Filed June 26, 2020
`
`On behalf of Illumina, Inc.
`By: Kerry S. Taylor
`
`Nathanael R. Luman
`Michael L. Fuller
`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
`
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`
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`
`
`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.
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`IPR2020-01177
`Patent 10,435,742
`
`
`
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`
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`
`
`PETITION FOR INTER PARTES REVIEW OF
`U.S. PATENT NO. 10,435,742
`
`
`
`On behalf of Illumina, Inc.
`By: Kerry S. Taylor
`
`Nathanael R. Luman
`Michael L. Fuller
`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.
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`IPR2020-01177
`Patent 10,435,742
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`PETITION FOR INTER PARTES REVIEW OF
`U.S. PATENT NO. 10,435,742
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`TABLE OF CONTENTS
`
`Page No.
`
`I.
`
`II.
`
`INTRODUCTION ......................................................................................... 1
`
`STATE OF THE ART ................................................................................... 4
`
`A. Deoxyribonucleotides Were Known ................................................... 4
`
`B.
`
`Nucleotide Analogues Were Known ................................................... 7
`
`1.
`
`Nucleotide analogues having a small 3′-OH cap
`and a labeled base were known ................................................. 7
`
`a.
`
`b.
`
`Small 3′-capping groups were desirable ......................... 8
`
`5-Substituted pyrimidine labels were
`common .......................................................................... 9
`
`III. THERE IS A REASONABLE LIKELIHOOD THAT THE
`CHALLENGED CLAIMS ARE UNPATENTABLE ................................ 10
`
`A.
`
`B.
`
`The Prior Art ..................................................................................... 10
`
`Grounds ............................................................................................. 11
`
`IV. CLAIM CONSTRUCTION ........................................................................ 11
`
`A.
`
`Claim 2’s “allyl ether” Means “an ether of –
`CH2CH=CH2” .................................................................................... 12
`
`B.
`
`No Other Terms Require Construction ............................................. 12
`
`V.
`
`LEVEL OF ORDINARY SKILL ................................................................ 13
`
`VI. GROUND 1: OBVIOUSNESS OVER TSIEN IN VIEW OF
`HIATT ......................................................................................................... 13
`
`A.
`
`Claim 1 .............................................................................................. 13
`
`- i -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`TABLE OF CONTENTS
`(cont’d)
`
`Page No.
`
`1.
`
`2.
`
`3.
`
`4.
`
`5.
`
`6.
`
`7.
`
`8.
`
`9.
`
`The structure of claim 1 is not new ......................................... 13
`
`Limitation R(a): “wherein R(a) represents a small,
`chemically cleavable, chemical group capping the
`oxygen at the 3′ position of the deoxyribose of the
`deoxyribonucleotide analogue” .............................................. 15
`
`Limitation R(b): “wherein R ... (b) does not
`interfere with recognition of the analogue as a
`substrate by a DNA polymerase” ............................................ 19
`
`The Stability Limitations: “wherein R ... (c) is
`stable during a DNA polymerase reaction” and
`“wherein the covalent bond between the 3′-oxygen
`and R is stable during a DNA polymerase
`reaction” .................................................................................. 20
`
`The Provisos: “wherein R ... (d) does not contain a
`ketone group, and (e) is not a –CH2CH=CH2
`group” and “wherein OR is not a methoxy group
`or an ester group” .................................................................... 21
`
`The Tag Limitation: “wherein tag represents a
`detectable fluorescent moiety” ................................................ 21
`
`Limitation Y: “chemically cleavable, chemical
`linker” ...................................................................................... 22
`
`Limitations Y(a) and (b): “wherein Y ... (a) does
`not interfere with recognition of the analogue as a
`substrate by a DNA polymerase” and “wherein Y
`... (b) is stable during a DNA polymerase reaction” ............... 23
`
`Limitation i): “wherein the thymine
`deoxyribonucleotide analogue: i) is recognized as a
`substrate by a DNA polymerase” ............................................ 25
`
`- ii -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`TABLE OF CONTENTS
`(cont’d)
`
`Page No.
`
`10. Limitation ii): “wherein the thymine
`deoxyribonucleotide analogue ... ii) is incorporated
`at the end of a growing strand of DNA during a
`DNA polymerase reaction” ..................................................... 26
`
`11. Limitation iii): “wherein the thymine
`deoxyribonucleotide analogue ... iii) produces a 3′-
`OH group on the deoxyribose upon cleavage of R” ............... 27
`
`12. Limitation iv): “wherein the thymine
`deoxyribonucleotide analogue ... iv) no longer
`includes a tag on the base upon cleavage of Y” ..................... 28
`
`13. Limitation v): “wherein the thymine
`deoxyribonucleotide analogue ... v) is capable of
`forming hydrogen bonds with adenine or an
`adenine nucleotide analogue” ................................................. 29
`
`14. Motivation ............................................................................... 30
`
`a.
`
`b.
`
`A 5-substituted analogue .............................................. 30
`
`The MOM capping group ............................................. 32
`
`15. Expectation of success ............................................................ 36
`
`B.
`
`Claim 2 .............................................................................................. 39
`
`VII. GROUND 2: OBVIOUSNESS OVER DOWER IN VIEW OF
`PROBER & HIATT ..................................................................................... 39
`
`A.
`
`Claim 1 .............................................................................................. 39
`
`1.
`
`2.
`
`The depicted structure ............................................................. 39
`
`Limitation R(a) ........................................................................ 42
`
`- iii -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`TABLE OF CONTENTS
`(cont’d)
`
`Page No.
`
`3.
`
`4.
`
`5.
`
`6.
`
`7.
`
`8.
`
`9.
`
`Limitation R(b) ....................................................................... 47
`
`The Stability Limitations ........................................................ 48
`
`The Provisos ............................................................................ 49
`
`The Tag Limitation ................................................................. 51
`
`Limitation Y ............................................................................ 52
`
`Limitations Y(a) and (b) ......................................................... 54
`
`Limitation i) ............................................................................ 55
`
`10. Limitation ii) ........................................................................... 56
`
`11. Limitation iii) .......................................................................... 57
`
`12. Limitation iv) .......................................................................... 57
`
`13. Limitation v) ........................................................................... 58
`
`14. Motivation ............................................................................... 59
`
`a.
`
`b.
`
`c.
`
`Combining Dower and Prober ...................................... 59
`
`Using a “small” blocking group ................................... 61
`
`The provisos .................................................................. 62
`
`15. Expectation of success ............................................................ 63
`
`B.
`
`Claim 2 .............................................................................................. 64
`
`VIII. GROUND 3: TSIEN ................................................................................... 64
`
`IX. GROUND 4: DOWER IN VIEW OF PROBER & METZKER ................ 69
`
`- iv -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`TABLE OF CONTENTS
`(cont’d)
`
`Page No.
`
`X. NO SECONDARY CONSIDERATIONS .................................................. 70
`
`XI. MANDATORY NOTICES PURSUANT TO 37 C.F.R.
`§42.8(A)(1) .................................................................................................. 70
`
`A.
`
`B.
`
`C.
`
`D.
`
`Real Party-In-Interest (37 C.F.R. §42.8(b)(1)) ................................. 70
`
`Related Matters (37 C.F.R. §42.8(b)(2)) ........................................... 70
`
`Lead and Backup Counsel (37 C.F.R. §42.8(b)(3)) .......................... 74
`
`Service Information (37 C.F.R. §42.8(b)(4)) .................................... 75
`
`XII. FEES ............................................................................................................ 75
`
`XIII. ADDITIONAL REQUIREMENTS UNDER 37 C.F.R. §42.104 ............... 75
`
`XIV. CONCLUSION ............................................................................................ 75
`
`
`
`
`
`- v -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`TABLE OF AUTHORITIES
`
`Page No(s).
`
`AC Techs. S.A. v. Amazon.com, Inc.,
`912 F.3d 1358 (Fed. Cir. 2019) .................................................................. 49, 62
`
`Acorda Therapeutics, Inc. v. Roxane Labs., Inc.,
`903 F.3d 1310 (Fed. Cir. 2018) ............................................................ 25, 27, 28
`
`In re Applied Materials, Inc.,
`692 F.3d 1289 (Fed. Cir. 2012) ........................................................................ 45
`
`Boston Sci. Scimed, Inc. v. Cordis Corp.,
`554 F.3d 982 (Fed. Cir. 2009) .......................................................................... 31
`
`In re Harris,
`409 F.3d 1339 (Fed. Cir. 2005) ........................................................................ 45
`
`Hospira, Inc. v. Fresenius Kabi USA, LLC,
`946 F.3d 1322 (Fed. Cir. 2020) ............................................................ 25, 27, 28
`
`Hybritech, Inc. v. Monoclonal Antibodies, Inc.,
`802 F.2d 1367 (Fed. Cir. 1986) ........................................................................ 38
`
`Kennametal, Inc. v. Ingersoll Cutting Tool Co.,
`780 F.3d 1376 (Fed. Cir. 2015) .................................................................. 17, 34
`
`MaxLinear, Inc. v. CF CRESPE LLC,
`880 F.3d 1373 (Fed. Cir. 2018) .................................................................. 67, 68
`
`Nestle USA, Inc. v. Steuben Foods, Inc.,
`884 F.3d 1350 (Fed. Cir. 2018) ........................................................................ 67
`
`New Hampshire v. Maine,
`532 U.S. 742 (2001) .......................................................................................... 68
`
`In re Peterson,
`315 F.3d 1325 (Fed. Cir. 2003) .................................................................. 44, 45
`
`- vi -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`TABLE OF AUTHORITIES
`(cont’d)
`
`Page No(s).
`
`Pfizer, Inc. v. Apotex, Inc.,
`480 F.3d 1348 (Fed. Cir. 2007) .................................................................. 17, 34
`
`PharmaStem Therapeutics, Inc. v. ViaCell, Inc.,
`491 F.3d 1342 (Fed. Cir. 2007) ................................................................. passim
`
`Pro-Mold & Tool Co. v. Great Lakes Plastics, Inc.,
`75 F.3d 1568 (Fed. Cir. 1996) .......................................................................... 33
`
`Regents of the Univ. of California v. Eli Lilly & Co.,
`119 F.3d 1559 (Fed. Cir. 1997) ........................................................................ 66
`
`Realtime Data, LLC v. Iancu,
`912 F.3d 1368 (Fed. Cir. 2019) ........................................................................ 32
`
`
`SimpleAir, Inc. v. Google LLC,
`884 F.3d 1160 (Fed. Cir. 2018) ........................................................................ 65
`
`Springs Window Fashions LP v. Novo Indus.
`323 F.3d 989 (Fed. Cir. 2003) ................................................................... passim
`
`Sud-Chemie, Inc. v. Multisorb Techs., Inc.,
`554 F.3d 1001 (Fed. Cir. 2009) .................................................................. 49, 62
`
`In re Swartz,
`232 F.3d 862 (Fed. Cir. 2000) .......................................................................... 38
`
`Vivid Techs., Inc. v. Am. Sci. & Eng’g. Inc.,
`200 F.3d 795 (Fed. Cir. 1999) .......................................................................... 13
`
`OTHER AUTHORITIES
`
`35 U.S.C. § 314 ...................................................................................................... 74
`
`35 U.S.C. § 325 ...................................................................................................... 74
`
`37 C.F.R. § 42.73 ................................................................................................... 68
`
`- vii -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`TABLE OF AUTHORITIES
`(cont’d)
`
`Page No(s).
`
`37 C.F.R. § 42.8 ......................................................................................... 70, 74, 75
`
`37 C.F.R. § 42.15 ................................................................................................... 75
`
`37 C.F.R. § 42.104 ................................................................................................. 75
`
`
`
`
`
`- viii -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`TABLE OF EXHIBITS
`
`Exhibit
`No.
`1001 U.S. Patent No. 10,407,458 (“Ju”) – (guanine with allyl proviso)
`
`Description
`
`1002 U.S. Patent No. 10,407,459 (“Ju”) – (adenine with allyl proviso)
`
`1003 U.S. Patent No. 10,457,984 (“Ju”) – (cytosine with allyl proviso)
`
`1004 U.S. Patent No. 10,435,742 (“Ju”) – (thymine with allyl proviso)
`
`1005
`
`1006
`
`1007
`
`1008
`
`1009
`
`1010
`
`1011
`
`1012
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`1013 U.S. Patent No. 7,790,869 (“Ju”)
`
`1014 U.S. Patent No. 7,713,698 (“Ju”)
`
`1015 U.S. Patent No. 8,088,575 (“Ju”)
`
`1016 U.S. Patent No. 9,718,852 (“Ju”) – (adenine)
`
`1017 U.S. Patent No. 9,719,139 (“Ju”) – (thymine)
`
`1018 U.S. Patent No. 9,708,358 (“Ju”) – (cytosine)
`
`1019 U.S. Patent No. 9,725,480 (“Ju”) – (guanine)
`
`Exhibit List, Page 1
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Exhibit
`No.
`1020 U.S. Patent No. 9,868,985 (“Ju”) – (method)
`
`Description
`
`1021
`
`1022
`
`1023
`
`1024
`
`1025
`
`1026
`
`1027
`
`1028
`
`1029
`
`2014-03-06 IPR2012-00007, Paper 140, Final Written Decision
`
`2014-03-06 IPR2012-00006, Paper 128, Final Written Decision
`
`2014-03-06 IPR2013-00011, Paper 130, Final Written Decision
`
`2019-06-21 IPR2018-00291, -00318, -00322, -00385, Final Written
`Decisions
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`2019-09-09 IPR2018-00797, Final Written Decision
`
`2015-07-17 Federal Circuit Opinion Affirming IPR2012-00006,
`IPR2012-00007 and IPR2013-00011
`
`1030 U.S. Patent No. 5,547,839 (“Dower”)
`
`1031 WO 91/06678 (“Tsien”)
`
`1032
`Exhibit number not used
`1033 Welch et al., “Syntheses of Nucleosides Designed for Combinatorial
`DNA Sequencing,” Chem. Eur. J., 5:951-960 (1999) (“Welch”)
`
`1034
`
`1035
`
`Exhibit number not used
`
`Exhibit number not used
`
`1036
`Exhibit number not used
`1037 Alberts et al., “Molecular Biology of the Cell,” Third Edition,
`Garland Publishing Inc., New York (1994)
`
`Exhibit List, Page 2
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Exhibit
`No.
`1038
`
`1039
`
`1040
`
`1041
`
`Description
`
`Exhibit number not used
`
`Metzker et al., “Termination of DNA synthesis by novel 3’-modified-
`deoxyribonucleoside 5’-triphosphates,” Nucleic Acids Research,
`22:4259-67 (1994) (“Metzker”)
`
`Sanger et al., “DNA sequencing with chain-terminating inhibitors,”
`Proc. Nat’l Acad. Sci. USA, 74:5463-5467 (1977) (“Sanger”)
`
`Prober et al., “A System for Rapid DNA Sequencing with Fluorescent
`Chain-Terminating Dideoxynucleotides,” Science, 238:336-341
`(1987) (“Prober”)
`
`1042 U.S. Patent No. 5,302,509 (“Cheeseman”)
`
`1043 U.S. Patent No. 5,763,594 (“Hiatt”)
`
`1044
`
`Pelletier et al., “Structures of Ternary Complexes of Rat DNA
`Polymerase β, a DNA Template-Primer, and ddCTP,” Science,
`264:1891-1903 (1994) (“Pelletier”)
`
`1045
`
`Exhibit number not used
`
`1046
`
`Rosenblum et al., “New dye-labeled terminators for improved DNA
`sequencing patterns,” Nucleic Acid Research, 25:4500-4504 (1997)
`(“Rosenblum”)
`
`1047
`
`Exhibit number not used
`
`1048
`
`1049
`
`1050
`
`Excerpts from 2019-01-14 Deposition Transcript of Dr. Menchen in
`IPR2018-00291, -00318, -00322, and -00797
`
`2018-05-04 IPR2018-00385, Paper 13, Patent Owner Preliminary
`Response
`
`Canard et al., “Catalytic editing properties of DNA polymerases,”
`Proc. Nat’l Acad. Sci. USA, 92:10859-10863 (1995) (“Canard”)
`
`1051
`
`Exhibit number not used
`
`Exhibit List, Page 3
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Exhibit
`No.
`1052 Yu et al., “Cyanine dye dUTP analogs for enzymatic labeling of DNA
`probes,” Nucleic Acids Research, 22:3226-3232 (1994) (“Yu”)
`
`Description
`
`1053
`
`1054
`
`1055
`
`Livak et al., “Detection of single base differences using biotinylated
`nucleotides with very long linker arms,” Nucleic Acids Research,
`20:4831-4837 (1992) (“Livak”)
`
`Stryer, “Biochemistry,” Fourth Edition, W.H. Freeman and Co., New
`York (1995) (“Stryer”)
`
`Watson & Crick, “Genetical Implication of the Structure of
`Deoxyribonucleic Acid,” Nature, 171:964-967 (1953) (“Watson &
`Crick”)
`
`1056 U.S. Patent No. 5,151,507 (“Hobbs”)
`
`1057
`
`Exhibit number not used
`
`1058
`
`Excerpts from Sept. 4-5, 2013 Deposition Transcript of Dr. George L.
`Trainor in IPR2012-00007
`
`1059
`
`Exhibit number not used
`
`1060
`
`1061
`
`1062
`
`1063
`
`Hovinen et al., “Synthesis of 3´-O-(ω-Aminoalkoxymethyl)thymidine
`5´-Triphosphates, Terminators of DNA Synthesis that Enable 3’-
`Labeling,” J. Chem. Soc. Perkin Trans. 1, 211-217 (1994)
`(“Hovinen”)
`
`Exhibit number not used
`
`Excerpt from Prosecution History of U.S. Patent No. 9,725,480
`
`Ireland et al., “Approach to the Total Synthesis of Chlorothricolide:
`Synthesis of (±)-19,20-Dihydro-24-O-methylchlorothricolide, Methyl
`Ester, Ethyl Carbonate,” J. Org. Chem. 51:635-648 (1986) (“Ireland”)
`
`1064
`
`Exhibit number not used
`
`Exhibit List, Page 4
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Exhibit
`No.
`
`1065
`
`1066
`
`1067
`
`1068
`
`1069
`
`Description
`
`Excerpt from Prosecution History of U.S. Patent No. 10,428,380
`[U.S. Appl. No. 16/150,191] (2019-03-12 Pre-interview first office
`action)
`
`Ruparel et al., “Design and synthesis of a 3´-O-allyl photocleavable
`fluorescent nucleotide as a reversible terminator for DNA sequencing
`by synthesis,” PNAS, Vol. 102, No. 17, 5932-37 (2005) (“Ruparel”)
`
`Ju et al., “Four-color DNA sequencing by synthesis using cleavable
`fluorescent nucleotide reversible terminators,” PNAS, Vol. 103, No.
`52, 19635-40 (2006) (“Ju”)
`
`2015-02-11 IPR2013-00517, Paper 87, Final Written Decision
`
`2016-05-09 Federal Circuit Opinion Affirming IPR2013-00517
`
`1070 U.S. Patent No. 5,449,767 (“Ward”)
`
`1071
`
`Exhibit number not used
`
`1072 WO 98/33939 (“Anazawa”)
`
`1073 Anazawa (English Translation of WO 98/33939)
`
`1074
`
`Exhibit number not used
`
`1075
`
`1076
`
`1077
`
`PROTECTIVE GROUPS IN ORGANIC SYNTHESIS (Theodora W.
`Greene & Peter G.M. Wuts eds., 3rd ed. 1999) (excerpts) (“Greene &
`Wuts”)
`
`Boss et al., “Cleavage of Allyl Ethers with Pd/C,” Angew. Chem. Int.
`Ed. Engl., 15:558-559 (1976) (“Boss”)
`
`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,” J. Am. Chem. Soc.,
`120:2184-2185 (1998) (“Qian”)
`
`Exhibit List, Page 5
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Exhibit
`No.
`
`1078
`
`1079
`
`1080
`
`1081
`
`1082
`
`1083
`
`1084
`
`Description
`
`Kamal et al., “A Mild and Rapid Regeneration of Alcohols from their
`Allylic Ethers by Chlorotrimethylsilane/Sodium Iodide,” Tetrahedron
`Letters, 40:371-372 (1999) (“Kamal”)
`
`2014-07-25 Final Written Decision in IPR2013-00128, Paper 92
`
`2014-10-28 Final Written Decision in IPR2013-00266, Paper 73
`
`2016-01-29 Federal Circuit Opinion Affirming IPR2013-00128 and
`IPR2013-00266
`
`IPR2017-02172, Paper 20 (P.T.A.B. 2018)
`
`IPR2017-02174, Paper 20 (P.T.A.B. 2018)
`
`Meng et al., “Design and Synthesis of a Photocleavable Fluorescent
`Nucleotide 3´-O-Allyl-dGTP-PC-Bodipy-FL-510 as a Reversible
`Terminator for DNA Sequencing by Synthesis,” J. Org. Chem. 71,
`3248-3252 (2006) (“Meng”)
`
`1085
`
`Bi et al., “Design and Synthesis of a Chemically Cleavable
`Fluorescent Nucleotide, 3´-O-Allyl-dGTP-allyl-Bodipy-FL-510, as a
`Reversible Terminator for DNA Sequencing by Synthesis,” J. Am.
`Chem. Soc., 128, 2542-2543 (2006) (“Bi”)
`1086 Meng thesis from Dr. Ju’s laboratory at Columbia University (2006)
`(“Meng Thesis”)
`
`1087
`
`Wu, et al., “3´-O-modified nucleotides as reversible terminators for
`pyrosequencing,” PNAS, Vol. 104, No. 42, 16462-16467 (2007)
`(“Wu”)
`1088 Kim thesis from Dr. Ju’s laboratory at Columbia University (2008)
`(“Kim Thesis”)
`1089 Wu thesis from Dr. Ju’s laboratory at Columbia University (2008)
`(“Wu Thesis”)
`
`Exhibit List, Page 6
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Exhibit
`No.
`
`1090
`
`Description
`
`Zhang thesis from Dr. Ju’s laboratory at Columbia University (2008)
`(“Zhang Thesis”)
`
`1091
`
`Guo et al., “Four-color DNA sequencing with 3´-O-modified
`nucleotide reversible terminators and chemically cleavable
`fluorescent dideoxynucleotides,” PNAS, Vol. 105, No. 27, 9145-9150
`(2008) (“Guo”)
`1092 Guo thesis from Dr. Ju’s laboratory at Columbia University (2009)
`(“Guo Thesis”)
`1093 Yu thesis from Dr. Ju’s laboratory at Columbia University (2010)
`(“Yu Thesis”)
`1094 Qui thesis from Dr. Ju’s laboratory at Columbia University (2011)
`(“Qui Thesis”)
`
`1095
`
`Exhibit number not used
`
`1096
`
`1097
`
`1098
`
`Lipshutz et al., “Hydrolysis of Acetals and Ketals Using LiBF4,”
`Synthetic Communications, 12:4, 267-277 (1982)
`
`Curriculum Vitae of Floyd Romesberg, Ph.D.
`
`Exhibit number not used
`
`1099 U.S. Patent No. 7,270,951 (“Stemple”)
`
`1100 Kraevskii et al., Molecular Biology 21:25-29 (1987) (“Kraevskii”)
`
`1101
`
`1102
`
`1103
`
`1104
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`Seitz et al., HYCRON, an Allylic Anchor for High-Efficiency Solid
`Phase Synthesis of Protected Peptides and Glycopeptides,” J. Org.
`Chem., 62:813-826 (1997) (“Seitz”)
`
`Exhibit List, Page 7
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Exhibit
`No.
`
`1105
`
`1106
`
`Description
`
`Greenberg et al., “Optimization and Mechanistic Analysis of
`Oligonucleotide Cleavage from Palladium-Labile Solid-Phase
`Synthesis Supports,” J. Org. Chem., 63:4062-4068 (1998)
`(“Greenberg”)
`
`Gullier et al., “Linkers and Cleavage Strategies in Solid-Phase
`Organic Synthesis and Combinatorial Chemistry,” Chem. Rev.,
`100:2091-2157 (2000) (“Guillier Review 2000”)
`
`1107
`
`Fields, Methods in Molecular Biology, Volume 35, Peptide Synthesis
`Protocols, Chapter 2, Humana Press 1994 (“Fields”)
`1108 Gigg et al., “The Allyl Ether as a Protecting Group in Carbohydrate
`Chemistry Part II”, J. Chem. Soc. (C), 1903-1911 (1968) (“Gigg”)
`
`1109
`
`IUPAC, Nomenclature of Organic Chemistry, Eds. Rigaudy et al.,
`International Union of Pure and Applied Chemistry, Organic
`Chemistry Division, Commission on Nomenclature of Organic
`Chemistry, Pergamon Press, 1979.
`
`1110
`
`CRC Handbook of Chemistry and Physics, eds. Weast et al., 72nd
`edition, CRC Press (1991)
`1111 McGraw-Hill Dictionary of Chemistry, ed. Parker, McGraw-Hill
`Book Co., 1984
`1112 Vollhardt et al., “Organic Chemistry,” W.H. Freeman and Co., New
`York (2d ed. 1994) (“Vollhardt”)
`
`1113
`
`Solomons, “Organic Chemistry”, Fourth Edition, John Wiley & Sons
`(1988) (“Solomons”)
`1114 Morrison et al., “Organic Chemistry,” Third Edition, Allyn and
`Bacon, Inc. (1973)
`
`1115
`
`Dominguez et al., “DNA polymerase mu (Pol μ), homologous to
`TdT, could act as a DNA mutator in eukaryotic cells,” The EMBO
`Journal, 19(7): 1731-1742 (2000) (“Dominguez”)
`
`Exhibit List, Page 8
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Exhibit
`No.
`
`Description
`
`1116
`
`1117
`
`1118
`
`1119
`
`1120
`
`1121
`
`1122
`
`1123
`
`1124
`
`1125
`
`1126
`
`1127
`
`Ito et al., “Compilation and alignment of DNA polymerase
`sequences,” Nucleic Acids Research, 19: 4045-4057 (1991) (“Ito”)
`
`Collins et al., “A rapid method for mRNA detection in single-cell
`Biopsies from preimplantation-stage bovine embryos,”
`Theriogenology, 43: 1227-1238 (1995) (“Collins”)
`
`Haber et al., “Diagnosis of Flame Chlorosis by Reverse
`Transcription–Polymerase Chain Reaction (RT-PCR),” Plant Disease,
`79(6): 626-630 (1995) (“Haber”)
`
`Sidorova et al., “A rapid RT-PCR based method for the detection of
`BCR-ABL translocation,” J. Clin Pathol: Mol Pathol 50: 266-268
`(1997) (“Sidorova”)
`
`Stromskaya et al., “Cell-specific effects of RAS oncogene and protein
`kinase C agonist TPA on P-glycoprotein function,” FEBS Letters,
`368: 373-376 (1995) (“Stromskaya”)
`
`Bechtereva et al., “DNA sequencing with thermostable Tet DNA
`polymerase from Thermus thermophilus,” Nucleic Acids Research,
`17: 10507 (1989) (“Bechtereva”)
`
`Asakura et al., “Cloning, Nucleotide Sequence, and Expression in
`Escherichia coli of DNA Polymerase Gene (polA) from Thermus
`thermophilus HB8,” Journal of Fermentation and Bioengineering,
`76(4): 265-269 (1993) (“Asakura”)
`
`Ikeda et al., “A Non-radioactive DNA Sequencing Method Using
`Biotinylated Dideoxynucleoside Triphosphates and ΔTth DNA
`Polymerase,” DNA Research, 2: 225-227 (1995) (“Ikeda”)
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit List, Page 9
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Exhibit
`No.
`1128
`
`1129
`
`1130
`
`Exhibit number not used
`
`Exhibit number not used
`
`Exhibit number not used
`
`Description
`
`1131 Declaration of Dr. Floyd Romesberg, Ph.D.
`
`1132
`
`List of documents considered by Floyd Romesberg, Ph.D.
`
`Excerpt from Prosecution History of U.S. Patent No. 10,435,742
`(Declaration of Jingyue Ju and Accompanying Documents)
`
`Excerpt from Prosecution History of U.S. Patent No. 10,435,742
`(2019-02-15 Pre-interview First Office Action)
`
`Excerpt from Prosecution History of U.S. Patent No. 10,435,742
`(2019-02-26 Applicant Arguments/Remarks Made in an Amendment)
`
`Excerpt from Prosecution History of U.S. Patent No. 10,435,742
`(2019-05-13 Applicant Arguments/Remarks Made in an Amendment)
`
`1133
`
`1134
`
`1135
`
`1136
`
`
`
`Exhibit List, Page 10
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`Illumina requests inter partes review of claims 1-2 of U.S. Patent No.
`
`10,435,742 (Ex. 1004) owned by The Trustees of Columbia University.
`
`I. INTRODUCTION
`
`Illumina manufactures and sells innovative DNA sequencing instruments and
`
`is a global leader in DNA sequencing technologies. Columbia, which has no
`
`commercial products, has been seeking royalties from Illumina for nearly a decade
`
`by repeatedly asserting the same family of invalid patents that contain functionally-
`
`defined claims extending well beyond any contribution by Columbia to DNA
`
`sequencing.
`
`Columbia’s initial patents from this family have never been asserted against
`
`Illumina. However, once Illumina launched its products using a different technology
`
`in 2006, Columbia veered from any purported invention in its patent disclosure to
`
`try to encompass Illumina’s products. When Columbia first attempted to monetize
`
`related patents covering modified nucleotides, Illumina petitioned for IPR. The
`
`Board held all challenged claims unpatentable:
`
`First Wave Determination
`IPR2012-00007 (Ex. 1021)
`
`IPR2012-00006 (Ex. 1022)
`
`IPR2013-00011 (Ex. 1023)
`
`Columbia’s Patent
`7,790,869
`(Ex. 1013)
`7,713,698
`(Ex. 1014)
`8,088,575
`(Ex. 1015)
`
`Result
`
`All challenged
`claims
`unpatentable
`
`
`
`- 1 -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`The Federal Circuit affirmed the Board’s decisions. Ex. 1029. The Court
`
`faulted Columbia for its limited patent disclosure, observing that “if novel and
`
`nonobvious chemistry was needed to practice the claimed inventions, Dr. Ju would
`
`have been obligated to disclose this chemistry in the patent.” Id. at 31.
`
`Undeterred, Columbia initiated a second wave of litigation, asserting five
`
`later-obtained patents covering the same type of modified nucleotides from the same
`
`patent family. Illumina again petitioned for IPR, and the Board again held all
`
`challenged claims unpatentable:
`
`Second Wave Determination
`IPR2018-00291 (Ex. 1024)
`
`IPR2018-00318 (Ex. 1024)
`
`IPR2018-00322 (Ex. 1024)
`
`IPR2018-00385 (Ex. 1024)
`
`IPR2018-00797 (Ex. 1028)
`
`
`
`Result
`
`All challenged
`claims
`unpatentable
`
`Columbia’s Patent
`9,718,852
`(Ex. 1016)
`9,719,139
`(Ex. 1017)
`9,708,358
`(Ex. 1018)
`9,725,480
`(Ex. 1019)
`9,868,985
`(Ex. 1020)
`
`In the second wave of IPRs, the Board expressed the same concern as the
`
`Federal Circuit regarding Columbia’s limited patent disclosure, determining that this
`
`weighed against many of Columbia’s arguments. See Ex. 1024: 44. Columbia has
`
`appealed these decisions, and Illumina expects another affirmance.
`
`Columbia now continues its quest to reach beyond the bounds of its
`
`disclosure. Having had eight patents invalidated, failing twice before the Board and
`
`- 2 -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`once before the Federal Circuit, Columbia resorted to a different audience—an
`
`Examiner—to re-litigate patentability. Columbia filed twelve additional patent
`
`applications from the same patent family, claiming overbroad and unpatentable
`
`subject matter.
`
` These
`
`twelve applications
`
`issued with claims covering
`
`indistinguishable subject matter from prior, invalidated, claims. All told, it may take
`
`20 IPR petitions for the Board to police Columbia’s repeated attempts to patent the
`
`same, overbroad claims to assert against Illumina.
`
`The claims deemed unpatentable in the second wave of IPRs are identical to
`
`the claims challenged in this IPR, with the exception that a single species of allyl
`
`capping group was removed from the claimed genus. Compare Ex. 1017: 34:2-35:6
`
`with Ex. 1004: 33:22-34:61 (adding the allyl proviso: “is not a –CH2CH=CH2 group”
`
`(claim 1) and “is not … an allyl ether group” (claim 2)). The only reason Columbia
`
`added these provisos is because Illumina argued, and the Board determined, that it
`
`would have been obvious to cap the claimed nucleotide with an allyl ether.
`
`Columbia’s drafting effort is nothing but an attempt to circumvent the Board’s prior
`
`determinations. With this effort, Columbia has veered away from Dr. Ju’s purported
`
`invention by excluding the unpatentable allyl capping group that he actually used in
`
`his own lab. Exs. 1066-1067, 1084-1094. All to try to cover an undisclosed capping
`
`group, developed and patented by Illumina, which is non-obvious over Columbia’s
`
`patent disclosures. Exs. 1068, 1069.
`
`- 3 -
`
`
`
`Illumina v. Columbia
`IPR Petition –Patent 10,435,742
`
`The Board should cancel claims 1-2 of the ’742 patent. Columbia’s
`
`specification only discloses two species of capping groups—methoxymethyl
`
`(“MOM”) and the unpatentable allyl group. Columbia now carves out the allyl
`
`group in the hope that the identical genus (minus allyl) will survive scrutiny.
`
`However, the MOM group was also a known, reversible capping group for use
`
`during polymerase-mediated DNA synthesis. Accordingly, the MOM group is
`
`another unpatentable species of the claimed genus.
`
`Moreover, during prosecution Columbia expressly relied upon
`
`the
`
`unpatentable allyl group to support and secure issuance of the instant claims despite
`
`the exclusionary allyl proviso. Columbia should not have been allowed to embrace
`
`such obvious subject matter to secure patent issuance and yet avoid the Board’s
`
`unpatentability determination. Columbia’s reliance on the unpatentable allyl group
`
`also renders the instant claims obvious.
`
`II. STATE OF THE ART
`
`The state of the art remains the same as in the eight prior Board determinations
`
`which invalidated Columbia’s claims.
`
`A. Deoxyribonucleotides Were Known
`
`Deoxyri
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