Illumina v. Columbia
`IPR Petition – U.S. Patent 10,435,742
`
`LIST OF DOCUMENTS CONSIDERED
`BY FLOYD ROMESBERG, PH.D.
`
`Exhibit
`No.
`1004 U.S. Patent No. 10,435,742 (“Ju”) – (thymine with allyl proviso)
`
`Description
`
`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)
`
`1020 U.S. Patent No. 9,868,985 (“Ju”) – (method)
`
`1030 U.S. Patent No. 5,547,839 (“Dower”)
`
`1031 WO 91/06678 (“Tsien”)
`1033 Welch et al., “Syntheses of Nucleosides Designed for Combinatorial
`DNA Sequencing,” Chem. Eur. J., 5:951-960 (1999) (“Welch”)
`1037 Alberts et al., “Molecular Biology of the Cell,” Third Edition,
`Garland Publishing Inc., New York (1994)
`
`1039
`
`1040
`
`1041
`
`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”)
`
`1
`
`Illumina Ex. 1132
`IPR Petition - USP 10,435,742
`
`
`IPR Petition – U.S. Patent 10,435,742
`
`LIST OF DOCUMENTS CONSIDERED
`BY FLOYD ROMESBERG, PH.D.
`
`Exhibit
`No.
`1004 U.S. Patent No. 10,435,742 (“Ju”) – (thymine with allyl proviso)
`
`Description
`
`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)
`
`1020 U.S. Patent No. 9,868,985 (“Ju”) – (method)
`
`1030 U.S. Patent No. 5,547,839 (“Dower”)
`
`1031 WO 91/06678 (“Tsien”)
`1033 Welch et al., “Syntheses of Nucleosides Designed for Combinatorial
`DNA Sequencing,” Chem. Eur. J., 5:951-960 (1999) (“Welch”)
`1037 Alberts et al., “Molecular Biology of the Cell,” Third Edition,
`Garland Publishing Inc., New York (1994)
`
`1039
`
`1040
`
`1041
`
`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”)
`
`1
`
`Illumina Ex. 1132
`IPR Petition - USP 10,435,742
`
`
`
`Illumina v. Columbia
`IPR Petition – U.S. Patent No. 10,435,742
`
`Exhibit
`No.
`
`1044
`
`1046
`
`Description
`
`Pelletier et al., “Structures of Ternary Complexes of Rat DNA
`Polymerase β, a DNA Template-Primer, and ddCTP,” Science,
`264:1891-1903 (1994) (“Pelletier”)
`
`Rosenblum et al., “New dye-labeled terminators for improved DNA
`sequencing patterns,” Nucleic Acid Research, 25:4500-4504 (1997)
`(“Rosenblum”)
`
`1050
`
`Canard et al., “Catalytic editing properties of DNA polymerases,”
`Proc. Nat’l Acad. Sci. USA, 92:10859-10863 (1995) (“Canard”)
`1052 Yu et al., “Cyanine dye dUTP analogs for enzymatic labeling of DNA
`probes,” Nucleic Acids Research, 22:3226-3232 (1994) (“Yu”)
`
`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”)
`
`1060
`
`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”)
`
`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”)
`
`1070 U.S. Patent No. 5,449,767 (“Ward”)
`
`2
`
`
`
`Illumina v. Columbia
`IPR Petition – U.S. Patent No. 10,435,742
`
`Exhibit
`No.
`
`1075
`
`1076
`
`1077
`
`Description
`
`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”)
`
`1096
`
`Lipshutz et al., “Hydrolysis of Acetals and Ketals Using LiBF4,”
`Synthetic Communications, 12:4, 267-277 (1982)
`
`1097
`
`Curriculum Vitae of Floyd Romesberg, Ph.D.
`
`1099 U.S. Patent No. 7,270,951 (“Stemple”)
`
`1100 Kraevskii et al., Molecular Biology 21:25-29 (1987) (“Kraevskii”)
`
`1104
`
`1105
`
`1106
`
`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”)
`
`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”)
`
`3
`
`
`
`Illumina v. Columbia
`IPR Petition – U.S. Patent No. 10,435,742
`
`Exhibit
`No.
`
`1109
`
`Description
`
`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
`
`1116
`
`1117
`
`1118
`
`1119
`
`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”)
`
`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”)
`
`4
`
`
`
`Illumina v. Columbia
`IPR Petition – U.S. Patent No. 10,435,742
`
`Exhibit
`No.
`
`1120
`
`1121
`
`1122
`
`1123
`
`Description
`
`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”)
`
`1132
`
`List of documents considered by Floyd Romesberg, Ph.D.
`
`
`
`33024807
`
`5
`
`
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