I 1111111111111111 1111111111 1111111111 111111111111111 IIIII IIIIII IIII IIII IIII
`US010407458B2
`
`c12) United States Patent
`Ju et al.
`
`US 10,407,458 B2
`(IO) Patent No.:
`*Sep.10,2019
`(45) Date of Patent:
`
`(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.
`
`(2018.01)
`(2006.01)
`
`C12Q 116876
`C40B 40/00
`(52) U.S. Cl.
`CPC ............. C07H 19114 (2013.01); C07H 19110
`(2013.01); C07H 21100 (2013.01); C12Q 1168
`(2013.01); C12Q 11686 (2013.01); C12Q
`116869 (2013.01); C12Q 116872 (2013.01);
`C12Q 116874 (2013.01); C12Q 116876
`(2013.01); C07B 2200111 (2013.01); Cl2Q
`25251117 (2013.01); Cl2Q 2525/186
`(2013.01); Cl2Q 2535/101 (2013.01); Cl2Q
`2535/122 (2013.01); Cl2Q 2563/107
`(2013.01); Cl2Q 2565/501 (2013.01); C40B
`40/00 (2013.01)
`
`(58) Field of Classification Search
`CPC .............................. C07H 19/04; C12Q 1/6869
`USPC ............................................. 536/4.1; 435/6.1
`See application file for complete search history.
`
`(56)
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`
`(21) Appl. No.: 16/149,098
`
`(22) Filed:
`
`Oct. 1, 2018
`
`(65)
`
`Prior Publication Data
`
`US 2019/0031704 Al
`
`Jan. 31, 2019
`
`(60)
`
`Related U.S. Application Data
`
`Continuation of application No. 15/915,983, filed on
`Mar. 8, 2018, which is a 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)
`
`Int. Cl.
`C07H 19114
`C12Q 1168
`C07H 21100
`C12Q 11686
`C12Q 116874
`C12Q 116872
`C12Q 116869
`C07H 19110
`
`(2006.01)
`(2018.01)
`(2006.01)
`(2018.01)
`(2018.01)
`(2018.01)
`(2018.01)
`(2006.01)
`
`4,711,955 A
`4,772,691 A
`4,804,748 A
`4,824,775 A
`4,863,849 A
`4,888,274 A
`5,043,272 A
`5,047,519 A
`5,118,605 A
`5,151,507 A
`5,174,962 A
`5,175,269 A
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`(Continued)
`
`FOREIGN PATENT DOCUMENTS
`
`CA
`CA
`
`4/2002
`2425112
`11/2002
`2408143
`(Continued)
`
`OTHER PUBLICATIONS
`
`Aug. 19, 2013 Petition 2 of 2 for Inter Partes Review of U.S. Pat.
`No. 7,566,537, issued Aug. 19, 2013.
`(Continued)
`
`Jezia Riley
`Primary Examiner -
`(74) Attorney, Agent, or Firm -
`Dunham LLP
`
`John P. White; Cooper &
`
`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.
`
`2 Claims, 28 Drawing Sheets
`Specification includes a Sequence Listing.
`
`Page 1
`
`Illumina Ex. 1001
`IPR Petition - USP 10,435,742
`
`

`

`US 10,407,458 B2
`Page 2
`
`(56)
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`Page 3
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`

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`US 10,407,458 B2
`Page 4
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