Illumina, Inc. vs The Trustees of Columbia University in the City of New York

Order Conduct of the Proceeding

Joint Motion to Preserve Record Under Seal

Patent Owner Notice of Appeal

Final Written Decision

Illumina Supplemental Reply Re Estoppel - IPR797

Patent Owner Reply to Petitioner Supplemental Brief

Hearing Transcript

Patent Owner Additional Brief

Illumina Supplemental Brief

Order - Conduct of the Proceeding - 37 CFR 42.5, 42.20(d)

Supplemental Mandatory Notices

Illumina Updated Exhibit List

Illumina Demonstratives for Oral Argument

Illumina Reply to Opposition to Exclude Columbia Evidence

Patent Owner Demonstratives

Columbia Exhibit List No. 6

Patent Owners Opposition To Petitioners Motion To Exclude

Oral Argument 37 U.S.C. § 316(a)(10) and 37 C.F.R. § 42.70

Patent Owner Request for Oral Argument

Illumina Request for Oral Argument

Illumina Motion to Exclude Columbia Evidence

Illumina Objections to Columbia Evidence Served with Sur-Reply

Transcript for the Deposition of Dr. Floyd Romesberg, February 1, 2019, in IPR2018-00291, -00318, -00322, -00385, and -00797

Patent Owner Sur-reply

Columbia Exhibit List No. 5

Metzker (1998) (Marked at Dr. Menchen Deposition)

Jannasch (1992) (Marked at Dr. Menchen Deposition)

Patent Owner Objections to Admissibility of Petitioner Evidence

Patent Owner Notice of Deposition of Floyd Romesberg, Ph.D. Concerning Second Declaration Filed January 22, 2019

Petitioners Reply

Petitioners Updated Exhibit List

U.S. 6,248,884

Ruparel and Ju et al., Proc. Natl. Acad. Sci. USA, (2005)

Sept. 4-5, 2013 Deposition Transcript of Dr. George L. Trainor in IPR2012-00007

U.S. 6,111,116

Genet et al., Tetrahedron, (1994)

2018-04-20 IPR2017-02174, Paper 20, Decision Denying Institution of Inter Partes Review

2018-04-20 IPR2017-02172, Paper 20, Decision Denying Institution of Inter Partes Review

Nucleic Acids Research publication information for Metzker et al., Termination of DNA synthesis (1994).

IUPAC, Nomenclature of Organic Chemistry, Eds. Rigaudy et al., 1979

Jensen, Organizations for Standardization of Quantities and Units, Metrologia (1994 1995)

Greene and Wuts, Protective Groups in Organic Synthesis, third edition, John Wiley & Sons (1999)

CRC Handbook of Chemistry and Physics, eds. Weast et al., 72nd edition, CRC Press (1991)

Morrison et al., Organic Chemistry, Third Edition, Allyn and Bacon, Inc. (1973)

McGraw-Hill Dictionary of Chemistry, ed. Parker, McGraw-Hill Book Co., 1984

Solomons, Organic Chemistry, Fourth Edition, John Wiley & Sons (1988)

U.S. 5,808.045

U.S. 6,627,436

Transcript for the Deposition of Steven M. Menchen, January 14, 2019

Transcript for the Deposition of Steven M. Menchen, January 15, 2019

Lemaire-Audoire and Genet et al., Tetrahedron Letters, (1994)

Lemaire-Audoire and Genet et al., Journal of Molecular Catalysis A: Chemical, (1997)

Reply Declaration of Floyd Romesberg, Ph.D.

Cyclist¿¿ Exo-Pfu DNA Sequencing Kit, Instruction Manual, Stratagene (1998)

Hedden et al., DNA Sequence Determination Using Exonuclease-Deficient Pfu DNA Polymerase in a Cycle Sequencing Format, March 13-17, 1994

Qinglin Meng thesis from Dr. Ju¿¿¿s laboratory at Columbia University (2006)

Kutateladze, FEBS, (1986)

The Race for the $1000 Genome, Science, (2006)

Gardner et al., Nucleic Acids Research, (1999)

IPR2012-00007, Paper 82, Opposition to Motion to Amend

IPR2012-00007, Paper 83, Reply to Patent Owner Response

WO 04/018493

WO 04/018497

Kraevskii et al., Molecular Biology (1987)

Ju et. al., PNAS USA, (2006)

U.S. 5,614,365

U.S. 5,885,813

Southworth et al., PNAS USA, (1996)

Fields, Methods in Molecular Biology, Volume 35, Peptide Synthesis Protocols, Chapter 2, Humana Press 1994

List of documents considered by Dr. Romesberg

Takashashi et al., Bulletin of the Chemical Society of Japan, (1972)

Yamamoto et al., Organometallics, (1986)

IPR2012-00007, Paper 79 Substitute Columbia Motion to Amend

ORDER Granting Petitioner¿¿¿s Motion for Pro Hac Vice Admission of Edward R. Reines

Unopposed Motion for Edward R. Reines to Appear Pro Hac Vice on Behalf of Illumina, Inc.

Declaration of Edward R. Reines ISO Pro Hac Vice Motion

In Re Edward R. Reines 14-MA004 (14-4) (Fed. Cir. 2014)

Personal Statement of Edward R. Reines

Petitioners Supplemental Power of Attorney

Petitioners Supplemental Mandatory Notice Adding Derek Walter and Edward R. Reines as Backup Counsel

Petitioners Updated Exhibit List

Illumina Notice of Menchen Deposition

Supplemental Mandatory Notices

Motion to Seal and for Protective Order

Illumina Response to Columbia Motion to Seal

Illumina Objections to Columbia Evidence

Transcript for the Deposition of Dr. Floyd Romesberg, October 9, 2018, in IPR2018-00797

Protective Order in D.Del. C.A. No. 17-973 (GMS)

Dr. Romesberg NIH Grant, Evolving Novel Polymerases for Genome Sequencing

Transcript for the Deposition of Dr. Floyd Romesberg, September 19-20, 2018, in IPR2018-00291, -00318, -00322, and -00385 (REVISED TRANSCRIPT)

Internal Illumina Email (PUBLIC)

Internal Solexa Email (PUBLIC)

Internal Illumina Email (PUBLIC)

Attachment to Ex. 2122 (PUBLIC)

Attachment to Ex. 2122 (PUBLIC)

Proposed Standing Protective Order

Documents Considered By Dr. Menchen For Exhibit 2114

Declaration of Steven M. Menchen, Ph.D., October 26, 2018 (IPR2018-00797)

Patent Owner's Motion to Seal

Patent Owner's Response (PUBLIC)

Columbia's Exhibit List No. 4

Internal Solexa Email (SEALED)

Internal Illumina Email (SEALED)

Attachment to Ex. 2122 (SEALED)

Attachment to Ex. 2122 (SEALED)

Patent Owner's Response (SEALED)

Internal lllumina Email (SEALED)

IPR2013-00128, Exhibit 1033, Deposition of Floyd Romesberg, Ph.D. (January 14, 2014)

IPR2013-00266, Exhibit 2037, Second Declaration of Floyd Romesberg, Ph.D. (March 21, 2014)

Jannasch (1992)

Lindahl & Nyberg (1972)

Hamed (2001)

Exhibit from Deposition of Dr. Floyd Romesberg, September 19-20, 2018, in IPR2018-00291, -00318, -00322, and -00385 (Handwritten calculations)

Pillai & Nandi (1977)

IPR2013-00266, Exhibit 1042, Deposition of Floyd Romesberg, Ph.D. (April 10, 2014)

IPR2013-00128, Substitute Exhibit 2009, Substitute Declaration of Floyd Romesberg, Ph.D. in Support of Patent Owner Motion to Amend (February 19, 2014)

Levine (1963)

Kit (1963)

U.S. Patent No. 6,664,079

Transcript for the Deposition of Dr. Floyd Romesberg, September 19-20, 2018, in IPR2018-00291, -00318, -00322, and -00385 (ORIGINAL TRANSCRIPT)

Qian (1999)

U.S. Patent No. 5,858,671

Tsuji (1982)

WO 96/27025

Hawley (1997)

IPR2017-02172, Paper 22, Decision Denying Petitioner¿¿¿s Request for Rehearing (August 2, 2018)

Eckert (1991)

Kang (1995)

U.S. Patent No. 6,013,445

Qian (2000)

Project Information for Dr. Romesberg NIH Grant, Evolving Novel Polymerases for Genome Sequencing

Genomeweb, Helicos and Columbia to Test Scripps Improved Polymerase for Next-Gen Sequencing, October 3, 2006

Bieg (1985)

Ochiai (1996)

Katritzky (1995)

WO 96/23807

Martinez (1997)

Parshall (1980)

Solexa, Inc. Form 425 Submission to the United States Securities and Exchange Commission (November 14, 2006)

Illumina suppl. mandatory notice adding N. Luman as add'l backup counsel

Illumina Objections to Columbia Evidence Submitted Prior to Trial Institution

SCHEDULING ORDER 37 C.F.R. sec 42.5

Patent Owner's Notice of Deposition of Floyd Romesberg, Ph.D.

Supplemental Mandatory Notices Pursuant to 37 CFR 42.8(b)(3)

Power of Attorney to Zachary L. Garrett

Proposal to Modify the Schedule

Trial Instituted Document

Order - 37 C.F.R. 42.10(c)

Patent Owner's Motion for Admission Pro Hac Vice of Zachary L. Garrett

Columbia's Exhibit List No. 3

Declaration of Zachary L. Garrett in Support of Patent Owner's Motion for Admission Pro Hac Vice

Order Denying Leave to File Reply to Preliminary Response

Supplemental Mandatory Notices Pursuant to 37 CFR 42.8(b)(3)

Power of Attorney to Robert S. Schwartz

Assignment data in connection with U.S. Patent Application Publication No. 2007/0166705 and U.S. Patent No. 7,541,444

Assignment data in connection with U.S. Patent No. 6,232,465

Froehler (1992)

IPR2018-00291, Petition for Inter Partes Review of U.S. Patent No. 9,718,852 (December 8, 2017)

Excerpts from the Prosecution History of U.S. Patent No. 9,868,985 not included in Ex. 1076

Metzker (2010)

Ronaghi (1998)

Excerpts from the Ex Parte Reexamination History of U.S. Patent No. 6,232,465

IPR2013-00517, Ex. 2011, Declaration of Floyd Romesberg, Ph.D. (May 5, 2014)

IPR2013-00517, Paper 32, Illumina Patent Owner Response (May 5, 2014)

Excerpts from the Ex Parte Reexamination History of U.S. Patent No. 5,808,045

Assignment data in connection with U.S. Patent No. 5,808,045

PCT Publication WO 98/33939 (Anazawa) (English translation)

Metzker (1998)

PCT Publication WO 00/53805 (Stemple)

Metzker (1994)

U.S. Patent No. 7,541,444

U.S. Patent No. 7,771,973

U.S. Patent Application Publication No. 2007/0166705

Boons (1996)

Ochiai (1996)

Olivero & Dunach (1995)

U.S. Patent No. 6,232,465

Solexa, Inc. Schedule 13D-A Submission to the United States Securities and Exchange Commission (Feb. 2, 2007)

Litosh (2011)

IPR2017-02172, Paper 6, Preliminary Response of Patent Owner Illumina Cambridge Ltd. (January 23, 2018)

IPR2017-02174, Paper 6, Preliminary Response of Patent Owner Illumina Cambridge Ltd. (January 23, 2018)

U.S. Patent No. 7,566,537

No. 2015-1123 (CAFC), Brief of Patent Owner-Appellant Illumina Cambridge Ltd., D.I. 27 (March 10, 2015)

IPR2013-00266, Paper 39, Patent Owner Illumina Reply to Petitioner Opposition to Illumina Motion to Amend (March 21, 2014)

Canard & Sarfati (1994)

IPR2013-00517, Paper 84, Oral Hearing Transcript (February 2, 2015)

IPR2013-00517, Paper 64, Illumina Motion for Observations on the Cross-Examination Testimony of Bruce Branchaud, Ph.D. and Michael Metzker, Ph.D. (September 2, 2014)

IPR2012-00007, Paper 5, Petition for Inter Partes Review of U.S. Pat. No. 7,790,869 (September 16, 2012)

IPR2013-00517, Exhibit 1025, Deposition of Floyd Romesberg, Ph.D. (July 28, 2014)

IPR2012-00007, Paper 38, Decision on Petition for Inter Partes Review (March 12, 2013)

PCT Publication WO 98/33939 (Japanese language version of Anazawa)

Translation Affidavit for Anazawa

Welch & Burgess (1999)

IPR2013-00517, Paper 68, Illumina Opposition to IBS Motion To Exclude Evidence

Excerpts from the Prosecution History of U.S. Patent No. 7,771,973

Declaration of Steven M. Menchen, Ph.D.

Genomeweb, Illumina Closes Solexa Acquisition, January 26, 2007

Lee (1981)

Lindahl (1993)

Mozingo (1955)

Johnson (1995)

IPR2018-00291, Institution Decision, Paper No. 16 (June 25, 2018)

Zielonacka-Lis (1989)

IPR2013-00128, Ex. 1029, Substitute Declaration of Floyd Romesberg, Ph.D. (Jan. 9, 2014)

IPR2018-00318, Institution Decision, Paper No. 16 (July 3, 2018)

IPR2018-00322, Institution Decision, Paper No. 16 (July 3, 2018)

Curriculum Vitae of Steven M. Menchen, Ph.D.

Patent Owner Preliminary Response

Illumina Suppl Mand. Notice Adding Wm Zimmerman as Add'l Backup Counsel

Granting Patent Owners Motion for Pro Hac Vice Admission of Robert S. Schwartz 37 C.F.R. sec 42.10

Granting Petitioners Motion for Pro Hac Vice Admission of William R. Zimmerman 37 C.F.R. sec 42.10

Supplemental Mandatory Notices Pursuant to 37 CFR 42.8(a)(3)

Illumina Updated Exhibit List

Illumina Motion for Zimmerman to Appear PHV

Illumina Supplemental Power of Attorney

Zimmerman Decl ISO PHV Motion

Patent Owner's Motion for Admission Pro Hac Vice

Declaration of Robert S. Schwartz

Columbia's Exhibit List No. 1 Under 37 CFR 42.63(e)

Notice of Accord Filing Date

Patent Owner's Mandatory Notices Pursuant to 37 CFR 42.8

U.S. 9,708,358 (Ju)

U.S. 9,719,139 (Ju)

IPR2012-00007 Paper 140

IPR2012-00006 Paper 128

IPR2012-00006 Federal Circuit Opinion

U.S. 7,790,869 (Ju)

Alberts (1994)

WO 9106678 (Tsien)

U.S. 5,547,839 (Dower)

Metzker (1994)

Wu and Metzker (2007)

Sanger (1977)

U.S. 5,302,509 (Cheeseman)

U.S. 9,718,852 (Ju)

U.S. 9,725,480 (Ju)

IPR2013-00011 Paper 130

Prober (1987)

U.S. 7,270,951 (Stemple)

Ramzaeva (1995)

Seela (1997)

Watson (1953)

Zavgorodny (1991)

IPR2012-00007 Paper 77

IPR2013-00266 Paper 73

U.S. 8,088,575 (Ju)

Stryer (1955)

U.S. 9,719,139 FH [Excerpts]

Pelletier (1994)

Welch (1999)

Welch (2005)

Seela (1991)

U.S. 4,804,748 (Seela)

Rosenblum (1997)

IPR2012-00007 Ex. 2094

U.S. 5,151,507 (Hobbs)

Seela (1995)

Ramzaeva (1997)

IPR2012-00006 Ex 2033

Boss (1976)

Qian (1998)

Kamal (1999)

Vollhardt (1994)

Yu (1994)

Livak (1992)

IPR2013-00517 Paper 87

Federal Circuit Opinion re IPR2013-00517

Gigg (1968)

IPR2013-00128 Paper 92

Federal Circuit Opinion Re IPR2013-00128 and -00126

Greenberg (1998)

Seitz (1997)

Guillier (2000)

Romesberg CV

Sears (1992)

U.S. 9,725,480 FH [Excerpts]

U.S. 9,718.852 FH [Excerpts]

U.S. 9868985 (Ju)

U.S. 9,868,985 PH [Excerpts]

Declaration of Ju re 9,868,985

Romesberg Documents Considered

WO 9853300 (Pallas)

WO 9833939 (Anazawa)

WO 9833939 (Anazawa) Translation

U.S. 5,424,186 (Fodor)

U.S. 9,708,358 FH [Excerpts]

Declaration of Romesberg

U.S. 7,713,698 (Ju)

U.S. 6,432,360 (Church)

Complaint 17cv973

Power of Attorney for Petitioner

Petition for Inter Partes Review of U.S. Patent No. 9,868,985