`US009718852B2
`
`c12) United States Patent
`Ju et al.
`
`(IO) Patent No.:
`(45) Date of Patent:
`
`US 9,718,852 B2
`* Aug. 1, 2017
`
`(54)
`
`MASSIVE PARALLEL METHOD FOR
`DECODING DNA AND RNA
`
`(71)
`
`(72)
`
`Applicant: The Trustees of Columbia University
`in the City of New York, New York,
`NY (US)
`
`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-
`claimer.
`
`(21)
`
`Appl. No.: 15/380,270
`
`(22)
`
`Filed:
`
`Dec. 15, 2016
`
`(65)
`
`Prior Publication Data
`
`US 2017/0088575 Al Mar. 30, 2017
`
`(60)
`
`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 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)
`
`(52)
`
`(58)
`
`(2006.01)
`(2006.01)
`
`Int. Cl.
`C07H 19114
`C12Q 1168
`U.S. Cl.
`CPC .......... . C07H 19114 (2013.01); C12Q 116872
`(2013.01); C12Q 116874 (2013.01)
`Field of Classification Search
`None
`See application file for complete search history.
`
`(56)
`
`References Cited
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`FOREIGN PATENT DOCUMENTS
`
`CA
`CA
`DE
`DE
`DE
`EP
`EP
`EP
`EP
`EP
`
`2425112
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`2408143
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`OTHER PUBLICATIONS
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`Office Action issued Sep. 21, 2007 in connection with U.S. Appl.
`No. 10/380,256.
`
`(Continued)
`
`Primary Examiner - Layla Berry
`(74) Attorney, Agent, or Firm -
`John P. White; Gary J.
`Gershik; Cooper & Dunham LLP
`
`ABSTRACT
`(57)
`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.
`
`1 Claim, 28 Drawing Sheets
`
`Page 1
`
`Illumina Ex. 1016
`IPR Petition - USP 10,435,742
`
`
`
`US 9,718,852 B2
`Page 2
`
`(56)
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`US 9,718,852 B2
`Page 3
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`Appl. No. 11/810,509.
`Notice of Allowance and Fee(s) Due issued Apr. 2, 2010 in
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`Office Action issued Oct. 28, 2010 in connection with U.S. Appl.
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`12/804,284.
`Aug. 4, 2011 Amendment in response to Office Action issued Feb.
`4, 2011 in connection with U.S. Appl. No. 12/804,284.
`Notice of Allowance issued Sep. 1, 2011 in connection with U.S.
`Appl. No. 12/804,284.
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`Office Action issued Dec. 1, 2014 in connection with U.S. Appl. No.
`13/959,660.
`Amendment filed Feb. 27, 2015 in connection with U.S. Appl. No.
`13/959,660.
`Notice of Allowance issued May 3, 2015 in connection with U.S.
`Appl. No. 13/959,660.
`
`Page 3
`
`
`
`US 9,718,852 B2
`Page 4
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