to do with whether increasing the concentration of
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`a blocking group would lead to effective incorporation.
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`5
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`Case: 19-2302 Document: 53 Page: 9 Filed: 09/25/2020
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`Therefore, even weighing the “new” materials, the PTAB’s determination is
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`comfortably supported by substantial evidence. Because these materials are
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`irrelevant, the motion should be denied for this additional reason.
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`CONCLUSION
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`For the reasons stated, Appellant’s motion should be denied.
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`Dated: September 25, 2020
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`Respectfully submitted,
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`/s/ Edward R. Reines
`Edward R. Reines
`Derek C. Walter
`WEIL, GOTSHAL & MANGES LLP
`201 Redwood Shores Parkway
`Redwood Shores, CA 94065
`(650) 802-3000
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`Brian G. Liegel
`WEIL, GOTSHAL & MANGES LLP
`1395 Brickell Avenue, Suite 1200
`Miami, FL 33131
`(305) 577-3100
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`Counsel for Appellee
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`Case: 19-2302 Document: 53 Page: 10 Filed: 09/25/2020
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`CERTIFICATE OF COMPLIANCE
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`The undersigned certifies that this brief complies with the type-volume
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`limitations of Federal Rule of Appellate Procedure 27(d)(2) because it contains
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`1,247 words.
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`The undersigned further certifies that this brief complies with the typeface
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`requirements of Fed. R. App. P. 32(a)(5) and the type style requirements of Fed. R.
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`App. P. 32(a)(6). This brief has been prepared in a proportionally spaced typeface
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`using Microsoft Word in Times New Roman 14-point font.
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`Dated: September 25, 2020
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`/s/ Edward R. Reines
`Edward R. Reines
`WEIL GOTSHAL & MANGES LLP
`201 Redwood Shores Parkway
`Redwood Shores, CA 94065
`Telephone: (650) 802-3000
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`Counsel for Appellee
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`7
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