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

Patent Owner Notice of Appeal

ORDER - Motions to Preserve Record Pending Appeal

Joint Motion to Preserve Record Under Seal

Errata

EXPUNGED

Termination Decision Document

Illumina Supplemental Reply Re Estoppel - IPR385

Patent Owner Reply to Petitioner Supplemental Brief

Hearing transcript

Illumina Supplemental Brief

Patent Owner Additional 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

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

Patent Owner Sur-reply

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

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

Columbia Exhibit List No. 5

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

Petitioner's Reply

Illumina Updated Exhibit List

WO 98_53300 ¿¿¿ Pallas

USP 6,111,116 - Benshon and Menchen

IPR2017-02174 Institution denial

IPR2017-02172 Institution denial

Metzker NAR publication information

USP 6,248,884 - Lam and Menchen

Ruparel and Ju, PNAS

Genet 1994

Trainor Sept. 4-5, 2013 transcript

Jensen, Metrologia

Solomons 1988

Morrison 1973

Cyclist DNA sequencing kit manual

Menchen 2019-01-14 depo transcript

IUPAC Nomenclature 1979

Greene and Wuts

CRC Handbook

McGraw-Hill dictionary excerpt 1984

USP 5,808,045 ¿¿¿ Hiatt

USP 6,627,436 ¿¿¿ Sorge

Hedden 1994

Menchen 2019-01-15 depo transcript

Lemaire-Audoire and Genet, Tetrahedron Ltrs 1994

Romesberg 2d declaration

Race for 1000 dollar genome, Science 2006

Lemaire-Audoire and Genet, 1997

Meng thesis 2006

Kutateladze FEBS [1986]

Gardner, NAR 1999

WO 04_018493 ¿¿¿ Solexa

WO 04_018497 ¿¿¿ Solexa

Kraevskii, Molecular Biology, 1987

IPR2012-00007 Paper 82

Takahashi 1972

Yamamoto 1986

Fields 1994

Documents Romesberg considered

IPR2012-00007 Paper 83

Ju, PNAS 2006

USP 5,614,365 ¿¿¿ Tabor

USP 5,885,813 ¿¿¿ Davis

Southworth, PNAS 1996

IPR2012-00007 Paper 79

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

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

Petitioners Supplemental Power of Attorney

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

Personal Statement of Edward R. Reines

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 Objections to Columbia Evidence

Illumina Response to Columbia Motion to Seal

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

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)

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

Internal Solexa Email (PUBLIC)

Internal Illumina Email (PUBLIC)

Internal Illumina Email (PUBLIC)

Attachment to Ex. 2122 (PUBLIC)

Attachment to Ex. 2122 (PUBLIC)

Proposed Standing Protective Order

Declaration of Steven M. Menchen, Ph.D., October 26, 2018 (IPR2018-00291, -00318, -00322, and -00385)

Documents Considered By Dr. Menchen For Exhibit 2116

Patent Owner's Response (PUBLIC)

Columbia's Exhibit List No. 4

Patent Owner's Motion to Seal

Patent Owner's Response (SEALED)

Attachment to Ex. 2122 (SEALED)

Internal Solexa Email (SEALED)

Internal lllumina Email (SEALED)

Internal Illumina Email (SEALED)

Attachment to Ex. 2122 (SEALED)

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

Jannasch (1992)

Levine (1963)

Kit (1963)

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

Qian (1999)

Kang (1995)

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

Metzker (2010)

Ronaghi (1998)

Genomeweb, Illumina Closes Solexa Acquisition, January 26, 2007

Lindahl (1993)

Johnson (1995)

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

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)

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)

Lindahl & Nyberg (1972)

Hamed (2001)

Pillai & Nandi (1977)

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)

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

Tsuji (1982)

Qian (2000)

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

Bieg (1985)

Ochiai (1996)

Katritzky (1995)

WO 96/27025

WO 96/23807

Martinez (1997)

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

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

Eckert (1991)

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

Hawley (1997)

Parshall (1980)

AMENDED SCHEDULING ORDER 37 C.F.R. sec 42.5

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

PANEL CHANGE ORDER

Proposal to Modify the Schedule

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

Illumina Objections to Admissibility of Columbia Evidence

Scheduling Order

Decision Institution of Inter Partes Review

Order Petitioner's Motion for Pro Hac Vice Admission of William R. Zimmerman

Order Patent Owner's Motions for Pro Hac Vice Admission of Zachary L. Garrett and Robert S. Schwartz

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

Power of Attorney to Zachary L. Garrett

Power of Attorney to Robert S. Schwartz

Supplemental Mandatory Notice Adding William R. Zimmerman as Backup Counsel

Patent Owner's Motion for Admission Pro Hac Vice (Garrett)

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

Columbia's Exhibit List No. 3 Under 37 CFR 42.63(e)

U.S. Patent No. 7,790,869

U.S. Patent No. 8,088,575

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

Metzker (1994)

Boons (1996)

Ochiai (1996)

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)

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)

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

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

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

U.S. Patent No. 7,713,698

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

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

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

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

Olivero & Dunach (1995)

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

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

Solexa, Inc. Fed. R. Civ. P. 7.1 Statement (Feb. 19, 2010)

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

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)

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

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. 9,718,852

Patent Owner Preliminary Response

Excerpts from the Prosecution History of U.S. Patent No. 9,725,480

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

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

Illumina Supplemental Power of Attorney

Illumina Updated Exhibit List

Illumina Motion for Zimmerman to Appear PHV

Zimmerman Decl ISO PHV Motion

Illumina's Supplemental Mandatory Notice

Patent Owner's Motion for Admission Pro Hac Vice

Declaration of Robert S. Schwartz

Columbia's Exhibit List No. 1

Notice of Accord Filing Date

Patent Owner's Mandatory Notices Pursuant to 37 CFR 42.8

Illumina's Supplemental Mandatory Notice - Related Matters

U.S. Patent No. 9,718,852 (Ju)

U.S. Patent No. 9,708,358 (Ju)

U.S. Patent No. 9,719,139 (Ju)

2014-03-06 IPR2012-00006, Paper 128, Final Written Decision

2014-03-06 IPR2013-00011, Paper 130, Final Written Decision

2015-07-17 Federal Circuit Opinion Affirming IPR2012-00006, IPR2012-00007 and IPR2013-00011

WO 91/06678 (Tsien)

U.S. Patent No. 9,725,480 (Ju)

2014-03-06 IPR2012-00007, Paper 140, Final Written Decision

U.S. Patent No. 7,790,869 (Ju)

Alberts, et al., Molecular Biology of the Cell (1994)

Prober, et al., A System for Rapid DNA Sequencing with Fluorescent Chain-Terminating Dideoxynucleotides (1987) (Prober)

U.S. Patent No. 5,547,839 (Dower)

Metzker, et al., Termination of DNA synthesis by novel 3-modified-deoxyribonucleoside 5-triphosphates (1994) (Metzker)

U.S. Patent No. 7,270,951 (Stemple)

Pelletier, et al., Structures of Ternary Complexes of Rat DNA Polymerase, a DNA Template-Primer, and ddCTP (1994) (Pelletier)

Rosenblum, et al., New dye-labeled terminators for improved DNA sequencing patterns (1997) (Rosenblum)

Seela, et al., Oligonucleotide Duplex Stability Controlled by the 7-Substituents of 7-Deazaguanine Bases (Seela 1995)

Wu and Metzker, et al., Termination of DNA synthesis by N6-alkylated, not 3-O-alkylated, photocleavable 2-deoxyadenosine triphosphates (2007) (Wu and Metzker)

Sanger et. al., DNA sequencing with chain-terminating inhibitors (1977) (Sanger)

U.S. Patent No. 5,302,509 (Cheeseman)

Welch, et al., Syntheses of Nucleosides Designed for Combinatorial DNA Sequencing (1999) (Welch)

Welch, et al., Corrgenda Syntheses of Nucleosides Designed for Combinatorial DNA Sequencing (2005) (Welch Corrigenda)

Seela, et al., 7-Deazapurine containing DNA (1991) (Seela 1991)

U.S. Patent No. 4,804,748 (Seela Patent)

Excerpts from 2013-09-04 Deposition Transcript of Dr. George L. Trainor in IPR2012-00007

U.S. Patent No. 5,151,507 (Hobbs)

Ramzaeva, et al., 88. 7-Substituted 7-Deasa-2'-deoxyguanosines Regioselective Halogenation of Pyrrolo2,3-d pyrimidine Nucleosides (1995) (Ramzaeva 1995)

Seela, et al., Duplex Stability of Oligonucleotides Containing 7-Substituted 7-Deaza- and 8-Aza-7-Deazapurine Nucleosides (Seela 1997)

Ramzaeva, et al., 123. 7-Deazaguanine DNA Oligonucleotides with Hydrophobic or Cationic Side Chains (Ramzaeva 1997)

2013-06-25 Declaration of Dr. George L. Trainor from IPR2012-00006

Boss, et al., Cleavage of Allyl Ethers with Pd/C (1976) (Boss)

Livak, et al., Detection of single base differences using biotinylated nucleotides with very long linker arms (1992) (Livak)

Qian, et al., Unexpected Enzymatic Fucosylation of the Hindered Tertiary Alcohol of 3-C-Methyl-N-Acetyllactosamine Produces a Novel Analogue of the LeX-Trisaccharide (1998) (Qian)

Kamal, et al., A Mild and Rapid Regeneration of Alcohols from their Allylic Ethers by Chlorotrimethylsilane/Sodium Iodide (1999) (Kamal)

Vollhardt, et al., Organic Chemistry (1994) (Vollhardt)

Yu, et al., Cyanine dye dUTP analogs for enzymatic labeling of DNA probes (1994) (Yu)

2015-02-11 Final Written Decision in IPR2013-00517

2016-05-09 Federal Circuit Opinion Affirming IPR2013-00517

2014-07-25 Final Written Decision in IPR2013-00128, Paper 92

2016-01-29 Federal Circuit Opinion Affirming IPR2013-00128 and IPR2013-00266

Seitz, et al., HYCRON, an Allylic Anchor for High-Efficiency Solid Phase Synthesis of Protected Peptides and Glycopeptides (1997) (Seitz)

Watson, et al., Genetical Implication of the Structure of Deoxyribonucleic Acid (1953) (Watson & Crick)

Zavgorodny, et al., 1-Alkylthioalkylation of Nucleoside Hydroxyl Functions and its Synthetic Applications A New Versatile Method in Nucleoside Chemistry (1991) (Zavgorodny)

Gigg, et al., The Allyl Ether as a Protecting Group in Carbohydrate Chemistry Part II (1968) (Gigg)

2013-08-30 Substitute Columbia Patent Owner Response in IPR2012-00007, Paper 77

2014-10-28 Final Written Decision in IPR2013-00266, Paper 73

Greenberg, et al., Optimization and Mechanistic Analysis of Oligonucleotide Cleavage from Palladium-Labile Solid-Phase Synthesis Supports (1998) (Greenberg)

U.S. Patent No. 8,088,575 (Ju)

Gullier, et al., Linkers and Cleavage Strategies in Solid-Phase Organic Synthesis and Combinatorial Chemistry (2000) (Gullier)

Stryer, Biochemistry (1995) (Stryer)

Curriculum Vitae of Floyd Romesberg, Ph.D.

Sears, et al., CircumVent Thermal Cycle Sequencing and Alternative Manual and Automated DNA Sequencing Protocols Using the Highly Thermostable VentR (exo) DNA Polymerase (1992) (Sears)

Declaration of Jingyue Ju from Prosecution History of U.S. Patent No. 9,725,480 (Ju)

List of documents considered by Floyd Romesberg, Ph.D.

Columbia's complaint for U.S. 9,725,480

Excerpts from Prosecution History of U.S. Patent No. 9,725,480 (Ju)

Declaration of Dr. Floyd Romesberg, Ph.D. for '480

U.S. 5,844,106 (Seela II)

Excerpts from Prosecution History of U.S. Patent No. 9,719,139 (Ju)

Excerpts from Prosecution History of U.S. Patent No. 9,718,852 (Ju)

Excerpts from Prosecution History of U.S. Patent No. 9,708,358 (Ju)

Petition for Inter Partes Review of U.S. Patent No. 9725480

Illumina, Inc. Power of Attorney