( 12 ) United States Patent
`Ju et al .
`
`( 10 ) Patent No . : US 10 , 435 , 742 B2
`( 45 ) Date of Patent :
`* Oct . 8 , 2019
`
`US010435742B2
`
`( 72 )
`
`( 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 )
`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 )
`Subject to any disclaimer , the term of this
`patent is extended or adjusted under 35
`U . S . C . 154 ( b ) by 0 days .
`This patent is subject to a terminal dis
`claimer .
`( 21 ) Appl . No . : 16 / 150 , 185
`( 22 ) Filed :
`Oct . 2 , 2018
`Prior Publication Data
`( 65 )
`US 2019 / 0031705 A1 Jan . 31 , 2019
`
`( * ) Notice :
`
`( 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 .
`C120 1 / 68
`CO7H 19 / 14
`C120 1 / 6869
`CO7H 21 / 00
`C12Q 1 / 686
`C120 1 / 6874
`C120 1 / 6872
`CO7H 19 / 10
`
`( 2018 . 01 )
`( 2006 . 01 )
`( 2018 . 01 )
`( 2006 . 01 )
`( 2018 . 01 )
`( 2018 . 01 )
`( 2018 . 01 )
`( 2006 . 01 )
`
`( 52 )
`
`( 56 )
`
`( 2018 . 01 )
`C12Q 1 / 6876
`C40B 40 / 00
`( 2006 . 01 )
`U . S . Cl .
`CPC . . . . . . . . . . . C120 1 / 6869 ( 2013 . 01 ) ; CO7H 19 / 10
`( 2013 . 01 ) ; C07H 19 / 14 ( 2013 . 01 ) ; COZH
`21 / 00 ( 2013 . 01 ) ; C12Q 1 / 68 ( 2013 . 01 ) ; C12Q
`1 / 686 ( 2013 . 01 ) ; C12Q 1 / 6872 ( 2013 . 01 ) ;
`C12Q 1 / 6874 ( 2013 . 01 ) ; C12Q 1 / 6876
`( 2013 . 01 ) ; CO7B 2200 / 11 ( 2013 . 01 ) ; C120
`2525 / 117 ( 2013 . 01 ) ; C12Q 2525 / 186
`( 2013 . 01 ) ; C12Q 2535 / 101 ( 2013 . 01 ) ; C12Q
`2535 / 122 ( 2013 . 01 ) ; C12Q 2563 / 107
`( 2013 . 01 ) ; C12Q 2565 / 501 ( 2013 . 01 ) ; C40B
`40 / 00 ( 2013 . 01 )
`( 58 ) Field of Classification Search
`CPC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C12Q 1 / 6869 ; CO7H 19 / 14
`USPC
`. . . . . . . . . . . 536 / 4 . 1 ; 435 / 6 . 1
`See application file for complete search history .
`References Cited
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`OTHER PUBLICATIONS
`U . S . Appl . No . 12 / 804 , 025 , filed Jul . 13 , 2010 , Balasubramanian et
`al .
`( Continued )
`Primary Examiner — Jezia Riley
`( 74 ) Attorney , Agent , or Firm — John P . White ; 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 analogue after the
`nucleotide analogue is incorporated into a growing strand of
`DNA in a polymerase reaction . The invention also provides
`nucleotide analogues which comprise unique labels attached
`to the nucleotide analogue 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 .
`
`CA
`
`Page 1
`
`Illumina Ex. 1004
`IPR Petition - USP 10,435,742
`
`

`

`US 10 , 435 , 742 B2
`Page 2
`
`( 56 )
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`US 10 , 435 , 742 B2
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`
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