I 1111111111111111 11111 1111111111 1111111111 111111111111111 111111111111111111
`US009725480B2
`
`c12) United States Patent
`Ju et al.
`
`(IO) Patent No.:
`(45) Date of Patent:
`
`US 9,725,480 B2
`* Aug. 8, 2017
`
`(54) MASSIVE PARALLEL METHOD FOR
`DECODING DNA AND RNA
`
`(71) Applicant: The Trustees of Columbia University
`in the City of New York, New York,
`NY (US)
`
`(72)
`
`Inventors: Jingyue Ju, Englewood Cliffs, NJ (US);
`Zengmin Li, Flushing, NY (US); John
`Robert Edwards, St. Louis, MO (US);
`Yasuhiro Itagaki, New York, NY (US)
`
`(73) Assignee: THE TRUSTEES OF COLUMBIA
`UNIVERSITY IN THE CITY OF
`NEW YORK, New York, NY (US)
`
`( *) Notice:
`
`Subject to any disclaimer, the term ofthis
`patent is extended or adjusted under 35
`U.S.C. 154(b) by O days.
`
`This patent is subject to a terminal dis(cid:173)
`claimer.
`
`(21) Appl. No.: 15/167,917
`
`(22) Filed:
`
`May 27, 2016
`
`(65)
`
`Prior Publication Data
`
`US 2016/0264612 Al
`Sep. 15, 2016
`Jul. 6, 2017
`US 2017/0190730 A2
`Related U.S. Application Data
`
`(60)
`
`(51)
`
`(52)
`
`Continuation of application No. 14/670,748, filed on
`Mar. 27, 2015, which is a continuation of application
`(Continued)
`
`Int. Cl.
`C07H 19114
`C12Q 1168
`
`(2006.01)
`(2006.01)
`(Continued)
`
`U.S. Cl.
`CPC ............. C07H 19114 (2013.01); C07H 21100
`(2013.01); C12Q 1168 (2013.01); C12Q 11686
`(2013.01);
`
`(58) Field of Classification Search
`CPC .............................. C07H 19/14; C12C 1/6869
`(Continued)
`
`(56)
`
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`2408143
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`
`OTHER PUBLICATIONS
`
`U.S. Application for a Method for Direct Nucleic Acid Sequencing;
`U.S. Appl. No. 09/266,187, filed Mar. 10, 1999.
`(Continued)
`
`Primary Examiner -
`Jezia Riley
`(74) Attorney, Agent, or Firm -
`John P. White; Gary J.
`Gershik; Cooper & Dunham LLP
`
`(57)
`
`ABSTRACT
`
`This invention provides methods for attaching a nucleic acid
`to a solid surface and for sequencing nucleic acid by
`detecting the identity of each nucleotide analog after the
`nucleotide analog is incorporated into a growing strand of
`DNA in a polymerase reaction. The invention also provides
`nucleotide analogs which comprise unique labels attached to
`the nucleotide analog through a cleavable linker, and a
`cleavable chemical group to cap the -OH group at the
`3'-position of the deoxyribose.
`
`(Continued)
`
`1 Claim, 28 Drawing Sheets
`
`Page 1
`
`Illumina Ex. 1019
`IPR Petition - USP 10,435,742
`
`

`

`US 9,725,480 B2
`Page 2
`
`Related U.S. Application Data
`
`No. 13/959,660, filed on Aug. 5, 2013, now Pat. No.
`9,133,511, which is a continuation of application No.
`13/672,437, filed on Nov. 8, 2012, now abandoned,
`which is a continuation of application No. 13/339,
`089, filed on Dec. 28, 2011, now abandoned, which is
`a continuation of application No. 12/804,284, filed on
`Jul. 19, 2010, now Pat. No. 8,088,575, which is a
`continuation of application No. 11/810,509, filed on
`Jun. 5, 2007, now Pat. No. 7,790,869, which is a
`continuation of application No. 10/702,203, filed on
`Nov. 4, 2003, now Pat. No. 7,345,159, which is a
`division of application No. 09/972,364, filed on Oct.
`5, 2001, now Pat. No. 6,664,079, and a continuation-
`in-part of application No. 09/684,670, filed on Oct. 6,
`2000, now abandoned.
`
`(60) Provisional application No. 60/300,894, filed on Jun.
`26, 2001.
`
`(51)
`
`(2006.01)
`(2006.01)
`
`Int. Cl.
`C07H 21100
`C40B 40/00
`(52) U.S. Cl.
`CPC ......... C12Q 116869 (2013.01); C12Q 116872
`(2013.01); C12Q 116874 (2013.01); C07B
`2200111 (2013.01); Cl 2Q 25251117 (2013.01);
`Cl2Q 2535/101 (2013.01); Cl2Q 2563/107
`(2013.01); C40B 40/00 (2013.01)
`(58) Field of Classification Search
`USPC ............................................. 435/6.1; 536/4.1
`See application file for complete search history.
`
`(56)
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`Addition Sequencing Scheme, nucleosides & Nucleotides. 18:197-
`201.
`Exhibit 2028, filed Jun. 24, 2013 in connection with IPR2012-
`00006: Hyman (1998) A New Method of Sequencing DNA, Ana(cid:173)
`lytical Biochemistry 174:423-436.
`Exhibit 2030, filed Jun. 24, 2013 in connection with IPR2012-
`00006: Canard and Sarfati (1994) DNA polymerase fluorescent
`substrates with reversible 3'-tags, Gene. 1481-6.
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`00006: Sarfati et al. (1987) Synthesis of Fluorescent or Biotinylated
`Nucleoside Compounds, Tetrahedron Letters. 43:3491-3497.
`Exhibit 2033, filed Aug. 30, 2013 in connection with IPR2012-
`00006: Jun. 25, 2013 Substitute Declaration of Dr. George L.
`Trainor [redacted].
`Exhibit 2034, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Jingyue Ju et. al. (2006) Four-color DNA sequencing by
`synthesis using cleavable fluorescent nucleotide reversible termi(cid:173)
`nators, Proceedings of the National Academy of Sciences. 103:
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`Exhibit 2035, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Batista et al. (2008) PRG-1 and 21U-RNAs Interact to Form
`the piRNA Complex Required for Fertility in C.elegans. Molecular
`Cell 31:1-12.
`Exhibit 2036, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Form 7 Review Context and Analysis, Biomedical Engi(cid:173)
`neering and Research to Aid Persons with Disabilities Programs
`Dec. 19-20, 2000 Panel Review, Fluorescence Imaging Chip System
`for Massive Parallel DNA Sequencing. Proposal No. BES-0097793.
`Exhibit 2037, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Oct. 1, 2006 Request for opinion on manuscript by J. Ju et.
`al., Proceedings of National Academy of Sciences, U.S.A.
`Exhibit 2038, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Correspondence between George Rupp, Chancellor, Colum(cid:173)
`bia University and Richard T. Schlossberg, President, The David
`and Lucile Packard Foundation (2001).
`Exhibit 2039, filed Jun. 25, 2013 in connection with IPR2012-
`00006: The David and Lucile Packard Foundation, Packard Fel(cid:173)
`lowships for Science and Engineering, http://www.packard.org/
`what -wefund/ conservation -and-science/packard-fellowships-for(cid:173)
`science-andengineering/ (last visited Jun. 25, 2013).
`Exhibit 2040, filed Jun. 25, 2013 in connection with IPR2012-
`00006: "Chemistry for Next-Generation Sequencing." http://www.
`illumina.corn/technology/sequencing_technology.ilrnn.
`Exhibit 2041, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Chiang et al. (2010) Mammalian microRNAs: experimental
`evaluation of novel and previously annotated genes, Genes & Dev.
`24:992, 993.
`Exhibit 2042, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Seo et al. (2004) Photocleavable fluorescent nucleotides for
`DNA sequencing on a chip constructed by site-specific coupling
`chemistry, Proc. Natl Acad. Sci. 101(15):5488-5493.
`Exhibit 2043, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Curriculum vitae of Mr. Raymond S. Sims.
`Exhibit 2044, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Prior Testimony of Mr. Raymond S. Sims.
`Exhibit 2045, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Documents reviewed by Mr. Raymond S. Sims in this
`Proceeding.
`Exhibit 2052, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Gary Schroth Proof of Chiang Paper.
`Exhibit 2074, filed Jun. 25, 2013 in connection with IPR2012-
`00006: Information about Dr. Ju's intellectual property sent to
`Illumina.
`Exhibit 2090, filed Jun. 26, 2013 in connection with IPR2012-
`00006: IPR Default Protective Order.
`Exhibit 2091, filed Jun. 26, 2013 in connection with IPR2012-
`00006: Declaration of Raymond S. Sims.
`
`Page 4
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`

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`Excerpt from Protective Groups in Organic Synthesis, 3rd Ed.
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`Exhibit 2094, filed Oct. 1, 2013 in connection with IPR2012-00006:
`Final transcript of the Sep. 4-6, 2013 deposition of Dr. George L.
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`Exhibit 2095, filed Oct. 1, 2013 in connection with IPR2012-00006:
`Final transcript of the Sep. 3, 2013 deposition of Raymond S. Sims.
`Nov. 12, 2013 Petitioner Motion to Exclude Evidence in connection
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`Exhibit 1056, filed Nov. 19, 2013 in connection with IPR2012-
`00006: Videotaped Deposition Transcript of Kevin Burgess, Ph.D.,
`Oct. 28, 2013, signed with errata.
`Nov. 12, 2013 Patent Owner Motion for Observations on the
`Cross-Examination Testimony of Kevin Burgess, Ph.D. in connec(cid:173)
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`Nov. 12, 2013 Patent Owner Motion to Exclude Evidence in
`connection with IPR2012-00006.
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`Exhibit 2103, filed Nov. 12, 2013 in connection with IPR2012-
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`Nov. 26, 2013 Petitioner Response to Motion for Observations in
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`Nov. 26, 2013 Patent Owner Opposition to Petitioner's Motion to
`Exclude in connection with IPR2012-00006.
`Nov. 26, 2013 Petitioner Opposition to Motion to Exclude in
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`Dec. 3, 2013 Petitioner Reply to Patent Owner's Opposition to
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`Dec. 3, 2013 Patent Owner Reply on Motion to Exclude in con(cid:173)
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`Exhibit 2105, filed Dec. 15, 2013 in connection with IPR2012-
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`2013 Oral Hearing in connection with IPR2012-00006, IPR2012-
`00007, and IPR2013-00011.
`Exhibit 1057, filed Dec. 16, 2013 in connection with IPR2012-
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`17, 2013 in connection with IPR2012-00006, IPR2012-00007, and
`IPR2013-00011.
`Feb. 10, 2014 Record of Dec. 17, 2013 Oral Hearing in connection
`with IPR2012-00006, IPR2012-00007, and IPR2013-00011.
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