Illumina Ex. 1054
`IPR Petition - USP 9,719,139
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`
`US. PATENT DOCUMENTS
`5/1994
`Takahashi et al.
`7/1994
`Ward et al.
`7/1994
`Prober et al.
`7/1995
`Hyman
`8/1995
`McClelland et al.
`9/1995
`Ward et al.
`12/1995
`Ward et al.
`5/1996
`Hyman
`7/1996
`Uhlen et al.
`8/1996
`Dower et al.
`8/1996
`Goodman et al.
`9/1996
`Douglas
`Brenner
`2/1997
`2/1997
`Hyman
`6/1997
`Wilding et al.
`8/1997
`Mathies
`8/1997
`Wong
`1/1998
`Shattuck et al.
`3/1998
`Mathies
`6/1998
`Hiatt et al.
`6/1998
`Lane et al.
`6/1998
`Southern
`8/1998
`Konrad
`8/1998
`Canard et al.
`9/1998
`Ju et al.
`9/1998
`Hiatt et al.
`9/1998
`Ju et al.
`10/1998
`Khan et al.
`11/1998
`Katzir
`12/1998
`Reeve et a1.
`12/1998
`Glazer
`1/1999
`Chee et al.
`2/1999
`Mathies
`2/1999
`Hiatt et al.
`3/1999
`Ju et al.
`3/1999
`Haff et al.
`6/1999
`Kumar et a1.
`8/1999
`Kwok
`9/1999
`Ju et al.
`Brenner
`10/1999
`12/1999
`Canard et al.
`12/1999
`Will
`12/1999
`Benson et a1.
`2/2000
`Mathies
`4/2000
`Ju et al.
`Koster
`6/2000
`7/2000
`Rosenthal et al.
`10/2000
`Anazawa et a1.
`1/2001
`JuVinall
`3/2001
`Makarov et al.
`3/2001
`Auer et al.
`4/2001
`Nyren et al.
`4/2001
`Hiatt et al.
`4/2001
`Sampson
`4/2001
`Rothschild et al.
`4/2001
`Schwartz et al.
`5/2001
`Hiatt et al.
`6/2001
`Anazawa et a1.
`6/2001
`Bogdanov
`7/2001
`Kwiatkowski
`8/2001
`Rothberg
`8/2001
`Tyagi et a1.
`9/2001
`Shi et al.
`9/2001
`Bensimon et a1.
`10/2001
`Livak et a1.
`10/2001
`Kwiatkowski et al.
`11/2001
`Van Ness et al.
`11/2001
`Egholm
`3/2002
`Van Ness et al.
`4/2002
`Kitamura et al.
`2/2003
`Seeger et al.
`4/2003
`O’Donnell
`9/2003
`Ness et al.
`9/2003
`Parce et al.
`9/2003
`Ju et al.
`10/2003
`Mehta et a1.
`10/2003
`Kwiatkowski
`12/2003
`Ju et al.
`
`5,308,990
`5,328,824
`5,332,666
`5,436,143
`5,437,975
`5,449,767
`5,476,928
`5,516,664
`5,534,424
`5,547,839
`5,547,859
`5,556,748
`5,599,675
`5,602,000
`5,637,469
`5,654,419
`5,658,736
`5,709,999
`5,728,528
`5,763,594
`5,770,365
`5,770,367
`5,789,167
`5,798,210
`5,804,386
`5,808,045
`5,814,454
`5,821,356
`5,834,203
`5,849,542
`5,853,992
`5,856,104
`5,869,255
`5,872,244
`5,876,936
`5,885,775
`5,908,755
`5,945,283
`5,952,180
`5,962,228
`6,001,566
`6,001,611
`6,008,379
`6,028,190
`6,046,005
`6,074,823
`6,087,095
`6,136,543
`6,175,107
`6,197,557
`6,207,831
`6,210,891
`6,214,987
`6,218,118
`6,218,530
`6,221,592
`6,232,465
`6,242,193
`6,245,507
`6,255,475
`6,274,320
`6,277,607
`6,287,821
`6,294,324
`6,309,829
`6,309,836
`6,312,893
`6,316,230
`6,361,940
`6,380,378
`6,524,829
`6,555,349
`6,613,508
`6,613,513
`6,627,748
`6,632,655
`6,639,088
`6,664,079
`
`6,664,399 B1
`6,713,255 B1
`6,780,591 B2
`6,787,308 B2
`6,818,395 B1
`6,833,246 B2
`6,864,052 B1
`6,911,345 B2
`6,934,636 B1
`6,982,146 B1
`7,037,687 B2
`7,056,661 B2
`7,056,666 B2
`7,057,026 B2
`7,057,031 B2
`7,074,597 B2
`7,078,499 B2
`7,105,300 B2
`7,329,496 B2
`7,345,159 B2
`7,414,116 B2
`7,427,673 B2
`7,459,275 B2
`7,566,537 B2
`7,622,279 B2
`7,635,578 B2
`7,713,698 B2
`2002/0012966 A1
`2002/0168642 A1
`2003/0008285 A1
`2003/0022225 A1
`2003/0027140 A1
`2003/0044871 A1
`2003/0054360 A1
`2003/0099972 A1
`2003/0166282 A1
`2003/0186256 A1
`2003/0190680 A1
`2003/0198982 A1
`2004/0014096 A1
`2004/0096825 A1
`2004/0185466 A1
`2005/0032081 A1
`2005/0239134 A1
`2006/0003352 A1
`2006/0057565 A1
`2006/0105461 A1
`2006/0240439 A1
`2006/0252938 A1
`2007/0166705 A1
`2007/0275387 A1
`2008/0131895 A1
`2008/0199868 A1
`2008/0319179 A1
`2009/0088332 A1
`
`12/2003
`3/2004
`8/2004
`9/2004
`11/2004
`12/2004
`3/2005
`6/2005
`8/2005
`1/2006
`5/2006
`6/2006
`6/2006
`6/2006
`6/2006
`7/2006
`7/2006
`9/2006
`2/2008
`3/2008
`8/2008
`9/2008
`12/2008
`7/2009
`11/2009
`12/2009
`5/2010
`1/2002
`11/2002
`1/2003
`1/2003
`2/2003
`3/2003
`3/2003
`5/2003
`9/2003
`10/2003
`10/2003
`10/2003
`1/2004
`5/2004
`9/2004
`2/2005
`10/2005
`1/2006
`3/2006
`5/2006
`10/2006
`11/2006
`7/2007
`11/2007
`6/2008
`8/2008
`12/2008
`4/2009
`
`Sabesan
`Makino et al.
`Williams et al.
`Balasubramanian et a1.
`Quake et al.
`Balasubramanian et a1.
`Drmanac et al.
`Quake et al.
`Skierczynski et al.
`Schneider et a1.
`Williams et al.
`Korlach et a1.
`Dower et al.
`Barnes et al.
`Olejnik et al.
`Ju
`Odedra et al.
`Parce et al.
`Dower et al.
`Ju et al.
`Milton et al.
`Balasubramanian et a1.
`Dower et al.
`Balasubramanian et a1.
`
`Monforte et al.
`Ju et al.
`Cutsforth et al.
`Gold et al.
`Olejnik
`Brown et al.
`Fischer et a1.
`Rothschild et al.
`Seela et a1.
`Anderson et al.
`Chenna et al.
`Ju et al.
`Ju et al.
`Gorenstein et a1.
`Lipkin et al.
`Ju et al.
`Tom-Moy et al.
`Smith et al.
`Sava et al.
`Milton et al.
`Ju
`Ju et al.
`Ju et al.
`Ju et al.
`Ju et al.
`
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`
`FOREIGN PATENT DOCUMENTS
`0 992 511 A
`4/2000
`0995804
`4/2000
`1182267
`2/2002
`1291354
`3/2003
`0808320
`4/2003
`1337541
`3/2007
`1218391
`4/2007
`1790736
`5/2007
`WO 89/09282
`10/1989
`WO 90/13666
`11/1990
`WO 91/06678
`5/1991
`WO 92/10587
`6/1992
`WO 93/05183
`3/1993
`WO 93/21340
`10/1993
`WO 94/14972
`7/1994
`WO 96/07669
`3/1996
`WO 96/23807
`8/1996
`WO 96/27025
`9/1996
`WO 97/08183
`3/1997
`WO 97/27317
`7/1997
`WO 97/35033
`9/1997
`WO 98/30720
`7/1998
`
`

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`
`Page 3
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`W0
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`W0
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`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`W0
`WO
`W0
`W0
`
`WO 98/44151
`WO 99/05315
`WO 00/02895
`WO 00/06770
`WO 00/09753
`WO 00/15844
`WO 00/18956
`WO 00/21974
`WO 00/50172
`WO 00/50642
`WO 00/53805
`WO 00/53812
`WO 00/70073
`WO 01/16375
`WO 01/23610
`WO 01/25247
`WO 01/27625 A
`WO 01/32930
`WO 01/57248
`WO 01/57249
`WO 01/92284
`WO 02/02813
`WO 02/22883 A1
`WO 02/29003
`W0 02/072892
`W0 02/079519 A1
`W0 02/088381
`W0 02/088382
`W0 03/002767
`W0 03/020968
`W0 03/048178
`W0 03/048387
`W0 03/085135
`WO 2004/007773
`WO 2004/055160
`WO 2004/018493
`WO 2004/018497
`WO 2004/108497
`WO 2005/084367
`WO 2006/073436
`WO 2007/002204
`WO 2007/053702
`WO 2007/053719
`WO/2007/062105
`WO 2008/069973
`WO 99/57321
`
`10/1998
`2/1999
`1/2000
`2/2000
`2/2000
`3/2000
`4/2000
`4/2000
`8/2000
`8/2000
`9/2000
`9/2000
`11/2000
`3/2001
`4/2001
`4/2001
`4/2001
`5/2001
`8/2001
`8/2001
`12/2001
`1/2002
`3/2002
`4/2002
`9/2002
`10/2002
`11/2002
`11/2002
`1/2003
`3/2003
`6/2003
`6/2003
`10/2003
`1/2004
`1/2004
`3/2004
`3/2004
`4/2004
`9/2005
`7/2006
`1/2007
`5/2007
`5/2007
`5/2007
`6/2008
`11/2009
`
`OTHER PUBLICATIONS
`
`U.S. Appl. No. 90/008,152, filed Aug. 3, 2006, Gitten.
`Arbo et al. (1993) “Solid Phase Synthesis of Protected Peptides
`Using New Cobalt (Ill) Amine Linkers,” Int. J. Petide.Protein Res.
`42: 138-154.
`Axelrod, V.D. et al. (1978) “Specific termination of RNA polymerase
`synthesis as a method of RNA and DNA sequencing” Nucleic Acids
`Res. 5(10) :3549-3563.
`Badman, E. R. et al. (2000) “A Parallel Miniature Cylindrical Ion
`Trap Array,” Anal. Chem. (2000) 72:3291-3297.
`Badman, E.R. et al. (2000) “Cylnidrical Ion Trap Array with Mass
`Selection by Variation in Trap Dimensions,” Anal. Chem. 72:5079-
`5086.
`Burgess, K. et al (1997) “Photolytic Mass Laddering for Fast Char-
`acterization of Oligomores on Single Resin Beads,” J. Org. Chem.
`62:5662-5663.
`(1993)
`and Glazer, A.N.
`Benson,
`S.C., Mathies, RA,
`“Heterodimeric DNA-binding dyes designed .
`.
`. application of the
`DNA complexes,” Nucleic Acids REs. 21 :5720-5726.
`Benson, S.C., Singh, P., and Glazer, A.N. (1993) “Heterodimeric
`DNA-binding dyes designed .
`.
`. spectroscopic properties,” Nucleic
`Acids REs. 21:5727-5735.
`Bergseid M., Baytan A.R., Wiley JP, Ankener W.M., Stolowitz,
`Hughs K.A., and Chestnut JD. (2000) “Small-molecule base .
`.
`.
`proteins,” BioTechniques 29: 1 126-1 133.
`Buck, G.A. et al. (1999) “Design Strategies and Performance of
`Custom DNA Sequencing Primers,” BioTechniques 27(3):528-536.
`Buschmann et
`al.
`(1999)
`“The Complex Formation of A,
`(n-Dicarboxylic Acidsd and A,
`(n-Diols with Cucurbituril and
`OL-Cyclodextrin,” Acata Chim. Slov. 46 (3):405-411.
`
`Canard, B. et al. (1995) “Catalytic editing properties of DNA
`polymerases,” Proc. Natl. Acad. Sci. USA 92:10859-10863.
`Caruthers, M.H. (1985) “Gene synthesis machines: DNA chemistry
`and its uses,” Science 230:281-285.
`Chee, M. et al. (1996) “Accessing genetic information with high
`density DNA arrays,” Science 274:610-614.
`Chen, X. And Kwok, P. -Y. (1997) “Template-directed dye-terminator
`incorporation (TDI) assay: a homogeneous DNA diagnostic .
`.
`.
`transfer,” Nucleic Acids Res. 25:347-353.
`Chiu, N. H., Tang, K.,Yip, P., Braun, A., Koster, H., and Cantor, CR.
`(2000) “Mass spectrometry of single-stranded .
`.
`. sequence,” Nucleic
`Acids Res. 28:E31.
`Edwards, J. et al. (2001) “DNA sequencing using biotinylated
`dideoxynucleotides and mass spectrometry,” Nucleic Acids Res.
`29(21)1041-1046.
`Elango, N. et al. (1983) “Amino Acid Sequence of Human Respira-
`tory Syncytial Virus Nucleocapsid Protein.” Nucleic Acids Research
`11(17):5941-5951.
`Fallahpour (2000) “Photochemical and Thermal reactions of Azido-
`Oligopyridines: Diazepinones, a New Class of Metal-Complex
`Ligands,” Helvetica Chimica Acta. 83:384-393.
`Fei, Z. et al. (1998) “MALDI-TOF mass spectrometric typing of
`single nucleotide polymorphisms with mass-tagged ddNTPs,”
`Nucleic Acids Research 26(11):2827-2828.
`Fu, DJ, et al (1998) “Sequencing exons 5 to 8 of the p53 gene by
`MALDI-TOF mass spectrometry,” Nat. Biotechnol, 16:381-384.
`Griffin, T.J. et al. (1999) “Direct Genetic Analysis by Matrix-Assisted
`Laser Desorption/Ionization Mass Spectrometry,” Proc. Nat. Acad.
`Sci. USA 96:6301-6306.
`Hacia J.G., Edgemon K., Sun B., Stern D., Fodor 8A., and Collins
`F.S. (1998) “Two Color Hybridization Analysis Using High .
`.
`.
`Transfer Dyes,” Nucleic Acids Res. 26:3865-6.
`HaffL.A.; et al. (1997) “Multiplex Genotyping of PCRProducts with
`Mass Tag-Labeled Primers,” Nucleic Acids Res. 25(18):3749-3750.
`Hafliger, D. et al. (1997) “Semi-nested RT-PCR Systems for Small
`Round Structured Viruses and Detection .
`.
`. Seafood,” International
`Journal of Food Microbiology, 37:27-36.
`Henner, W.D. et al. (1983) “Enzyme Action at 3‘ Termini of Ionizing
`Radiation-Induced DNA Strand Breaks,”
`J. Biol. Chem.
`258(24):15198-15205.
`Hultman et al. (1989) “Direct Solid Phase Sequencing of Genomic
`and Plasmid DNA Using Magnetic Beads as Solid Support,” Nucleic
`Acids Research 17(3):4937-4946.
`Hyman, ED, (1988) “A new method of sequencing DNA,” Analyti-
`cal Biochemistry 174:423-436.
`Ireland, R.E. And Varney, MD. (1986) “Approach to the total syn-
`thesis of chlorothricolide synthesis of (+/)-19.20-dihydro-24-O- .
`.
`.
`ethyl carbonate,” J. Org. Chem. 51:635-648.
`Kamal, A., Laxman, E., and Rao, NV. (1999) “A mild and rapid
`regeneration of alcohols from their allylic ethers .
`.
`. iodide,” Tetra-
`hedron Lett 40:371-372.
`Ikeda, K. et al. (1995) “A Non-Radioactive DNA Sequencing Method
`Using Biotinylated Dideoxynucleoside Triphosphates and Delta
`TTH DNA Polymerase,” DNA Research 2(31):225-227.
`Jiang-Baucom, P. et al. (1997) “DNA Typing of Human Leukocyte
`Antigen Sequence Polymorphisms by Peptide Nucleic Acid Probes
`and .
`.
`. Spectrometry,” Anal. Chem. 69:4894-4896.
`Jingyue Ju, et al. (1996) “Cassette labeling for facile construction of
`energy transfer fluorescent primers,” Nuc. Acids Res. 24(6):1144-
`1 148.
`Ju J., Glazer, AN, and Mathies, RA. (1996) “Energy transfer prim-
`ers: A new fluorescence labeling paradigm for DNA sequencing and
`analysis,” Nature Medicine 2: 246-249.
`Ju J., Ruan C., Fuller, C.W., Glazer, AN, and Mathies, RA. (1995)
`“Fluorescence energy transfer dye-labeled primers for .
`.
`. analysis,”
`Proc. Natl. Acad. Sci. USA 92:4347-4351.
`Jurinke, C., van de Boom, D., Collazo, V., Luchow, A., Jacob, A., and
`Koster H. (1997) “Recovery of nucleic acids from immobilized .
`.
`.
`spectrometry,” Anal. Chem 69:904-910.
`Kim, S. et al.
`(2003) “Multiplex Genotyping of the Human
`[32-adrenergic Receptor Gene Using Solid-phase Capturable .
`.
`.
`Spectrometry,” Analytical Biochemistry 316:251-258.
`
`

`

`US 8,088,575 B2
`
`Page 4
`
`Kim Sobin et al. (2002) “Solid Phase Capturable Dideoxynucleotides
`for Multiplex Genotyping Using Mass Spectrometry,” Nucleic Acids
`Research 30(16):e85.1-e85.6.
`Kokoris, M. et al. (2000) High-throughput SNP Genotyping With the
`Masscode System, Molecular Diagnosis 5(4):329-340.
`Kolb et al. (2001) “Click Chemistry: Diverse Chemical Function
`From a Few Good Reactions,” Angew. Chem. Int. Ed. 40:2004-2021.
`Kraevskii, A.A. et al.
`(1987) “Substrate Inhibitors of DNA
`Biosynthesis,” Molecular Biology 21 :25-29.
`Lee, L.G., et al. (1992) “DNA sequencing with dye labeled termina-
`tors and T7 DNA polymerase effect of dyes and dNTPs .
`.
`. frag-
`ments” Nucleic Acids Res. 20:2471-2483.
`Lee, L.G. et al, (1997) “New energy transfer dyes for DNA sequenc-
`ing” Nucleic Acids Res. 25:2816-2822.
`Lewis et al., (2002) “Click Chemistry in Situ: Acetylcholinesterase as
`a Reaction Vessel for Array of Building Blocks,” Angew. Chem. Int.
`Ed. 41(6):1053-1057.
`Leroy, E .M. et al. (2000) “Diagnosis of Ebola Haemorrhagic Fever by
`RT-PCR in an Epidemic Setting,” Journal of Medical Virology
`60:463-467.
`Li, J. (1999) “Single Oligonucleotide Polymorphism Determination
`Using Primer Extension and Time-of-Flight Mass Spectrometry,”
`Electrophoresis 20: 1258-1265.
`Liu, H. et al. (2000) “Development of Multichannel Devices with an
`Array of Electrospray Tips for High-Throughput Mass Spectrom-
`etry,” Anal. Chem. 72:3303-3310.
`Lyamichev, A. et al. (1999) “Polymorphism Identification and Quan-
`titative Detection of Genomic DNA by Invasive Cleavage of
`Oligonucleotide Probes,” Nat. Biotech 17:292-296.
`Metzker, ML. et al. (1994) “Termination of DNA synthesis by novel
`3‘ modified deoxyribonucleoside 5' triphosphates,” Nucleic Acids
`Res. 22: 4259-4267.
`Monforte, J.A. and Becker, CH. (1997) “High-throughput DNA
`analysis by time-of-flight mass spectrometry,” Nat. Med. 3(3):360-
`362.
`Olejnik, J. et al. (1999) “Photocleavable peptide DNA conjugates:
`synthesis and applications to DNA analysis using MALDI MS,”
`Nucleic Acids Res. 27:4626-4631.
`Olejnik, J. et al. (1995) “Photocleavable biotin derivatives: a versatile
`approach for the isolation of biomolecules,” Proc. Natl. Acad. Sci.
`USA. 92:7590-7594.
`Pelletier, H. et al. (1994) “Structures ofternary complexes ofrat DNA
`polymerase [3, a DNA template-primer, and ddCTP,” Science
`264:1891-1903.
`Prober, J.M. etal.(1987) “A, system for rapid DNA sequencing with
`fluorescent
`chain-terminating
`dideoxynucleotides,”
`Science
`238:336-341.
`Ronaghi, M., Uhlen, M., and Nyren, P. (1998) “A sequencing Method
`based on real-time pyrophosphate,” Science 281:364-365.
`Rosenblum, B.B. et al. (1997) “New dye-labeled terminators for
`improved DNA sequencing patterns,” Nucleic Acids Res. 25:4500-
`4504.
`Roskey, M.T., Juhasz, P., Smirnov, I.P, Takach, E.J., Martin, SA,
`and Haff, LA. (1996) “DNA sequencing .
`.
`. mass spectrometry,”
`Proc. Natl. Acad. Sci. USA. 93:4724-4729.
`Ross, P et al. (1998) High Level Multiplex Genotyping by MALDI-
`TOF Mass Spectrometry. Nat. Biotech 16:1347-1351.
`Ross, P.L. et al.
`(1997) “Discrimination of Single-Nucleotide
`Polymorphisms in Human DNA Using Peptide Nucleic Acid
`Probes .
`.
`. Spectrometry,” Anal. Chem. 69:4197-4202.
`Saxon, E. and Bertozzi, CR. (2000) “Cell surface engineering by a
`modified Staudinger reaction,” Science 287:2007-2010.
`Schena, M., Shalon, D. and Davis, R. Brown PC. (1995) “Quantita-
`tive monitoring of gene expression patterns with a cDNA microar-
`ray,” Science 270: 467-470.
`Seo et al.
`(2003) “Click Chemistry to Construct Fluorescent
`Oligonucleotides for DNA Sequencing,” J. Org. Chem. 68:609.
`Speicher, M.R., Ballard, S.G., and Ward, DC. (1996) “Karyotyping
`human chromosomes by combinatorial multi-fluor FISH,” Nature
`Genetics 12: 368-375.
`Stoerker, J. et al. (2000) “Rapid Genotyping by MALDI-monitored-
`nuclease selection from probe Libraries,” Nat. Biotech 18: 1213-
`1216.
`
`Tang, K., Fu, D.J., Julien, D., Braun, A., Cantor, CR, and Koster, H.
`(1999) “Chip-based genotyping by mass spectrometry,” Proc. Natl.
`Acad. Sci. USA. 96: 10016-10020.
`Tong, X. and Smith, L.M. (1992) “Solid-Phase Method for the Puri-
`fication of DNA Sequencing Reactions,”Anal. Chem. 64:2672-2677.
`Wendy, Jen. et al. (2000) “New Strategies for Organic Catalysis: The
`First Enantioselective Orgacnocatalytic 1,3-Dipolar Cycloaddition,”
`J. Am. Chem. Soc. 122:9874-9875.
`Welch MB, Burgess K, (1999) “Synthesis of fluorescent, photolabile
`3‘-O-protected nucleoside triphosphates .
`.
`. scheme,” Nucleosides
`and Nucleotides 18: 197-201.
`Woolley, A. T. et al. (1997) “High-Speed DNA Genotyping Using
`Microfabricated Capillary Array Electrophoresis Chips,” Anal.
`Chem. 69:2181-2186.
`International Preliminary Examination Report issued on Mar. 18,
`2005 in connection with PCT/US03/21818.
`International Preliminary Examination Report issued on Jun. 13,
`2003 in connection with PCT/US01/31243.
`International Preliminary Examination Report issued on Feb. 25,
`2003 in connection with PCT/US01/28967.
`International Preliminary Examination Report issued on Mar. 17,
`2003 in connection with PCT/US02/09752.
`International Preliminary-Report on Patentability issued on Sep. 5,
`2006 in connection with PCT/US05/006960.
`International Search Report issued May 13, 2002 in connection with
`PCT/US01/31243.
`International Search Report issued Jan. 23, 2002 in connection with
`PCT/US01/28967.
`International Search Report issued Sep. 18, 2002 in connection with
`PCT/US02/09752.
`International Search Report issued Sep. 26, 2003 in connection with
`PCT/US03/21818.
`International Search Report issued Jun. 8, 2004 in connection with
`PCT/US03/39354.
`International Search Report issued Nov. 4, 2005 in connection with
`PCT/US05/06960.
`International Search Report issued Dec. 15, 2006 in connection with
`PCT/US05/13883.
`Partial European Search Report issued Apr. 26, 2007 in connection
`with European Patent Application No. 07004522 .4.
`Supplementary European Search Report issued Feb. 16, 2004 in
`connection with European Patent Application No. 01 97 7533.
`Supplementary European Search Report-issued Feb. 9, 2007 in con-
`nection with European Patent Application No. 03 76 4568.6.
`Supplementary European Search Report issued May 25, 2005 in
`connection with European Patent Application No. 02 72 8606.1.
`Supplementary European Search Report issued Jun. 7, 2005 in con-
`nection with European Patent Application No. 01 96 8905.
`Supplementary European Search Report issued Sep. 9, 2008 in con-
`nection with PCT International Application No. PCT/US05/06960.
`Written Opinion of the International Searching Authority issued Oct.
`27, 2005 in connection with PCT/US05/06960.
`Written Opinion ofthe International Searching Authority issued Dec.
`15, 2006 in connection with PCT/US05/13883.
`Li et al. (2003) “A photocleavable Fluorescent Nucleotide for DNA
`Sequencing and Analysis,” PNAS 100(2):414-419.
`Meng et al. (2006) “Design and Synthesis of a Photocleavable Fluo-
`rescent .
`.
`. Sequencing by Synthesis,” J. Org. Chem 71:3248-3252.
`Ruparel et al.
`(2005) “Design and Synthesis of a 3'-O-Allyl
`Photocleavable
`Fluorescent Nucleotide
`as
`a Reversible
`Terminator .
`. .by Synthesis,” PNAS 102(17):5932-5937.
`Seo et al. (2004) “Photocleavable Fluorescent Nucleotides for DNA
`Sequencing on a Chip Constructed by Site-Specific Coupling Chem-
`istry,” PNAS 101(15):5488-5493.
`Seo et al. (2004) “Four-Color DNA Sequencing by Synthesis on a
`Chip Using Photocleavable Fluorescent Nucleotides,” PNAS
`102(17):5926-5931.
`Tuncel et al. (1999) “Catalytically Self-Threading Polyrotaxanes,”
`Chem. Comm. 1509-1510.
`Kurata et al., Fluorescent quenching-based quantitative detection of
`specific DNNRNA using BODIPY® FL-labeled probe of primer,
`Nucleic Acids .
`.
`. p. e34 (2001).
`
`

`

`US 8,088,575 B2
`
`Page 5
`
`Welch et a1., Synthesis of Nucleosides Designed for Combinatorial
`DNA Sequencing, Chemistry, European Journal, 5:951-960 (1999).
`Wada et a1., 2-(Azidomethyl)benzoyl as a new protecting group in
`nucleosides, Tetrahedron Letters, 42:1069-1072 (2001).
`Sarfati et a1., Synthesis of fluorescent derivatives of 3'-O-(6-
`aminohexanoyl)-pyrimidine nucleosides 5‘triphosphates .
`.
`. tagged
`at C-3', JCS Perkin Trans, 1163-1171 (1995).
`Rasolonjatovo et
`a1., 6-N-
`(N-Methylanthranylamido)-4-Oxo-
`Hexanoic Acid: A New Fluorescent Protecting Group Applicable .
`.
`.
`Nucleotides, 17:2021-2025 (1998).
`Marquez et
`a1., Selective Fluorescence Quenching of 2,3-
`Diazabicyclo[2.2.2] oct-2-ene by Nucleotides, Organic Letters,
`5:3911-3914 (2003).
`Nazarenko et al., Effect of primary and secondary structure of
`oligodeoxyribonucleotides on the fluorescent properties of conju-
`gated dyes, Nucleic Acids Research, 30:2089-2095.
`Kvam et a1., Characterization of singlet oxygen-induced guanine
`residue damage after photochemical treatment of free .
`.
`. DNA,
`Biochemica et Biophysica Acta., 1217:9-15 (1994).
`Crespo-Hernandez et a1., Part 1. Photochemical and Photophysical
`Studies of Guanine Derivatives: Intermediates .
`.
`. Photobiology,
`71(5):534-543 (2000).
`314. Buschmann et a1., Spectroscopic Study and Evaluation of Red-
`Absorbing Fluorescent Dyes, Bioconjugate Chem., 14:195-204
`(2003).
`Torimura et a1., Fluorescence-Quenching Phenomenon by Photo
`induced Electron Transfer between a Fluorescent Dye and
`Nucleotide Base, Analytical Sciences, 17:155-160 (2001).
`Markiewicz et a1., Anew method of synthesis offluorescently labeled
`oligonucleotides and their application in DNA sequencing, Nucleic
`Acids Research, 25:3672-3690 (1997).
`Maier et a1., Synthesis and Properties of New Fluorescein-Labeled
`Oligonucleotides; Nucleosides, Nucleotides, and Nucleic Acids
`14:961-965 (1995).
`Bergmann et a1., Allyl As Internucleotide Protecting Group in DNA
`Synthesis to be Cleaved Off by Ammonia, Tetrahedron, 51:6971-
`6976 (1995).
`Guibé, Allylic Protecting Groups and Their Use in a Complex Envi-
`ronment Part
`I: Allylic Protection of Alcohols, Tetrahedron,
`53: 13509-13556 (1997).
`Guibé, Allylic Protecting Groups and Their Use in a Complex Envi-
`ronment Part II: Allylic Protecting .
`.
`. Methodology, Tetrahedron,
`54:2967-3042 (1998).
`ether,
`stability of allyl
`relative
`Kloosterrnan et
`al., The
`allyloxycarbonyLester and prop-2 enylidene acetal .
`.
`. Palladium
`catalysts, Tetrahedron Letters, 26:5045-5048 (1985).
`Kitamura et a1., (P(C6H5)3)CpRu+Catalyzed Deprotection of Allyl
`Carboxylic Esters, J. Org. Chem., 67:4975-4977 (2002).
`Hayakawa et a1., O-Allyl Protection of Guanine and Thymine Resi-
`dues in Oligodeoxyribonucleotides, J. Org. Chem., 58:5551-5555
`(1993).
`Veeneman et al., An Efficient Approach to the Synthesis of
`Thymidine Derivatives Containing Phosphate-lsoteric Methylene
`Acetyl Linkages, Tetrahedron, 47:1547-1562 (1991).
`Zavgorodny et a1.,
`l-Alkylthioalkylation of Nucleoside Hydroxl
`Functions and Its Synthetic Application: A New Versatile Method
`in .
`.
`. Tetrahedron Letters, 32:7593-7596 (1991).
`Seeger, Single Molecule Fluorescence: High-Performance Molecu-
`lar Diagnosis and Screening, Bioforum, Git Verlag, Darmstadt, DE
`vol. 21, No. (1998) (German text).
`Rao et a1., Four Color FRET Dye Nucleotide Terminators for DNA
`Sequencing, Nucleosides, Nucleotides & Nucleic Acids, 20:673-
`676. (2001).
`J. Brunckova et a1., Tetrahedron Letters, vol. 35, pp. 6619-6622
`(1994) (Exhibit 4).
`S. Nishino et a1., Heteroatom Chemistry, vol. 2, pp. 187-196 (1991).
`M. Krecmerova, Coll. Czech. Chem. Commun., vol. 55, pp. 2521-
`2536 (1990).
`P.J.L.M. Quaedflieg et a1., Tetretrahedron Letters, vol. 33, pp. 3081-
`3084 (1992).
`J. I. Yamashita et a1., Chem Pharm. Bull., vol. 35, pp. 2373-2381
`(1987).
`
`S.G. Zavgorodny et a1., Nucleosides, Nucleotides and Nucleic Acids,
`19 (10-12), 1977-1991 (2000).
`Canard et a1., DNA polymerase fluorescent substrates with reversible
`3‘-tags, Gene, 148L 1-6 (1994).
`of 3'-O-(u)-Aminoalkoxymethyl)
`Hovinen
`et
`a1.,
`Synthesis
`thymidine 5'-Triphosphates, Terminators of DNA Snythesis that
`Enable 3'-Labelling, J. Chem. Soc. Perkin Trans.,l:2l 1-21.
`Nickel W, et a1. (1992) “Interactions of azidothymidine triphosphate
`with the cellular DNA polymersases alpha .
`.
`. primase”. Journal of
`Biological Chemistry. 267(2): 848-854.
`Hanshaw et a1. (2004) “An Indicator displacement system for fluo-
`rescent detection of phosphate oxyanions under .
`.
`. conditions”
`Tetrahedron Letters, vol. 45, pp. 8721-8724.
`Bai et a1. (2003) “Photocleavage of a 2-nitrobenzyl linker bridging a
`fluorophore to the 5' endofDNA,” PNAS, vol. 11, No. 2, pp. 409-413.
`Nielsen et a1. (2004) “Multiplexed sandwich assays in microarray
`format,” Journal of Immunological Methods, vol. 290, pp. 107-120.
`Zhang et a1. (2002) “Synthesis of Releasable Electrophore Tags for
`Applications in Mass Spectrometry,” Bioconjugate Chem, vol. 13,
`pp. 1002-1012.
`Katherine J. Gibson and Stephen J. Benkovic (1987) “Synthesis and
`application of dervatizable oligonucleotides,” Nucleic Acids
`Research, vol. 15, No. 16, pp. 6455-6467.
`Tatyana S. Godovikova et a1. (1999) “5-[3 -(E)-(4-Azido-2, 3, 5,
`6-tetrafluorobenzamido) propenyl-l]-2‘ .
`.
`. Reaction,” Bioconjugate
`Chem., vol. 10, pp. 529-537.
`Amy L. Kimzey and William S. Dynan (1998) “Specific Regions
`of .
`.
`. Photocross-linking,” The Journal of Biological Chemistry, vol.
`273, No. 22, pp. 13768-13775.
`Huber et a1., Analytica Chimica Acta, 393:213 (1999).
`Pastinen ,Genomic Res., 7:606 (1997).
`Ronaghi, BioTechniques, 25:876 (1998).
`Weiss, Science, 283:1676 (1999).
`Finzi, Science, 267:378 (1995).
`Hu, BBRC, 254:466 (1999).
`Caetono-Anolies, Biotechnology, 12:619 (1994).
`Extended European Search Report issued Jul. 18, 2007 in connection
`with European Patent Application No. 070045224.
`International Search Report issued Oct. 29, 2007 in connection with
`PCT International Application No. PCT/US 07/ 13559.
`\Iotification of Transmittal of International Search Report and Writ-
`ten Opinion, issued Nov. 23, 2007.
`\Iotification of Transmittal of International Search Report and Writ-
`ten Opinion, issued Sep. 9, 2008 in connection with International
`Application No. PCT/US06/24157.
`\Iotification of Transmittal of International Search Report and Writ-
`ten Opinion, issued Feb. 6, 2008 in connection with International
`Application No. PCT/US06/42739.
`\Iotification Concerning Transmittal of International Preliminary
`Report on Patentability .
`.
`. issued May 15, 2008 in connection with
`PCT/US2006/042698.
`\Iotification of Transmittal of the International Search Report and
`Written Opinion, issued May 22, 2008 in connection with Interna-
`tional Application No. PCT/US06/45180.
`\Iotification of Transmittal of the international Search Report and
`Written Opinion, issued Aug. 16, 2008 in connection with Interna-
`tional Application No. PCT/US07/24646.
`Official Action issued May 21, 2007 in connection with European
`Patent Application No. 01968905 .8.
`Official Action issued Mar. 31, 2006 in connection with European
`Patent Application No. 01968905 .8.
`Official Action issued Mar. 3, 2007 in connection with European
`Patent Application No. 070045224.
`Official Action issued Mar. 14, 2008 in connection with European
`Patent Application No. 070045224.
`Communication Pursuant to Article 94(3) EPC issued Apr. 30, 2009
`in connection with counterpart European Patent Application No.
`070045224.
`Mathews, Christopher K. and Van Holde, K.E. (1985) “Chemical
`Synthesis of Oligonucleotides,” Biochemistry, 2nd Edition, pp. 127-
`128.
`Office Action issued Oct. 25, 2002 in connection with US. Appl. No.
`09/972,364.
`
`
`
`

`

`US 8,088,575 B2
`Page 6
`
`
`
`Office Action issued Mar. 14, 2003 in connection with US. Appl. \Io.
`09/972,364.
`Office Action issued Aug. 10, 2007 in connection with US. Appl. \Io.
`11/119,231.
`Office Action issued Sep. 21, 2007 in connection with US. Appl. \Io.
`10/380,256.
`Office Action issued Nov. 14, 2007 in connection with US. Appl. \Io.
`10/735,081.
`Office Action issued Sep. 3, 2008 in connection with US. Appl. \Io.
`11/894,808.
`Office-Action issued Jun. 24, 2008 in connection with US. Appl. \Io.
`11/894,690.
`Office Action issued Jul. 8, 2008 in connection with US. Appl. \Io.
`10/591,520.
`Restriction Requirement issued in connection with US. Appl. \Io.
`10/521,206.
`Notice of Allowance issued Sep. 6, 2007 in connection with US.
`App1.No. 10/702,203.
`Jun. 5, 2009 Office Action issued in connection with US. Appl. \Io.
`11/894,690.
`Notice of Allowance issued Apr. 2, 2010 in connection with US.
`App1.No. 11/810,509.
`US. Appl. No. 09/658,077, filed Sep. 11, 2000, Ju et al.
`US. Appl. No. 09/684,670, filed Oct. 6, 2000, Ju et al.
`US. Appl. No. 09/823,181, filed Mar. 30, 2001, Ju et al.
`US. Appl. No. 09/972,364, filed Oct. 5, 2001, Ju et al.
`U.S.App1.No. 10/194,882, filed Jul. 12, 2002, Ju et al.
`US. Appl. No. 10/380,256, filed Mar. 30, 2001, Ju et al.
`US. Appl. No. 10/591,520, filed Sep. 1, 2006, Ju et al.
`US. Appl. No. 11/894,690, filed Aug. 20, 2007, Ju et al.
`US. Appl. No. 11/894,808, filed Aug. 20, 2007, Ju et al.
`US. Appl. No. 11/922,385, filed Dec. 14, 2007, Ju et al.
`US. Appl. No. 12/084,338, filed Apr. 28,2008, Ju et al.
`US. Appl. No. 12/085,343, filed May 19, 2008, Ju et al.
`Bai, X., Kim, S., Li, Z., Turro, NJ. and Ju, J. (2004) “Design and
`Synthesis of a Photocleavable Biotinylated Nucleotide for DNA
`Analysis by Mass Spectrometry,” Nucleic Acids Research,
`32(2):534-541.
`Bi, L., Kim DH, and Ju, J. (2006) “Design and Synthesis of a
`Chemically Cleavable Fluorescent Nucleotide, 3‘-O-Allyl-dGTP-al-
`lyl-Bodipy-FL-5 10, as a Reversible Terminator for DNA Sequencing
`by Synthesis” J. Am. Chem. Soc., 128:2542-2543.
`Braslaysky, 1.; Hebert, B.; Kartalov, E.; et al. (2003) “Sequence
`information can be obtained from single DNA molecules.” Proc.
`Natl. Acad. Sci. 100(7):3960-3964.
`Collins, F. S.; Morgan, M.; Patrinos, A. (2003) “The Human Genome
`Project: Lessons from Large-Scale Biology.” Science, 300, pp. 286-
`290.
`
`Drmanac, S.; Kita, D.; Labat, 1.; et al. (1998) “Accurate sequencing
`by hybridization for DNA diagnostics and individual genomics.” Nat.
`Biotech., 16:54-58.
`Green, T.W. et al. and Wuts, PG.M. “Protective Groups in Organic
`Synthesis” 3rd ed. NewYork: John Wiley & Sons, Inc., 1999. 96-99,
`190-191, 260-261, 542-543, and 750-751.
`Huang, B.G. et al. “Synthesis and in vitro Antitumor Activity of Some
`Amino-deoxy 3-hexofuranosylpyrrolo[2,3-d]pyrimidines.” Carbo-
`hydrate Research, 1998, 308(3-4):319-328.
`Ju, J. et al. (2006) “Four-color DNA Sequencing by Synthesis Using
`Cleavable Fluorescent Nucleotide Reversible Terminators,” Proc.
`Natl. Acad. Sci. USA, 103(52): 19635-40.
`Kan, C.W.; Doherty, E. A. S.; Barron, A. E. (2003) “A novel
`thermogelling matrix for microchannel DNA sequencing based on
`poly-N-alkoxyalkylacrylamide copolymers,” Electrophoresis, 24,
`pp. 4161-4169.
`Kasianowicz, J.J., Brandin, B., Branton, D. and Deainer, D.W. (1996)
`“Characterization of Individual Polynucleotide Molecules Using a
`Membrane Channel,” Proc. Natl. Acad. Sci. USA 93:13770-13773.
`Loubinoux et al. (1998), Protection Des Phenols Par Le Groupement
`Azidomethylene Application a La Synthese De Phenols Instables,
`Tetrahedron, 44(19):6055-6064.
`Lu, G. and Burgess, K. (2006) “A Diversity Oriented Synthesis of
`3'-O-Modified Nucleoside Triphosphates for DNA ‘Sequencing by
`Synthesis’” Bioorg. Med. Chem, Lett., 16:3902-3905.
`Margulies, M.; Egholm, M.; Altman, W. E.(2005) “Genome
`Sequencing in Microfabricated High-Density Picolitre Reactors.”
`Nature, 437:376-380.
`Metzker ML. (2005) “Emerging Technologies in DNA Sequencing.”
`Genome Res., 15:1767-1776.
`Mitra, R. D.; Shendure J.; Olejnik, J.; et al. (2003) “Fluorescent in situ
`sequencing on polymerase colonies.” Anal. Biochem. 320:55-65.
`Shendure, J.; Porreca, G. 1.; Reppas, N. B.; et al. (2005) “Accurate
`Multiplex Polony Sequencing of an Evolved Bacterial Genome.”
`Science 309: 1728-1732.
`Smith, L.M., Sanders, J.Z., Kaiser, R.J., et al. (1986) “Fluorescence
`Detection in Automated DNA Sequence Analysis,” Nature 321 :674-
`679.
`Thu, Z., Chao, J., Yu, H, et al. (1994) “Directly Labeled DNA Probes
`Using Fluorescent Nucleotides with Different Length Linkers,”
`Nucleic Acids Res., 22:3418-3422.
`Zavgorodny et al.
`(1991), 1-Alkylthioalkylation ofNucleoside
`Hydroxyl Functions and Its Synthetic Applications: A New Versatile
`Method in Nucleo side Chemistry, Tetrahedron—Letters, 32(5 1):7593 -
`7596.
`Notice of Allowance issued Feb. 24, 2009 in connection with US.
`App1.No. 11/894,690.
`Notice of Allowance issued Mar. 23, 2009 in connection with US.
`App1.No. 11/894,808.
`
`

`

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`Jan. 3, 2012
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