`
`On behalf of Illumina, Inc.
`By: Kerry S. Taylor
`
`Nathanael R. Luman
`Michael L. Fuller
`William R. Zimmerman (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
`
`
`
`
`
`
`
`
`
`
`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
`IPR2020-01065 Patent 10,407,459
`IPR2020-01177 Patent 10,435,742
`IPR2020-01125 Patent 10,457,984
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`ILLUMINA’S OBJECTIONS TO ADMISSIBILITY OF
`COLUMBIA EVIDENCE FILED WITH PATENT OWNER’S RESPONSE
`
`An identical paper is being filed in each of the above four proceedings.
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`
`
`Pursuant to 37 C.F.R. § 42.64(b)(1), Petitioner Illumina, Inc., timely objects
`
`to the admissibility of evidence submitted by Patent Owner Trustees of Columbia
`
`University in the City of New York with its Response to the petition.
`
`Objections
`
`Incomplete, Relevance, Misleading (FRE 106,
`401, 403):
`The document does not stand for the proposition for
`which it is cited as supposed admissions made by
`Illumina. In addition, to the extent that Columbia is
`relying upon statements regarding supposed
`admissions made by Illumina, such reliance is
`misleading because Columbia has mischaracterized
`the statements made in this document and has taken
`statements out of context. Also, the excerpts provide
`an incomplete version of the reexamination
`proceeding that, when taken in isolation, are
`misleading in the manner in which they are used.
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`
`Exhibit Number and
`Description
`2054 - Excerpts from the
`Ex Parte Reexamination
`History of U.S. Patent
`No. 5,808,045
`
`2059 - Tabor, S. & C. C.
`Richardson, “A single
`residue in DNA
`polymerases of the
`Escherichia coli DNA
`polymerase I family is
`critical for distinguishing
`between deoxy- and
`dideoxyribonucleotides,”
`Proc. Natl. Acad. Sci.
`U.S.A., 92(14):6339-
`6343 (1995)
`
`- 1 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`Relevance, Misleading (FRE 106, 401, 402,
`403):
`
` ¶
`
` 24 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes enzyme
`fidelity and utility for sequencing-by-synthesis.
`
`¶¶ 26-27 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the patents-at-issue.
`
` 28 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of the prior art.
`
` ¶
`
` ¶
`
` 29 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited, contradicts prior findings by the Board,
`and improperly mischaracterizes the teachings of the
`prior art.
`
` ¶
`
` 30 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of the prior art.
`
`¶¶ 33-38 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the teachings of Metzker and the testimony of Dr.
`Romesberg.
`
` ¶
`
` 39 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of the prior art.
`
`
`- 2 -
`
`2071 - Declaration of
`Kenneth A. Johnson,
`March 30, 2021,
`IPR2020-00988, -01065,
`-01125, -01177, -01323
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`¶¶ 40-41 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the teachings of Hovinen and/or Kwiatkowski.
`
`¶¶ 43-49 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the teachings of Metzker and/or Canard.
`
` ¶
`
` 50 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of the prior art.
`
` ¶
`
` 52 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of Hovinen, Kwiatkowski, and Metzker.
`
` ¶
`
` 53 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of the prior art.
`
` ¶
`
` 54 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of Greene and Wuts and the teachings of
`the prior art.
`
` ¶
`
` ¶
`
` 55 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of Tsien.
`
` 56 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`
`- 3 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`teachings of the cited references and that of the prior
`art.
`
`¶¶ 58-63 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the teachings of Hiatt.
`
`¶¶ 64-65 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`sequencing-by-synthesis.
`
`¶¶ 68-75 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the teachings of the cited references, sequencing-by-
`synthesis, and the testimony of Dr. Romesberg.
`
`¶¶ 77-78 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the teachings of Tsien, Hiatt, and the prior art.
`
`¶¶ 80-81 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the teachings of Tsien and the other cited references.
`
` ¶
`
` 82 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of Metzker.
`
`¶¶ 84-88 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the teachings of the cited references.
`
`
`- 4 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`¶¶ 90-100 are misleading, incomplete, and irrelevant
`because they lack support for the contentions for
`which they are cited and improperly mischaracterize
`the teachings of Hiatt.
`
`¶¶ 103-105 are misleading, incomplete, and
`irrelevant because they lack support for the
`contentions for which they are cited and improperly
`mischaracterize the teachings of Hiatt.
`
`¶¶ 107-109 are misleading, incomplete, and
`irrelevant because they lack support for the
`contentions for which they are cited and improperly
`mischaracterize the teachings of Tsien and Dower.
`
` 110 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`testimony of Dr. Romesberg.
`
` ¶
`
` ¶
`
` 112 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`testimony of Dr. Romesberg and the teachings of
`Tsien.
`
` ¶
`
` 114 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`testimony of Dr. Romesberg and the documents in
`this proceeding.
`
`¶¶ 115-116 are misleading, incomplete, and
`irrelevant because they lack support for the
`contentions for which they are cited and improperly
`mischaracterize the teachings of the cited references.
`
` ¶
`
` 117 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`
`- 5 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`it is cited and improperly mischaracterizes the
`teachings of Hiatt.
`
`¶¶ 118-119 are misleading, incomplete, and
`irrelevant because they lack support for the
`contentions for which they are cited and improperly
`mischaracterize the teachings of Hovinen.
`
` ¶
`
` 120 is misleading, incomplete, and irrelevant
`because it lacks support for the contentions for which
`it is cited and improperly mischaracterizes the
`teachings of Tsien.
`
`¶¶ 121-122 are misleading, incomplete, and
`irrelevant because they lack support for the
`contentions for which they are cited and improperly
`mischaracterize the patents-at-issue.
`
`Improper Testimony by Expert Witness (FRE
`702):
`¶ 24 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
`¶¶ 26-27 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
` ¶
`
` 28 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
` ¶
`
` ¶
`
` 29 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
` 30 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
`
`- 6 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`¶¶ 33-38 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
` ¶
`
` 39 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
`¶¶ 40-41 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`¶¶ 43-49 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
` ¶
`
` 50 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
` 52 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
` ¶
`
` ¶
`
` 53 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
` ¶
`
` 54 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
` ¶
`
` 55 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
` ¶
`
` 56 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
`
`- 7 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`¶¶ 58-63 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`¶¶ 64-65 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`¶¶ 68-75 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`¶¶ 77-78 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`¶¶ 80-81 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
` ¶
`
` 82 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
`¶¶ 84-88 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`¶¶ 90-100 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`¶¶ 103-105 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`¶¶ 107-109 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`
`- 8 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`Exhibit Number and
`Description
`
`Objections
`
`¶ 110 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
` ¶
`
` 112 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
` ¶
`
` 114 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
`¶¶ 115-116 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
` ¶
`
` 117 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
`¶¶ 118- are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
` ¶
`
` 120 is not based on sufficient facts and data, and
`does not reliably apply facts and data using
`scientific principles.
`
`¶¶ 121-122 are not based on sufficient facts and
`data, and do not reliably apply facts and data
`using scientific principles.
`
`- 9 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`Exhibit Number and
`Description
`2072 - Deposition
`Transcript for Videotaped
`Deposition of Floyd
`Romesberg, Ph.D., March
`15, 2021, IPR2020-
`00988, -01065, -01125, -
`01177, -01323
`2074 - EP 3 034 627
`(“Columbia’s EP’627
`patent”)
`
`2075 - Illumina’s October
`29, 2019 Opposition
`against Columbia’s
`EP’627 patent
`
`2076 - Illumina’s March
`25, 2021 Response in
`support of its Opposition
`against Columbia’s
`EP’627 patent
`
`Objections
`
`Misleading (FRE 403):
`Columbia’s citations to selected portions of this
`document are taken out of context and misleading.
`
`Relevance, Misleading (FRE 401, 403):
`Columbia’s reliance on this document is misleading
`because the document relates to European patent
`law.
`
`Hearsay (FRE 802):
`The exhibit includes out-of-court statements offered
`for the truth of the matter asserted.
`Incomplete, Relevance, Misleading (FRE 106,
`401, 403):
`This document, when taken in isolation, provides an
`incomplete version of the European Opposition
`proceeding. Further, Columbia’s reliance on this
`document is misleading because the document
`relates to European patent law that does not
`correspond with U.S. patent law. Also, Columbia’s
`citations to selected portions of this document are
`taken out of context and misleading.
`
`Hearsay (FRE 802):
`The exhibit includes out-of-court statements offered
`for the truth of the matter asserted.
`Incomplete, Relevance, Misleading (FRE 106,
`401, 403):
`This document, when taken in isolation, provides an
`incomplete version of the European Opposition
`proceeding. Further, Columbia’s reliance on this
`document is misleading because the document
`relates to European patent law that does not
`correspond with U.S. patent law. Also, Columbia’s
`
`- 10 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`Exhibit Number and
`Description
`
`Objections
`
`2077 - U.S. Patent No.
`7,057,026 (“Barnes”)
`
`2078 - Johnson, K. A.,
`“Conformational
`coupling in DNA
`polymerase fidelity,”
`Annu. Rev. Biochem.,
`62:685-713 (1993)
`2079 - Preliminary
`Opinion of Opposition
`Division re: Illumina’s
`Opposition against
`Columbia’s EP’627
`patent
`
`citations to selected portions of this document are
`taken out of context and misleading.
`
`Hearsay (FRE 802):
`The exhibit includes out-of-court statements offered
`for the truth of the matter asserted.
`Relevance (FRE 401, 403):
`The date markings on this document are after the
`asserted priority date of Columbia’s patents.
`Columbia’s reliance on this document is misleading
`because the document does not represent the
`knowledge of a person of ordinary skill in the art at
`the time of Columbia’s alleged invention.
`
`Hearsay (FRE 802):
`The exhibit includes out-of-court statements offered
`for the truth of the matter asserted.
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`
`Incomplete, Relevance, Misleading (FRE 106,
`401, 403):
`This document, when taken in isolation, provides an
`incomplete version of the European Opposition
`proceeding. Further, Columbia’s reliance on this
`document is misleading because the document
`relates to European patent law that does not
`correspond with U.S. patent law.
`
`Hearsay (FRE 802):
`The exhibit includes out-of-court statements offered
`for the truth of the matter asserted.
`
`- 11 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`Exhibit Number and
`Description
`2080 - Sluis-Cremer, N.,
`D. Arion & M. A.
`Parniak, “Molecular
`mechanisms of HIV-1
`resistance to nucleoside
`reverse transcriptase
`inhibitors (NRTIs),” Cell
`Mol Life Sci,
`57(10):1408-1422 (2000)
`2081 - Koshland JR., D.
`E., “Enzyme flexibility
`and enzyme action,”
`Journal of Cellular and
`Comparative Physiology
`54(S1):245-258 (1959)
`2082 - IPR2018-00291, -
`00318, -00322, -00385, -
`00797, March 5, 2019
`Oral Hearing Transcript
`(Paper 62)
`
`2083 - Timsit, Y, “DNA
`structure and polymerase
`fidelity,” J Mol Biol,
`293(4):835-853 (1999)
`2084 - Goodman, M. F.
`& D. K. Fygenson,
`“DNA polymerase
`fidelity: From genetics
`toward a biochemical
`understanding,” Genetics,
`148(4):1475-1482 (1998)
`
`Objections
`
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`
`Incomplete, Relevance, Misleading (FRE 106,
`401, 403):
`This document, when taken in isolation, provides an
`incomplete version of the previous IPR proceeding.
`In addition, Columbia’s citations to selected portions
`of this document are taken out of context and
`misleading.
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`
`- 12 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`Objections
`
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`
`Exhibit Number and
`Description
`2085 - Goodman, M. F.
`& B. Tippin, “Sloppier
`copier DNA polymerases
`involved in genome
`repair,” Curr Opin Genet
`Dev, 10(2):162-168
`(2000)
`2086 - Kunkel, T. A.,
`“The mutational
`specificity of DNA
`polymerasebeta during in
`vitro DNA synthesis.
`Production of frameshift,
`base substitution, and
`deletion mutations,” J
`Biol Chem, 260(9):5787-
`5796 (1985)
`2087 - Wong, I., S. S.
`Patel & K. A. Johnson,
`“An induced-fit kinetic
`mechanism for DNA
`replication fidelity: direct
`measurement by single-
`turnover kinetics,”
`Biochemistry, 30(2):526-
`537 (1991)
`
`- 13 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`Objections
`
`Relevance (FRE 401, 403):
`This exhibit is not cited to or otherwise relied upon
`in Patent Owner’s Response and therefore lacks
`relevance.
`
`Exhibit Number and
`Description
`2088 - Tan, X., C. K. Chu
`& F. D. Boudinot,
`“Development and
`optimization of anti-HIV
`nucleoside analogs and
`prodrugs: A review of
`their cellular
`pharmacology, structure-
`activity relationships and
`pharmacokinetics,” Adv
`Drug Deliv Rev,
`39(1-3):117-151 (1999)
`
`
`
`
`Dated: April 6, 2021
`
`
`
`
`
`Respectfully submitted,
`
`
`
`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.
`
`- 14 -
`
`
`
`Illumina v. Columbia
`IPR2020-00988, -01065, -01177, & -01125
`
`CERTIFICATE OF SERVICE
`
`I hereby certify that a true and correct copy of the foregoing ILLUMINA’S
`
`OBJECTIONS TO ADMISSIBILITY OF COLUMBIA EVIDENCE FILED
`
`WITH PATENT OWNER’S RESPONSE is being served on April 6, 2021, via
`
`email, pursuant to agreement of the parties, to counsel for the Trustees of Columbia
`
`University in the City of New York, at the email addresses below:
`
`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
`
`
`
`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.
`
`
`
`Dated: April 6, 2021
`
`
`
`34720600
`
`
`
`