Case IPR2020-00988
`Patent No. 10,407,458
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`Filed: March 30, 2021
`
`
`
`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.
`_______________
`
`IPR2020-00988 (Patent 10,407,458)
`
`
`
`PATENT OWNER’S UPDATED EXHIBIT LIST
`
`
`
`
`
`
`
`
`
`
`
`Patent No. 10,407,458
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`Filed: March 30, 2021
`
`
`
`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.
`_______________
`
`IPR2020-00988 (Patent 10,407,458)
`
`
`
`PATENT OWNER’S UPDATED EXHIBIT LIST
`
`
`
`
`
`
`
`
`
`
`
`
`Case IPR2020-00988
`Patent No. 10,407,458
`
`
`Pursuant to 37 C.F.R. § 42.63(e), Patent Owner The Trustees of Columbia
`
`University in the City of New York hereby provides an updated list of its exhibits
`
`in this proceeding.
`
`Exhibit No. Description
`
`EXHIBIT LIST
`
`2001
`
`2002
`
`2003
`
`2004
`
`2005
`
`2006
`
`2007
`
`2008
`
`2009
`
`2010
`
`Defendant Illumina, Inc.’s Response to Plaintiffs’ Opening Claim
`Construction Brief
`
`Metzker, et al., “Elimination of residual natural nucleotides from
`3’-O-modified-dNTP syntheses by enzymatic mop-up,”
`BioTechniques, 25:814-817 (1998)
`PCT Publication WO 00/53805 (“Stemple”)
`
`Defendant Illumina, Inc.’s Initial Invalidity Contentions, The
`Trustees of Columbia University in the City of New York and
`Qiagen Sciences, LLC v. Illumina, Inc., 19-cv-01681 (D. Del.)
`U.S. Patent No. 6,087,095 (“Rosenthal”)
`
`Welch & Burgess, “Synthesis of fluorescent, photolabile 3’-O-
`protected nucleoside triphosphates for the base addition
`sequencing scheme,” Nucleosides & Nucleotides, 18:197-201
`(1999)
`Canard & Sarfati, “DNA polymerase fluorescent substrates with
`reversible 3’-tags,” Gene, 148:1-6 (1994)
`
`IPR2017-02172 Petition for Inter Partes Review of U.S. Patent
`No. 7,566,537
`
`IPR2017-02172 Preliminary Response of Patent Owner Illumina
`Cambridge Ltd.
`
`IPR2017-02174 Preliminary Response of Patent Owner Illumina
`Cambridge Ltd.
`
`2011
`
`IPR2013-00517 Illumina’s Patent Owner Response
`
`
`
`1
`
`
`
`Case IPR2020-00988
`Patent No. 10,407,458
`
`
`2012
`
`IPR2013-00517 Final Written Decision
`
`2013
`
`IPR2013-00517 Deposition of Floyd Romesberg, Ph.D., July 8,
`2014
`
`2014
`
`IPR2018-00291 Petitioner’s Reply
`
`2015
`
`U.S. Patent No. 5,808,045
`
`2016
`
`Curriculum Vitae of Kenneth A. Johnson, Ph.D.
`
`2017
`
`2018
`
`2019
`
`IPR2018-00291, IPR2018-00318, IPR2018-00322, IPR2018-
`00385, IPR2018-00797 Illumina’s Demonstratives for Oral
`Hearing
`IPR2018-00291, IPR2018-00318, IPR2018-00322, IPR2018-
`00385, IPR2018-00797 Illumina’s Reply to Patent Owner’s
`Opposition to Motion to Exclude
`IPR2018-00291 Institution Decision
`
`2020
`
`Declaration of Kenneth A. Johnson
`
`2021
`
`WO 96/23807 (“Kwiatkowski”)
`
`2022
`
`2023
`
`2024
`
`Ronaghi, et al. “A sequencing method based on real-time
`pyrophosphate,” Science, 281(5375):363-365 (1998)
`
`Brief of Patent Owner-Appellant Illumina Cambridge Ltd.,
`Illumina Cambridge Ltd. v. Intelligent Bio-Systems, Inc., D.I. 27,
`2015-1123 (Fed. Cir.)
`U.S. Patent No. 5,858,671 (“Jones”)
`
`2025
`
`U.S. Patent No. 6,013,445 (“Albrecht”)
`
`2026
`
`Excerpts from the Prosecution History of U.S. Patent No.
`9,718,852
`
`
`
`2
`
`
`
`Case IPR2020-00988
`Patent No. 10,407,458
`
`
`2027
`
`2028
`
`2029
`
`2030
`
`2031
`
`2032
`
`2033
`
`2034
`
`Complaint for Patent Infringement, The Trustees of Columbia
`University in the City of New York and Qiagen Sciences, LLC v.
`Illumina, Inc., D.I. 1, 19-cv-01681 (D. Del.)
`Docket, The Trustees of Columbia University in the City of New
`York and Qiagen Sciences, LLC v. Illumina, Inc., 19-cv-01681
`(D. Del.)
`Amended Complaint for Patent Infringement, The Trustees of
`Columbia University in the City of New York and Qiagen
`Sciences, LLC v. Illumina, Inc., D.I. 12, 19-cv-01681 (D. Del.)
`Exhibit 7 to Complaint for Patent Infringement, The Trustees of
`Columbia University in the City of New York and Qiagen
`Sciences, LLC v. Illumina, Inc., D.I. 1-7, 19-cv-01681 (D. Del.)
`Exhibit 8 to Complaint for Patent Infringement, The Trustees of
`Columbia University in the City of New York and Qiagen
`Sciences, LLC v. Illumina, Inc., D.I. 1-8, 19-cv-01681 (D. Del.)
`Docket, The Trustees of Columbia University in the City of New
`York and Qiagen Sciences, LLC v. Illumina, Inc., 19-2302 (Fed.
`Cir.)
`Zhu, Z., et al., “Directly labeled DNA probes using fluorescent
`nucleotides with different length linkers,” Nucleic Acids Res.,
`22:3418-3422 (1994)
`IPR2018-00291, Petition for Inter Partes Review of U.S. Patent
`No. 9,718,852
`
`2035
`
`U.S. Patent No. 7,566,537
`
`2036
`
`2037
`
`Joint Claim Construction Brief, The Trustees of Columbia
`University in the City of New York and Qiagen Sciences, LLC v.
`Illumina, Inc., D.I. 54, 19-cv-01681 (D. Del.)
`Excerpts of Joint Claim Construction Appendix (Declaration of
`John Kuriyan, Ph.D. in Support Of Plaintiffs’ Opening Claim
`Construction Brief; Expert Declaration of Dr. Floyd Romesberg in
`Support of Illumina’s Response to Plaintiffs’ Opening Claim
`Construction Brief), The Trustees of Columbia University in the
`City of New York and Qiagen Sciences, LLC v. Illumina, Inc., D.I.
`55, 19-cv-01681 (D. Del.)
`2038-2045 Reserved
`
`
`
`3
`
`
`
`Case IPR2020-00988
`Patent No. 10,407,458
`
`
`2046
`
`Protective Order, The Trustees of Columbia University in the City
`of New York and Qiagen Sciences, LLC v. Illumina, Inc., 19-cv-
`01681 (D. Del.)
`2047-2053 Reserved
`
`2054
`
`Excerpts from the Ex Parte Reexamination History of U.S. Patent
`No. 5,808,045
`
`2055-2058 Reserved
`
`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)
`2060-2070 Reserved
`
`2071
`
`2072
`
`2073
`
`Declaration of Kenneth A. Johnson, March 30, 2021, IPR2020-
`00988, -01065, -01125, -01177, -01323
`
`Deposition Transcript for Videotaped Deposition of Floyd
`Romesberg, Ph.D., March 15, 2021, IPR2020-00988, -01065, -
`01125, -01177, -01323
`Curriculum Vitae of Kenneth A. Johnson, Ph.D.
`
`2074
`
`EP 3 034 627 (“Columbia’s EP’627 patent”)
`
`2075
`
`2076
`
`Illumina’s October 29, 2019 Opposition against Columbia’s EP’627
`patent
`
`Illumina’s March 25, 2021 Response in support of its Opposition
`against Columbia’s EP’627 patent
`
`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)
`
`
`
`4
`
`
`
`Case IPR2020-00988
`Patent No. 10,407,458
`
`
`2079
`
`2080
`
`2081
`
`2082
`
`2083
`
`2084
`
`2085
`
`2086
`
`2087
`
`2088
`
`2089
`
`Preliminary Opinion of Opposition Division re: Illumina’s
`Opposition against Columbia’s EP’627 patent
`
`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)
`Koshland JR., D. E., “Enzyme flexibility and enzyme action,”
`Journal of Cellular and Comparative Physiology 54(S1):245-258
`(1959)
`IPR2018-00291, -00318, -00322, -00385, -00797, March 5, 2019
`Oral Hearing Transcript (Paper 62)
`
`Timsit, Y, “DNA structure and polymerase fidelity,” J Mol Biol,
`293(4):835-853 (1999)
`
`Goodman, M. F. & D. K. Fygenson, “DNA polymerase fidelity:
`From genetics toward a biochemical understanding,” Genetics,
`148(4):1475-1482 (1998)
`Goodman, M. F. & B. Tippin, “Sloppier copier DNA polymerases
`involved in genome repair,” Curr Opin Genet Dev, 10(2):162-168
`(2000)
`Kunkel, T. A., “The mutational specificity of DNA polymerase-
`beta during in vitro DNA synthesis. Production of frameshift, base
`substitution, and deletion mutations,” J Biol Chem, 260(9):5787-
`5796 (1985)
`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)
`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)
`Ito, J. & D. K. Braithwaite, “Compilation and alignment of DNA
`polymerase sequences,” Nucleic Acids Res, 19(15):4045-4057
`(1991)
`
`
`
`Dated: March 30, 2021
`
`
`
`
`
`
`
`Respectfully submitted,
`
`/John P. White/
`
`
`
`
`
`
`By:
`
`5
`
`
`
`Case IPR2020-00988
`Patent No. 10,407,458
`
`
`
`
`
`
`
`
`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
`
`
`
`Case IPR2020-00988
`Patent No. 10,407,458
`
`
`
`CERTIFICATE OF SERVICE
`
`I hereby certify that a true and correct copy of the foregoing PATENT
`
`OWNER’S UPDATED EXHIBIT LIST and EXHIBITS 2054, 2059, 2071-2089
`
`are being served on March 30, 2021, 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: March 30, 2021
`
`
`
`
`
`By:
`
`
`
`/John P. White/
`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
`
`
`
`
`
`
Accessing this document will incur an additional charge of $.
After purchase, you can access this document again without charge.
Accept $ Charge
Still Working On It
This document is taking longer than usual to download. This can happen if we need to contact the court directly to obtain the document and their servers are running slowly.
Give it another minute or two to complete, and then try the refresh button.
A few More Minutes ... Still Working
It can take up to 5 minutes for us to download a document if the court servers are running slowly.
Thank you for your continued patience.
This document could not be displayed.
We could not find this document within its docket. Please go back to the docket page and check the link. If that does not work, go back to the docket and refresh it to pull the newest information.
Your account does not support viewing this document.
You need a Paid Account to view this document. Click here to change your account type.
Your account does not support viewing this document.
Set your membership
status to view this document.
With a Docket Alarm membership, you'll
get a whole lot more, including:
- Up-to-date information for this case.
- Email alerts whenever there is an update.
- Full text search for other cases.
- Get email alerts whenever a new case matches your search.
One Moment Please
The filing “” is large (MB) and is being downloaded.
Please refresh this page in a few minutes to see if the filing has been downloaded. The filing will also be emailed to you when the download completes.
Your document is on its way!
If you do not receive the document in five minutes, contact support at support@docketalarm.com.
Sealed Document
We are unable to display this document, it may be under a court ordered seal.
If you have proper credentials to access the file, you may proceed directly to the court's system using your government issued username and password.
Access Government Site
