I 1111111111111111 11111 111111111111111 1111111111 1111111111 111111111111111111
`US009868985B2
`
`c12) United States Patent
`Ju et al.
`
`(IO) Patent No.:
`(45) Date of Patent:
`
`US 9,868,985 B2
`*Jan. 16, 2018
`
`(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.: 15/647,657
`
`(22) Filed:
`
`Jul. 12, 2017
`
`(65)
`
`(60)
`
`(51)
`
`(52)
`
`Prior Publication Data
`
`US 2017/0313737 Al
`Nov. 2, 2017
`Related U.S. Application Data
`
`Continuation of application No. 15/167,917, filed on
`May 27, 2016, now Pat. No. 9,725,480, which is a
`(Continued)
`
`Int. Cl.
`C12Q 1168
`C07H 19114
`
`(2006.01)
`(2006.01)
`(Continued)
`
`U.S. Cl.
`CPC ........... C12Q 116869 (2013.01); C07H 19114
`(2013.01); C07H 21100 (2013.01); C12Q 1168
`(2013.01);
`
`(58) Field of Classification Search
`CPC ........................ C12Q 1/6869; C12Q 2525/117
`(Continued)
`
`(56)
`
`References Cited
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`(Continued)
`
`FOREIGN PATENT DOCUMENTS
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`CA
`CA
`
`4/2002
`2425112
`11/2002
`2408143
`(Continued)
`
`OTHER PUBLICATIONS
`
`Non-Final Office Action issued by the U.S. Patent and Trademark
`Office dated Feb. 8, 2017 in connection with U.S. Appl. No.
`15/380,284.
`
`(Continued)
`
`Primary Examiner -
`Jezia Riley
`(74) Attorney, Agent, or Firm -
`Dunham LLP
`
`John P. White; Cooper &
`
`(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)
`
`2 Claims, 28 Drawing Sheets
`
`Page 1
`
`Illumina Ex. 1020
`IPR Petition - USP 10,435,742
`
`

`

`US 9,868,985 B2
`Page 2
`
`Related U.S. Application Data
`
`continuation of application No. 14/670,748, filed on
`Mar. 27, 2015, which is a continuation of application
`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-in-part 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, which is 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 11686 (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 2535/122
`(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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`US 9,868,985 B2
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`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:
`19635-19640.
`
`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 proprety 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.
`Exhibit 2092, filed Oct. 10, 2013 in connection with IPR2012-
`00006: Rough Transcript of the Sep. 4, 2013 deposition of Dr.
`George L. Train or.
`Exhibit 2093, filed Oct. 1, 2013 in connection with IPR2012-00006:
`Excerpt from Protective Groups in Organic Synthesis, 3rd Ed.
`(Theodora W. Greene and Peter G.M. Wuts ed., John Wiley & Sons,
`Inc. 1999).
`Exhibit 2094, filed Oct. 1, 2013 in connection with IPR2012-00006:
`Final transcript of the Sep. 4-6, 2013 deposition of Dr. George L.
`Trainor.
`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
`with IPR2012-00006.
`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)
`tion with IPR2012-00006.
`Nov. 12, 2013 Patent Owner Motion to Exclude Evidence in
`connection with IPR2012-00006.
`Exhibit 2099, filed Nov. 12, 2013 in connection with IPR2012-
`00006: Welch, M., et al (2005) Corrigenda to Syntheses of
`
`Page 4
`
`

`

`US 9,868,985 B2
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`00006: Welch, M (1999) "Base Additions Sequencing Scheme
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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
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`Nov. 26, 2013 Petitioner Opposition to Motion to Exclude in
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`Dec. 3, 2013 Patent Owner Reply on Motion to Exclude in con(cid:173)
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`00007, and IPR2013-00011.
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`00518: Excerpts from the '537 Patent File History.
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`Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
`7,790,869.
`Sep. 17, 2012 Motion to Waive Page Limit and Proposed Petition
`in connection with Petition for Inter Partes Review of U.S. Pat. No.
`7,790,869.
`Dec. 21, 2012 Preliminary Response under 37 C.F.R. 42.107 in
`connection with IPR2012-00007.
`Mar. 12, 2013 Decision on Petition for Inter Partes Review in
`connection with IPR2012-00007.
`Mar. 26, 2013 Request for Reconsideration in connection with
`IPR2012-00007.
`Mar. 26, 2013 Request for Rehearing. under 37 C.F.R. 42.71 of
`Decision to Institute Inter Partes Review in connection with
`IPR2012-00007.
`Apr. 26, 2013 Opposition to Request for Reconsideration (Rehear(cid:173)
`ing) Under 37 C.F.R. 42.71.(C) in connection with IPR2012-00007.
`May 10, 2013 Decision on Request for Rehearing in connection
`with IPR2012-00007.
`Aug. 30, 2013 Substitute Patent Owner Response Under 37 C.F.R.
`42.120 in connection with IPR2012-00007.
`Aug. 30, 2013 Substitute Patent Owner Motion to Amend Under 37
`C.F.R. 42.121 in connection with IPR2012-00007.
`Sep. 27, 2013 Petitioner Opposition to Motion to Amend in con(cid:173)
`nection with IPR2012-00007.
`Sep. 27, 2013 Petitioner Reply to Response to Petition in connection
`with IPR2012-00007.
`Nov. 18, 2013 Substitute Patent Owner Reply on Motion to Amend
`in connection with IPR2012-00007.
`Exhibit 1022, filed Sep. 16, 2012 in connection with IPR2012-
`00007: Excerpts of File History of U.S. Pat. No. 7,790,869.
`Exhibit 1053, filed Sep. 27, 2013 in connection with IPR2012-
`00007: Sep. 27, 2013 Declaration of Kevin Burgess.
`Exhibit 2001, filed Dec. 21, 2012 in connection with IPR2012-
`00007: Composition of a Nucleotide.
`Exhibit 2033, filed Aug. 30, 2013 in connection with IPR2012-
`00007: Jun. 25, 2013 Substitute Declaration of Dr. George L.
`Trainor [redacted].
`Nov. 12, 2013 Petitioner Motion to Exclude Evidence in connection
`with IPR2012-00007.
`Nov. 12, 2013 Patent Owner Motion for Observations on the
`Cross-Examination Testimony of Kevin Burgess, Ph.D. in connec(cid:173)
`tion with IPR2012-00007.
`Nov. 12, 2013 Patent Owner Motion to Exclude Evidence in
`connection with IPR2012-00007.
`Nov. 26, 2013 Petitioner's Response to Motion for Observations in
`connection with IPR2012-00007.
`Nov. 26,. 2013 Patent Owner's Opposition to Petitioner's Motion to
`Exclude in connection with IPR2012-00007.
`
`Page 5
`
`

`

`US 9,868,985 B2
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`Nov. 26, 2013 Petitioner's Opposition to Motion to Exclude in
`connection with IPR2012-00007.
`Dec. 3, 2013 Petitioner Reply to Patent Owner's Opposition to
`Motion to Exclude in connection with IPR2012-00007.
`Dec. 3, 2013 Patent Owner Reply on Motion to Exclude in con(cid:173)
`nection with IPR2012-00007.
`Mar. 6, 2014 Final Written Decision in connection with IPR2012-
`00007.
`Jan. 29, 2013 Petition for Inter Partes Review of U.S. U.S. Pat. No.
`7,057,026.
`Feb. 7, 2013 Revised Petition for Inter Partes Review of U.S. Pat.
`No. 7,057,026.
`May 1, 2013 Preliminary Response under 37 C.F.R. 42.107 m
`connection with IPR2013-00128.
`Jul. 29, 2013 Decision on Petition for Inter Partes Review m
`connection with IPR2013-00128.
`Oct. 24, 2013 Patent Owner Motion to Amend the Patent m
`connection with IPR2013-00128.
`Exhibit 1006, filed Jan. 29, 2013 in connection with IPR2013-
`00128: Beckman Coulter CEQTM 2000 DNA Analysis System
`User's Guide, Jun. 2000.
`Exhibit 1010, filed Jan. 29, 2013 in connection with IPR2013-
`00128: Kamal, Tetrahedron Letters 40(2):371-372, 1999.
`Exhibit 1011, filed Jan. 29, 2013 in connection with IPR2013-
`00128: Jung, J.C.S. Chem. Comm. (7):315-316, 1978.
`Exhibit 1015, filed Jan. 29, 2013 in connection with IPR2013-
`00128: Jan. 28, 2013 Declaration of Dr. Bruce Branchaud.
`Exhibit 1016, filed Jan. 29, 2013 in connection with IPR2013-
`00128: Excerpts from the '026 Patent File History.
`Exhibit 1020, filed Jan. 29, 2013 in connection with IPR2013-
`00128: Transcript oflnitial Conference Call Held on Aug. 29, 2013.
`Exhibit 2001, filed May 1, 2013 in connection with IPR2013-00128:
`The Trustees of Columbia University in the City of New York v.
`Illumina, Inc., 1: 12-cv-00376-GMS----Columbia's Amended Com(cid:173)
`plaint.
`Exhibit 2002, filed May 1, 2013 in connection with IPR2013-00128:
`The Trustees of Columbia University in the City of New York v.
`Illumina,
`Inc.,
`l:12-cv-00376-GMS----Columbia's Amended
`Answer.
`Exhibit 2003, filed May 1, 2013 in connection with IPR2013-00128:
`The Trustees of Columbia University in the City of New York v.
`Illumina,
`Inc.,
`l:12-cv-00376-GMS-IBS's Responses
`to
`Illumina's Requests for Admission.
`Exhibit 2004, filed May 1, 2013 in connection with IPR2013-00128:
`The Trustees of Columbia University in the City of New York v.
`Illumina, Inc.,
`l:12-cv-00376-GMS-Columbia's Responses to
`Illumina's Requests for Admission.
`Exhibit 2006, filed Oct. 24, 2013 in connection with IPR2013-
`00128: Green & Wuts, Protective Groups in Organic Synthesis,
`excerpts from "Protection From the Hydroxyl Group," (1999).
`Exhibit 2007, filed Oct. 24, 2013 in connection with IPR2013-
`00128: Katagiri et al., "Selective Protection of the Primary
`Hydroxyl Groups of Oxetanocin A," Chem. Pharm. Bull. 43:884-
`886 (1995).
`Exhibit 1029, filed Jan. 24, 2014 in connection with IPR2013-
`00128: Jan. 9, 2014 Substitute Declaration of Floyd Romesberg,
`Ph.D.
`Exhibit 2012, filed Oct. 24, 2013 in connection with IPR2013-
`00128: Oct. 3, 2013 Deposition Transcript of Bruce Branchaud,
`Ph.D.
`Exhibit 2016, filed Oct. 24, 2013 in connection with IPR2013-
`00128: Ruby, Methods in Enzymology (1990).
`Exhibit 2025, filed Oct. 24, 2013 in connection with IPR2013-
`00128: U.S. Pat. No. 7,057,026 file history.
`Exhibit 1025, filed Jan. 24, 2014 in connection with IPR2013-
`00128: Substitute Eric Vermaas Declaration, Dec. 20, 2013.
`
`Exhibit 1021, filed Dec. 23, 2013 in connection with IPR2013-
`00128: Excerpts from Protective Groups in Organic Synthesis
`(Theodora W. Greene & Peter G. M. Wuts eds., John Wiley & Sons,
`Inc. 3rd ed. 1999) (1991).
`Exhibit 1022, filed Dec. 23, 2013 in connection with IPR2013-
`00128: Signed Deposition Transcript of Dr. Bruce Branchaud on
`Oct. 3, 2013.
`Jan. 24, 2014 Intelligent Bio-Systems Opposition to Illumina's
`Motion to Amend in connection with IPR2013-00128.
`Exhibit 1030, filed Jan. 24, 2014 in connection with IPR2013-
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`Murine Erythroleukemia Cell DNA Using a Cleavable Biotinylated
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`Exhibit 1033, filed Jan. 24, 2014 in connection with IPR2013-
`00128: Deposition of Floyd Romesberg, Ph.D., from Jan. 14, 2014.
`Exhibit 1034, filed Jan. 24, 2014 in connection with IPR2013-
`00128: 1999/2000 Pierce Chemical Company catalog (1999).
`Exhibit 1035, filed Jan. 24, 2014 in connection with IPR2013-
`00128: Second Declaration of Dr. Bruce Branchaud, dated Jan. 23,
`2014.
`Exhibit 1039, filed Jan. 24, 2014 in connection with IPR2013-
`00128: Excerpts from the file history of European Patent Applica(cid:173)
`tion No. 02781434.2.
`Exhibit 1041, filed Jan. 24, 2014 in connection with IPR2013-
`00128: Lukesh et al., "A Potent, Versatile Disulfide-Reducing Agent
`from Aspartic Acid" J. Am. Chem. Soc., 134, 4057-59 (2012).
`Exhibit 1042, filed Jan. 24, 2014 in connection with IPR2013-
`00128: Klausner, "Dupont's DNA Sequencer Uses New Chemistry"
`Nat. Biotech., 5, 1111-12 (1987).
`Exhibit 1043, filed Jan. 24, 2014 in connection with IPR2013-
`00128: Murakami et al., "Structure of a Plasmodium yoelii gene(cid:173)
`encoded protein homologous to the Ca2+-ATPase of rabbit skeletal
`muscle sarcoplasmic retic