( 12 ) United States Patent
`Ju et al .
`
`( 10 ) Patent No . : US 10 , 407 , 459 B2
`( 45 ) Date of Patent :
`* Sep . 10 , 2019
`
`US010407459B2
`
`( 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 / 149 , 114
`( 22 ) Filed :
`Oct . 1 , 2018
`Prior Publication Data
`( 65 )
`US 2019 / 0085014 A1 Mar . 21 , 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 .
`CO7H 19 / 14
`C120 1 / 68
`CO7H 21 / 00
`C12Q 1 / 686
`C12Q 1 / 6874
`C120 1 / 6872
`C12Q 1 / 6869
`CO7H 19 / 10
`
`( 2006 . 01 )
`( 2018 . 01 )
`( 2006 . 01 )
`( 2018 . 01 )
`( 2018 . 01 )
`( 2018 . 01 )
`( 2018 . 01 )
`( 2006 . 01 )
`
`( 58 )
`
`( 56 )
`
`( 2018 . 01 )
`C12Q 1 / 6876
`C40B 40 / 00
`( 2006 . 01 )
`( 52 ) U . S . CI .
`CPC . . . . . . . . . . . . . CO7H 19 / 14 ( 2013 . 01 ) ; CO7H 19 / 10
`( 2013 . 01 ) ; C07H 21 / 00 ( 2013 . 01 ) ; C120 1 / 68
`( 2013 . 01 ) ; C12Q 1 / 686 ( 2013 . 01 ) ; C12Q
`1 / 6869 ( 2013 . 01 ) ; C120 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 )
`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 .
`References Cited
`U . S . PATENT DOCUMENTS
`12 / 1987 Ward et al .
`4 , 711 , 955 A
`4 , 772 , 691 A
`9 / 1988 Herman
`2 / 1989 Seela
`4 , 804 , 748 A
`4 / 1989 Dattagupta et al .
`4 , 824 , 775 A
`4 , 863 , 849 A
`9 / 1989 Melamede
`12 / 1989 Radding et al .
`4 , 888 , 274 A
`8 / 1991 Hartley
`5 , 043 , 272 A
`9 / 1991 Hobbs , Jr . et al .
`5 , 047 , 519 A
`6 / 1992 Urdea
`5 , 118 , 605 A
`5 , 151 , 507 A
`9 / 1992 Hobbs , Jr . et al .
`5 , 174 , 962 A
`12 / 1992 Brennan
`( Continued )
`FOREIGN PATENT DOCUMENTS
`2425112
`4 / 2002
`2408143
`11 / 2002
`( Continued )
`OTHER PUBLICATIONS
`Kre?merová ( 1990 ) “ Synthesis of 5 ' - O - Phosphonomethyl Deriva
`tives of Pyrimidine 2 ' - Deoxynucleosides . ” Coll . Czech . Chem .
`Commun . , 55 : 2521 - 2536 .
`( Continued )
`Primary Examiner — Jezia Riley
`( 74 ) Attorney , Agent , or Firm — John P . White ; 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 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. 1002
`IPR Petition - USP 10,435,742
`
`

`

`US 10 , 407 , 459 B2
`Page 2
`
`( 56 )
`
`References Cited
`U . S . PATENT DOCUMENTS
`12 / 1992 Stavrianopoulos
`5 , 175 , 269 A
`5 , 242 , 796 A
`9 / 1993 Prober et al .
`4 / 1994 Cheeseman
`5 , 302 , 509 A
`5 , 308 , 990 A
`5 / 1994 Takahashi et al .
`7 / 1994 Ward et al .
`5 , 328 , 824 A
`7 / 1994 Prober et al .
`5 , 332 , 666 A
`1 / 1995 Reilly et al .
`5 , 383 , 858 A
`5 , 424 , 186
`A
`6 / 1995 Fodor et al .
`7 / 1995 Hyman
`5 , 436 , 143 A
`8 / 1995 McClelland et al .
`5 , 437 , 975 A
`9 / 1995 Ward et al .
`5 , 449 , 767 A
`12 / 1995 Ward et al .
`5 , 476 , 928 A
`5 / 1996 Hyman
`5 , 516 , 664 A
`5 , 534 , 424 A
`7 / 1996 Uhlen et al .
`5 , 547 , 839 A
`8 / 1996 Dower et al .
`8 / 1996 Goodman et al .
`5 , 547 , 859 A
`9 / 1996 Douglas
`5 , 556 , 748 A
`5 , 599 , 675 A
`2 / 1997 Brenner
`2 / 1997 Hyman
`5 , 602 , 000 A
`3 / 1997 Tabor et al .
`5 , 614 , 365 A
`6 / 1997 Wilding et al .
`5 , 637 , 469 A
`8 / 1997 Mathies et al .
`5 , 654 , 419 A
`8 / 1997 Wong
`5 , 658 , 736 A
`1 / 1998 Shattuck - Eidens et al .
`5 , 709 , 999 A
`2 / 1998 Brenner et al .
`5 , 714 , 330 A
`3 / 1998 Mathies et al .
`5 , 728 , 528 A
`5 , 763 , 594 A
`6 / 1998 Hiatt et al .
`6 / 1998 Lane et al .
`5 , 770 , 365 A
`6 / 1998 Southern et al .
`5 , 770 , 367 A
`5 , 789 , 167 A
`8 / 1998 Konrad
`5 , 798 , 210 A
`8 / 1998 Canard et al .
`5 , 804 , 386 A
`9 / 1998 Ju
`9 / 1998 Hiatt et al .
`5 , 808 , 045 A
`9 / 1998 Ju
`5 , 814 , 454 A
`10 / 1998 Khan et al .
`5 , 821 , 356 A
`11 / 1998 Katzir et al .
`5 , 834 , 203 A
`5 , 844 , 106 A
`12 / 1998 Seela et al .
`12 / 1998 Reeve et al .
`5 , 849 , 542 A
`5 , 853 , 992 A
`12 / 1998 Glazer et al .
`1 / 1999 Chee et al .
`5 , 856 , 104 A
`1 / 1999 Jones
`5 , 858 , 671 A
`2 / 1999 Mathies et al .
`5 , 869 , 255 A
`5 , 872 , 244 A
`2 / 1999 Hiatt et al .
`5 , 876 , 936 A
`3 / 1999 Ju
`3 / 1999 Haff et al .
`5 , 885 , 775 A
`5 , 885 , 813 A
`3 / 1999 Davis et al .
`5 , 908 , 755 A
`6 / 1999 Kumar et al .
`5 , 945 , 283 A
`8 / 1999 Kwok et al .
`5 , 948 , 648 A
`9 / 1999 Khan et al .
`9 / 1999 Ju
`5 , 952 , 180 A
`9 / 1999 Hannessian
`5 , 959 , 089 A
`10 / 1999 Brenner
`5 , 962 , 228 A
`12 / 1999 Canard et al .
`6 , 001 , 566 A
`12 / 1999 Will
`6 , 001 , 611 A
`12 / 1999 Benson et al .
`6 , 008 , 379 A
`1 / 2000 Albrecht et al .
`6 , 013 , 445 A
`2 / 2000 Mathies et al .
`6 , 028 , 190 A
`6 , 046 , 005 A
`4 / 2000 Ju et al .
`6 , 074 , 823 A
`6 / 2000 Koster
`7 / 2000 Rosenthal et al .
`6 , 087 , 095 A
`8 / 2000 Benson et al .
`6 , 111 , 116 A
`10 / 2000 Anazawa et al .
`6 , 136 , 543 A
`6 , 175 , 107 B1
`1 / 2001 Juvinall
`3 / 2001 Makarov et al .
`6 , 197 , 557 B1
`3 / 2001 Auer et al .
`6 , 207 , 831 B1
`4 / 2001 Nyren et al .
`6 , 210 , 891 B1
`4 / 2001 Hiatt et al .
`6 , 214 , 987 B1
`4 / 2001 Sampson et al .
`6 , 218 , 118 B1
`4 / 2001 Rothschild et al .
`6 , 218 , 530 B1
`4 / 2001 Schwartz et al .
`6 , 221 , 592 B1
`5 / 2001 Hiatt et al .
`6 , 232 , 465 B1
`6 / 2001 Anazawa et al .
`6 , 242 , 193 B1
`6 / 2001 Bogdanov
`6 , 245 , 507 B1
`6 / 2001 Lam et al .
`6 , 248 , 884 B1
`6 , 255 , 083 B1
`7 / 2001 Williams
`
`7 / 2001 Kwiatkowski
`6 , 255 , 475 B1
`8 / 2001 Rothberg et al .
`6 , 274 , 320 B1
`6 , 277 , 607 B1 8 / 2001 Tyagi et al .
`6 , 287 , 821 B1
`9 / 2001 Shi et al .
`6 , 294 , 324 B1
`9 / 2001 Bensimon et al .
`6 , 309 , 829 B1 10 / 2001 Livak et al .
`6 , 309 , 836 B1 10 / 2001 Kwiatkowski
`6 , 312 , 893 B111 / 2001 Van Ness et al .
`6 , 316 , 230 B111 / 2001 Egholm et al .
`6 , 335 , 155 B1
`1 / 2002 Wells et al .
`6 , 361 , 940 B1
`3 / 2002 Van Ness et al .
`6 , 380 , 378 B1
`4 / 2002 Kitamura et al .
`6 , 432 , 360 B1
`8 / 2002 Church
`6 , 495 , 680 B1 12 / 2002 Gong
`6 , 524 , 829 B1 2 / 2003 Seeger
`6 , 555 , 349 B1
`4 / 2003 O ' Donnell
`6 , 613 , 508 B1
`9 / 2003 Ness et al .
`6 , 613 , 513 B1
`9 / 2003 Parce et al .
`6 , 627 , 436 B2
`9 / 2003 Sorge et al .
`6 , 627 , 748 B1
`9 / 2003 Ju et al .
`6 , 632 , 655 B1 10 / 2003 Mehta et al .
`6 , 639 , 088 B2 10 / 2003 Kwiatkowski
`6 , 664 , 079 B2 12 / 2003 Ju et al .
`6 , 664 , 399 B1 12 / 2003 Sabesan
`6 , 713 , 255 B1
`3 / 2004 Makino et al .
`6 , 780 , 591 B2
`8 / 2004 Williams et al .
`6 , 787 , 308 B2
`9 / 2004 Balasubramanian et al .
`6 , 818 , 395 B1 11 / 2004 Quake et al .
`6 , 833 , 246 B2 12 / 2004 Balasubramanian
`6 , 858 , 393 B1
`2 / 2005 Anderson et al .
`6 , 864 , 052 B1
`3 / 2005 Drmanac et al .
`6 , 911 , 345 B2
`6 / 2005 Quake et al .
`6 , 934 , 636 B1
`8 / 2005 Skierczynski et al .
`6 , 982 , 146 B1
`1 / 2006 Schneider et al .
`7 , 037 , 687 B2
`5 / 2006 Williams et al .
`7 , 056 , 661 B2
`6 / 2006 Korlach et al .
`7 , 056 , 666 B2
`6 / 2006 Dower et al .
`7 , 057 , 026 B2
`6 / 2006 Barnes et al .
`7 , 057 , 031 B2
`6 / 2006 Olejnik et al .
`7 , 074 , 597 B2
`7 / 2006 Ju
`7 , 078 , 499 B2
`7 / 2006 Odedra et al .
`7 , 105 , 300 B2
`9 / 2006 Parce et al .
`7 , 270 , 951 B1
`9 / 2007 Stemple et al .
`7 , 279 , 563 B2 10 / 2007 Kwiatkowski
`7 , 329 , 496 B2
`2 / 2008 Dower et al .
`7 , 345 , 159 B2
`3 / 2008 Ju et al .
`7 , 393 , 533 B1
`7 / 2008 Crotty et al .
`7 , 414 , 116 B2
`8 / 2008 Milton et al .
`7 , 427 , 673 B2
`9 / 2008 Balasubramanian et al .
`7 , 459 , 275 B2 12 / 2008 Dower et al .
`7 , 541 , 444 B2
`6 / 2009 Milton et al .
`7 , 566 , 537 B2
`7 / 2009 Balasubramanian et al .
`7 , 622 , 279 B2
`11 / 2009 Ju
`7 , 635 , 578 B2 12 / 2009 Ju et al .
`7 , 713 , 698 B2
`5 / 2010 Ju et al .
`7 , 771 , 973 B2
`8 / 2010 Milton et al .
`7 , 785 , 790 B1
`8 / 2010 Church et al .
`7 , 790 , 869 B2
`9 / 2010 Ju et al .
`7 , 883 , 869 B2
`2 / 2011 Ju et al .
`7 , 982 , 029 B2
`7 / 2011 Ju et al .
`8 , 088 , 575 B2
`1 / 2012 Ju et al .
`8 , 158 , 346 B2
`4 / 2012 Balasubramanian et al .
`8 , 298 , 792 B2
`10 / 2012 Ju et al .
`8 , 399 , 188 B2
`3 / 2013 Zhao et al .
`8 , 796 , 432 B2
`8 / 2014 Ju et al .
`8 , 889 , 348 B2 11 / 2014 Ju
`9 , 115 , 163 B2
`8 / 2015 Ju et al .
`9 , 133 , 511 B2
`9 / 2015 Ju et al .
`9 , 159 , 610 B2 10 / 2015 Zhang et al .
`9 , 175 , 342 B2
`11 / 2015 Ju et al .
`9 , 255 , 292 B2
`2 / 2016 Ju et al .
`9 , 297 , 042 B2
`3 / 2016 Ju et al .
`9 , 708 , 358 B2
`7 / 2017 Ju et al .
`9 , 718 , 852 B2
`8 / 2017 Ju et al .
`9 , 719 , 139 B2
`8 / 2017 Ju et al .
`9 , 725 , 480 B2
`8 / 2017 Ju et al .
`9 , 868 , 985 B2
`1 / 2018 Ju et al .
`2002 / 0012966 AL
`1 / 2002 Shi et al .
`2002 / 0168642 A1 11 / 2002 Drukier
`
`Page 2
`
`

`

`( 56 )
`
`References Cited
`U . S . PATENT DOCUMENTS
`2003 / 0008285 A11 / 2003 Fischer
`2003 / 0022225 Al
`1 / 2003 Monforte et al .
`2003 / 0027140 A1 2 / 2003 Ju et al .
`2003 / 0044871 Al
`3 / 2003 Cutsforth et al .
`2003 / 0054360 Al
`3 / 2003 Gold et al .
`2003 / 0099972 A1
`5 / 2003 Olejnik et al .
`2003 / 0166282 A
`9 / 2003 Brown et al .
`2003 / 0180769 AL
`9 / 2003 Metzker
`2003 / 0186256 AL 10 / 2003 Fischer
`2003 / 0190680 A
`10 / 2003 Rothschild et al .
`2003 / 0198982 A
`10 / 2003 Seela et al .
`2004 / 0014096 AL
`1 / 2004 Anderson et al .
`2004 / 0096825 A1 5 / 2004 Chenna et al .
`2005 / 0032081 A1
`2 / 2005 Ju et al .
`2005 / 0170367 AL
`8 / 2005 Quake et al .
`2005 / 0239134 AL 10 / 2005 Gorenstein et al .
`2006 / 0003352 A11 / 2006 Lipkin et al .
`2006 / 0057565 A1 3 / 2006 Ju et al .
`2006 / 0105461 A1
`5 / 2006 Tom - Moy et al .
`2006 / 0160081 A1
`7 / 2006 Milton et al .
`2006 / 0160113 AL
`7 / 2006 Korlach et al .
`2006 / 0240439 Al 10 / 2006 Smith et al .
`2006 / 0252038 AL 11 / 2006 Ju
`2007 / 0166705 Al
`7 / 2007 Milton et al .
`2009 / 0088332 Al 4 / 2009 Ju et al .
`2009 / 0240030 A1 9 / 2009 Ju et al .
`2010 / 0159531 A1 6 / 2010 Gordon et al .
`2010 / 0323350 A112 / 2010 Gordon et al .
`2011 / 0014611 A1 1 / 2011 Ju et al .
`2011 / 0124054 Al 5 / 2011 Olejnik et al .
`2012 / 0052489 Al
`3 / 2012 Gordon et al .
`2012 / 0142006 A16 / 2012 Ju et al .
`2013 / 0264207 Al 10 / 2013 Ju et al .
`2014 / 0315191 Al 10 / 2014 Ju et al .
`2015 / 0037788 AL
`2 / 2015 Ju
`2015 / 0080232 A1 3 / 2015 Ju et al .
`2015 / 0111759 Al 4 / 2015 Ju et al .
`2015 / 0119259 Al 4 / 2015 Ju et al .
`2015 / 0197800 A1
`7 / 2015 Ju et al .
`2015 / 0368710 Al 12 / 2015 Fuller et al .
`2016 / 0024570 A1
`1 / 2016 Ju et al .
`2016 / 0024574 AL
`1 / 2016 Ju et al .
`2016 / 0041179 A1
`2 / 2016 Ju et al .
`2016 / 0090621 A1
`3 / 2016 Ju et al .
`2016 / 0264612 A1 9 / 2016 Ju et al .
`2017 / 0088574 A1
`3 / 2017 Ju et al .
`2017 / 0088575 Al
`3 / 2017 Ju et al .
`2017 / 0088891 Al
`3 / 2017 Ju et al .
`2017 / 0313737 AL 11 / 2017 Ju et al .
`2018 / 0201642 A17 / 2018 Ju et al .
`FOREIGN PATENT DOCUMENTS
`6 / 1993
`4141178
`20122767
`8 / 2007
`112007002932 . 3
`8 / 2015
`0251786 B1
`11 / 1994
`0995804
`4 / 2000
`1182267
`2 / 2002
`1291354
`3 / 2003
`0808320
`4 / 2003
`1337541 B1
`3 / 2007
`1218391
`4 / 2007
`0992511
`3 / 2009
`10 / 2013
`2209911 B1
`2000 0013276
`6 / 2000
`12 / 2001
`2001 0029012
`3 / 2011
`2446083
`2446084
`3 / 2011
`9 / 2011
`2457402
`WO 1989 / 09282
`10 / 1989
`WO 89 / 10977
`11 / 1989
`WO 1989 / 11548
`11 / 1989
`WO 1990 / 13666
`11 / 1990
`WO 91 / 06678
`5 / 1991
`
`DE
`DE
`DE
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`GB
`GB
`GB
`GB
`GB
`WO
`WO
`WO
`WO
`WO
`
`US 10 , 407 , 459 B2
`Page 3
`
`WO
`WO
`WO
`WO
`WO
`WO
`Wo
`wo
`wo
`WO
`WO
`wo
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`wo
`WO
`WO
`WO
`WO
`wo
`WO
`WO
`wo
`WO
`WO
`WO
`wo
`WO
`WO
`WO
`WO
`WO
`WO
`wo
`WO
`WO
`WO
`WO
`wo
`WO
`Wo
`WO
`WO
`wo
`WO
`WO
`WO
`WO
`wo
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`wo
`WO
`WO
`WO
`wo
`WO
`WO
`WO
`WO
`WO
`
`WO 1991 / 06678
`WO1992 / 10587
`WO 1993 / 05183
`WO 93 / 12340
`WO 1993 / 21340
`WO 1994 / 14972
`WO 1996 / 07669
`WO 96 / 23807
`WO 1996 / 23807
`WO 96 / 27025
`WO 1996 / 27025
`WO 1997 / 08183
`WO 1997 / 27317
`WO 1997 / 35033
`WO 1998 / 30720
`WO 98 / 33939
`WO 1998 / 33939
`WO 1998 / 44151
`WO 98 / 53300
`WO 1999 / 05315
`WO 1999 / 49082
`WO 1999 / 57321
`WO 2000 / 02895
`WO 2000 / 06770
`WO 2000 / 09753
`WO 2000 / 15844
`WO 2000 / 18956
`WO 2000 / 21974
`WO 2000 / 50172
`WO 2000 / 50642
`WO 00 / 53812
`WO 2000 / 53805
`WO 2000 / 53812
`WO 2000 / 70073
`WO 2001 / 16375
`WO 2001 / 23610
`WO 2001 / 25247
`WO 2001 / 27625
`WO 2001 / 32930
`WO 2001 / 57248
`WO 2001 / 57249
`WO 01 / 92284
`WO 2001 / 92284
`WO 2002 / 02813
`WO 02 / 21098
`WO 2002 / 22883
`WO 02 / 29003
`WO 2002 / 29003
`WO 2002 / 72892
`WO 2002 / 079519
`WO 2002 / 88381
`WO 2002 / 88382
`WO 2003 / 02767
`WO 2003 / 20968
`WO 2003 / 48178
`WO 2003 / 48387
`WO 2003 / 85135
`WO 04 / 18493
`WO 04 / 18497
`WO 2004 / 018493
`WO 2004 / 18493
`WO 2004 / 18497
`WO 2004 / 018497
`WO 2004 / 055160
`WO 2005 / 084367
`WO 2006 / 73436
`WO 2007 / 002204
`WO 2007 / 62105
`WO 2008 / 069973
`WO 2012 / 083249
`WO 2012 / 162429
`WO 2013 / 154999
`WO 2013 / 191793
`WO 2014 / 144883
`WO 2014 / 144898
`WO 2015 / 123430
`
`5 / 1991
`6 / 1992
`3 / 1993
`10 / 1993
`10 / 1993
`7 / 1994
`3 / 1996
`8 / 1996
`8 / 1996
`9 / 1996
`9 / 1996
`3 / 1997
`7 / 1997
`9 / 1997
`7 / 1998
`8 / 1998
`8 / 1998
`10 / 1998
`11 / 1998
`2 / 1999
`9 / 1999
`11 / 1999
`1 / 2000
`2 / 2000
`2 / 2000
`3 / 2000
`4 / 2000
`4 / 2000
`8 / 2000
`8 / 2000
`9 / 2000
`9 / 2000
`9 / 2000
`11 / 2000
`3 / 2001
`4 / 2001
`4 / 2001
`4 / 2001
`5 / 2001
`8 / 2001
`8 / 2001
`12 / 2001
`12 / 2001
`1 / 2002
`3 / 2002
`3 / 2002
`4 / 2002
`4 / 2002
`9 / 2002
`10 / 2002
`11 / 2002
`11 / 2002
`1 / 2003
`3 / 2003
`6 / 2003
`6 / 2003
`10 / 2003
`3 / 2004
`3 / 2004
`3 / 2004
`3 / 2004
`3 / 2004
`3 / 2004
`7 / 2004
`9 / 2005
`7 / 2006
`1 / 2007
`5 / 2007
`6 / 2008
`6 / 2012
`11 / 2012
`10 / 2013
`12 / 2013
`9 / 2014
`9 / 2014
`8 / 2015
`
`Page 3
`
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`US 10 , 407 , 459 B2
`Page 4
`
`( 56 )
`
`10 / 2015
`11 / 2015
`
`References Cited
`FOREIGN PATENT DOCUMENTS
`WOWO 2015 / 148402
`WOWO 2015 / 179284
`OTHER PUBLICATIONS
`Kurata et al . ( 2001 ) “ Fluorescent quenching - based quantitative
`detection of specific DNA / RNA using BODIPY® FL - labeled probe
`of primer , ” Nucleic Acids Research , vol . 29 , No . 6 , p . e34 .
`Kvam et al . , ( 1994 ) " Characterization of singlet oxygen - induced
`guanine residue damage after photochemical treatment of free
`nucleosides and DNA , ” Biochemica et Biophysica Acta . , 1217 : 9
`15 .
`Lee , L . G . , et al . ( 1992 ) “ DNA sequencing with dye labeled termi
`nators and T7 DNA polymerase effect of dyes and dNTPs on
`incorporation of dye terminators and probability analysis of termi
`nation fragments , ” Nucleic Acids Res . 20 : 2471 - 2483 .
`Lee L . G . et al , ( 1997 ) “ New energy transfer dyes for DNA sequenc
`ing , ” Nucleic Acids Res . 25 : 2816 - 2822 .
`Leroy , E . M . et al . ( 2000 ) “ Diagnosis of Ebola Haemorrhagic Fever
`by RT - PCR in an Epidemic Setting , ” Journal of Medical Virology
`60 : 463 - 467 .
`Lewis et al . ( 2002 ) “ Click Chemistry in Situ : Acetylcholinesterase
`as a Reaction Vessel for the Selective Assembly of a Femtomolar
`Inhibitor from an Array of Building Blocks , ” Angew . Chem . Int . Ed .
`41 ( 6 ) : 1053 - 1057 .
`Li , J . ( 1999 ) “ Single Oligonucleotide Polymorphism Determination
`Using Primer Extension and Time - of - Flight Mass Spectrometry , "
`Electrophoresis 20 : 1258 - 1265 .
`Li et al . ( 2003 ) “ A photocleavable Fluorescent Nucleotide for DNA
`Sequencing and Analysis , ” PNAS 100 ( 2 ) : 414 - 419 .
`Liu , H . et al . ( 2000 ) “ Development of Multichannel Devices with an
`Array of Electrospray Tips for High - Throughput Mass Spectrom
`etry , ” Anal . Chem . 72 : 3303 - 3310 .
`Loubinoux , B . et al . “ Protection Des Phenols Par Le Groupement
`Azidomethylene Application A La Synthese De Phenols Instables , "
`Tetrahedron , 1998 , 44 ( 19 ) : 6055 ( English Abstract Only ) .
`Lu , G . and Burgess , K . ( 2006 ) “ A Diversity Oriented Synthesis of
`3 - O - Modified Nucleoside Triphosphates for DNA Sequencing by
`Synthesis ” Bioorg . Med . Chem . Lett . , 16 : 3902 - 3905 .
`Lyamichev ,
`V . et al . ( 1999 ) “ Polymorphism Identification and
`Quantitative Detection of Genomic DNA by Invasive Cleavage of
`Oligonucleotide Probes , ” Nat . Biotech 17 : 292 - 296 .
`Maier et al . ( 1995 ) “ Synthesis and Properties of New Fluorescein
`Labeled Oligonucleotides , ” Nucleosides and Nucleotides , 14 : 961
`965 .
`Margulies , M . , Egholm , M . ; Altman , W . E . ( 2005 ) “ Genome Sequenc
`ing in Microfabricated High - Density Picolitre Reactors . ” Nature ,
`437 : 376 - 380 .
`Markiewicz et al . ( 1997 ) “ A new method of synthesis of fluorescently
`labeled oligonucleotides and their application in DNA sequencing ,
`Nucleic Acids Research , 25 : 3672 - 3690 .
`Marquez et al . ( 2003 ) “ Selective Fluorescnece Quenching of 2 , 3
`Diazabicyclo [ 2 . 2 . 2 ] oct - 2 - ene by Nucleotides , ” Organic Letters , 5 : 3911
`3914 .
`Mathews C . K . et al . ( 1985 ) “ Chemical Synthesis of Oligonucle
`otides , ” Biochemistry , 2nd Edition , pp . 127 - 128 .
`Meng et al . ( 2006 ) “ Design and Synthesis of a Photocleavable
`Fluorescent Nucleotide 3 ' - O - Allyl - dGTP - PC - Biodipy - FL - 510 as a
`Reversible Terminator for DNA Sequencing by Synthesis , ” J . Org .
`Chem 71 : 3248 - 3252 .
`Metzker , M . L . et al . ( 1994 ) “ Termination of DNA synthesis by
`novel 3 ' modified deoxyribonucleoside 5 ' triphosphates , ” Nucleic
`Acids Res . 22 : 4259 - 4267 .
`Metzker M . L . ( 2005 ) “ Emerging Technologies in DNA Sequenc
`ing . ” Genome Res . , 15 : 1767 - 1776 .
`Mitra , R . D . ; Shendure J . ; Olejnik , J . ; et al . ( 2003 ) “ Fluorescent in
`situ sequencing on polymerase colonies . ” Anal . Biochem . 320 : 55
`65 .
`
`Monforte , J . A . and Becker , C . H . ( 1997 ) “ High - throughput DNA
`analysis by time - of - flight mass spectrometry , " Nat . Med . 3 ( 3 ) : 360
`362 .
`Nazarenko et al . ( 2002 ) “ Effect of primary and secondary structure
`of oligodeoxyribonucleotides on the fluorescent properties of con
`jugated dyes , " Nucleic Acids Research , 30 : 2089 - 2095 .
`Nickel et al . ( 1992 ) “ Interactions of Azidothymidine triphosphate
`with the Cellular DNA polymerases alpha , delta , and episilon and
`with DNA Primase , " J . Biol . Chem . 267 ( 2 ) : 848 - 854 .
`Nielsen et al . ( 2004 ) “ Multiplexed Sandwich Assays in Microarray
`Format , ” Journal of Immunological Methods , vol . 290 , pp . 107 - 120 .
`Nishino et al . ( 1991 ) “ Efficient Deanilidation of Phosphoranilidates
`by the Use of Nitrites and Acetic Anhydride . ” Heteroatom Chem
`istry , vol . 2 , pp . 187 - 196 .
`Olejnik , J . et al . ( 1995 ) “ Photocleavable biotin derivatives : a
`versatile approach for the isolation of biomolecules , " Proc . Natl .
`Acad . Sci . USA . 92 : 7590 - 7594 .
`Olejnik , J . et al . ( 1999 ) “ Photocleavable peptide DNA conjugates :
`synthesis and applications to DNA analysis using MALDI MS , "
`Nucleic Acids Res . 27 : 4626 - 4631 .
`Pastinen et al . ( 1997 ) “ Minisequencing : A Specific Tool for DNA
`Analysis and Diagnostics on Oligonucleotide Arrays , " Genomic
`Res . , 7 : 606 - 614 .
`Pelletier , H . et al . ( 1994 ) " Structures of ternary complexes of rat
`DNA polymerase B , a DNA template - primer and ddCTP , ” Science
`264 : 1891 - 1903 .
`Prober , J . M . et al . ( 1987 ) “ A system for rapid DNA sequencing with
`fluorescent chain - terminating dideoxynucleotides , ” Science 238 : 336
`341 .
`Quaedflieg et al . ( 1992 ) “ An Alternative Approach Toward the
`Synthesis of ( 3 ' - > 5 ' ) Methylene Acetal Linked Dinucleosides . "
`Tetrahedron Letters , vol . 33 , pp . 3081 - 3084 .
`Rao et al . ( 2001 ) “ Four Color FRET Dye Nucleotide Terminators
`for DNA Sequencing , " Nucleosides , Nucleotides and Nucleic Acids ,
`20 : 673 - 676 .
`Rasolonjatovo et al . ( 1998 ) “ g - N - ( N - Methlanthranylamido ) - 4 - Oxo
`Hexanoic Acid : A New Fluorescnet Protecting Group Applicable to
`a New DNA Sequencing Method , ” Nucleosides and Nucleotides ,
`17 : 2021 - 2025 .
`Ronaghi , ( 1998 ) “ PCR - Introduced Loop Structure as Primer in
`DNA Sequencing . ” Bio Techniques , 25 : 876 .
`Ronaghi , M . , Uhlen , M . , and Nyren , P . ( 1998 ) “ A Sequencing
`Method Based on Real - time Pyrophosphate , ” Science 281 : 364 - 365 .
`Rosenblum , B . B . et al . ( 1997 ) “ New dye - labeled terminators for
`improved DNA sequencing patterns , ” Nucleic Acides Res . 25 : 4500
`4504 .
`Roskey , M . T . , Juhasz , P . , Smirnov , I . P . , Takach , E . J . , Martin , S . A . ,
`and Haff , L . A . ( 1996 ) “ DNA sequencing by delayed extraction
`matrix - assisted laser desorption / ionization time of flight mass spec
`trometry , ” Proc . Natl . Acad . Sci . USA . 93 : 4724 - 4729 .
`Ross , P . L . et al . ( 1997 ) “ Discrimination of Single - Nucleotide
`Polymorphisms in Human DNA Using Peptide Nucleic Acid Probes
`Detected by MALDI - TOF Mass Spectrometry , ” Anal . Chem . 69 : 4197
`4202 .
`Ross , P . et al . ( 1998 ) High Level Multiplex Genotyping by MALDI
`TOF Mass Spectrometry . Nat . Biotech 16 : 1347 - 1351 .
`Ruparel et al . ( 2005 ) “ Design and Synthesis of a 3 ' - 0 - Allyl Photocleav
`able Fluorescent Nucleotide as a Reversible Terminator for DNA
`Sequencing by Synthesis , ” PNAS 102 ( 17 ) : 5932 - 5937 .
`Sarfati et al . , ( 1995 ) “ Synthesis of fluorescnet derivatives of 3 ' - 0
`( 6 - aminohexanoyl ) - pyrimidine nucleosides 5 ' - triphosphates that act
`as DNA polymerase substrates reversibly tagged at C - 3 ' , ” JCS
`Perkin Trans , 1163 - 1171 .
`Saxon , E . and Bertozzi , C . R . ( 2000 ) “ Cell surfac engineering by a
`modified Staudinger reaction , ” Science 287 ; 2007 - 2010 .
`Schena , M . , Shalon , D . and Davis , R . Brown P . O . ( 1995 ) " Quan
`titative monitoring of gene expression patterns with a cDNA
`microarray , ” Science 270 : 467 - 470 .
`Seeger ( 1998 ) “ Single Molecule Fluorescence : High - Performance
`Molecular Diagnosis and Screening , ” Bioforum , Git Verlag , Darmstadt ,
`DE vol . 21 , ( German text ) .
`Seo et al . ( 2003 ) “ Click Chemistry to Construct Fluorescent Oli
`gonucleotides for DNA Sequencing , " J . Org . Chem . 68 : 609 - 612 .
`
`Page 4
`
`

`

`US 10 , 407 , 459 B2
`Page 5
`
`( 56 )
`
`References Cited
`OTHER PUBLICATIONS
`Seo et al . ( 2004 ) “ Photocleavable Fluorescent Nucleotides for DNA
`Sequencing on a Chip Constructed by Site - Specific Coupling Chem
`istry , ” PNAS 101 ( 15 ) : 5488 - 5493 .
`Seo et al . ( 2005 ) “ Four - Color DNA Sequencing by Synthesis on a
`Chip Using Photocleavable Fluorescent Nucleotides , ” PNAS 102
`( 17 ) : 5926 - 593 .
`Shendure , J . ; Porreca , G . J . ; Reppas , N . B . , et al . ( 2005 ) “ Accurate
`Multiplex Polony Sequencing of an Evolved Bacterial Genome . "
`Science 309 : 1728 - 1732 .
`Smith , L . M . , Sanders , J . Z . , Kaiser , R . J . , et al . ( 1986 ) “ Fluorescence
`Detection in Automated DNA Sequence Analysis , ” Nature 321 : 674
`679 .
`Speicher , M . R . , Ballard , S . G . , and Ward , D . C . ( 1996 ) “ Karyotyping
`human chromosomes by combinatorial multi - fluor FISH , ” Nature
`Genetics 12 : 368 - 375 .
`Stoerker , J . et al . ( 2000 ) “ Rapid Genotyping by MALDI - monitored
`nuclease selection from probe Libraries , ” Nat . Biotech 18 : 1213
`1216 .
`Tang , K . , Fu , D . J . , Julien , D . , Braun , A . , Cantor , C . R . , and Koster ,
`H . ( 1999 ) “ Chip - based genotyping by mass spectrometry , ” Proc .
`Natl . Acad . Sci . USA . 96 : 10016 - 10020 .
`Tong , X . and Smith , L . M . ( 1992 ) “ Solid - Phase Method for the
`Purification of DNA Sequencing Reactions , ” Anal . Chem . 64 : 2672
`2677 .
`Torimura et al . ( 2001 ) “ Fluorescence - Quenching Phenomenon by
`Photoinduced Electron Transfer between a Fluorescent Dye and
`Nucleotide Base , ” Analytical Sciences , 17 : 155 - 160 .
`Tuncel et al . ( 1999 ) “ Catalytically Self - Threading Polyrotaxanes , "
`Chem . Comm . 1509 - 1510 .
`Veeneman et al . ( 1991 ) “ An Efficient Approach to the Synthesis of
`Thymidine Derivatives containing Phosphate - Isoteric Methylene
`Acetyl Linkages , " Tetrahedron , 47 : 1547 - 1562 .
`Wada et al . ( 2001 ) “ 2 - ( Azidomethyl ) benzoyl as a new protecting
`group in nucleosides , ” Tetrahedron Letters , 42 : 1069 - 1072 .
`Weiss ( 1999 ) “ Fluorescent SpectroScopy of Single Biomolecules . ”
`Science , 283 : 1676 .
`Welch et al . ( 1999 ) “ Synthesis of Nucleosides Designed for Combinato
`rial DNA Sequencing , ” Chemistry , European Journal , 5 : 951 - 960 .
`Welch MB , Burgess K , ( 1999 ) “ Synthesis of fluorescent , photolabile
`3 ' - O - protected nucleoside triphosphates for the base addition sequenc
`ing scheme , " Nucleosides and Nucleotides 18 : 197 - 201 .
`Wendy , Jen . Et al . ( 2000 ) “ New Strategies for Organic Catalysis :
`The First Enantioselective Orgacnocatalytic 1 , 3 - Dipolar Cycload
`dition , " J . Am . Chem . Soc . 122 : 9874 - 9875 .
`Woolley , A . T . et al . ( 1997 ) “ High - Speed DNA Genotyping Using
`Microfabricated Capillary Array Electrophoresis Chips , ” Anal . Chem .
`69 : 2181 - 2186 .
`Yamashita et al . ( 1987 ) “ Studies on Antitumor Agents VII . Antitu
`mor Activities of 0 - Alkoxyalkyl Derivatives of 2 ' - Deoxy - 5
`trifluoromethyluridine . ” Chem Pharm . Bull . , vol . 35 , pp . 2373
`2381 .
`Zavgorodny , S . et al . ( 1991 ) " 1 - Alkylthioalkylation of Nucleoside
`Hydroxyl Functions and its synthetic Applications : A New Versatile
`Method in Nucleoside Chemistry , ” Tetrahedron Letters , 32 ( 51 ) :
`7593 - 7596 .
`Zavgorodny et al . ( 2000 ) “ S , X - Acetals in Nucleoside Chemistry .
`III . Synthesis of 2 ' - and 3 ' - 0 - Azidomethyl Derivatives of
`Ribonucleosides " Nucleosides , Nucleotides and Nucleic Acids ,
`19 ( 10 - 12 ) : 1977 - 1991 .
`Zhang et al . ( 2002 ) “ Synthesis of Releasable Electrophore Tags for
`Applications in Mass Spectrometry , ” Bioconjugate Chem . , vol . 13 ,
`pp . 1002 - 1012 .
`Zhu , Z . , Chao , J . , Yu , H , et al . ( 1994 ) “ Directly Labeled DNA
`Probes Using Fluorescent Nucleotides with Different Length Link
`ers , " Nucleic Acids Res . , 22 : 3418 - 3422 .
`U . S . Appl . No . 09 / 266 , 187 , filed Mar . 10 , 1999 , Stemple et al .
`Sep . 16 , 2012 Petition for Inter Partes Review of U . S . Pat . No .
`7 , 713 , 698 , issued May 11 , 2010 .
`
`Sep . 16 , 2012 Motion to Waive Page Limit and Proposed Petition
`in connection with Petition for Inter Partes Review of U . S . Pat . No .
`7 , 713 , 698 , issued May 11 , 2010 .
`Dec . 20 , 2012 Preliminary Response under 37 C . F . R . 42 . 107 in
`connection with IPR2012 - 00006 .
`Mar . 12 , 2013 Decision on Petition for Inter Partes Review in
`connection with IPR2012 - 00006 .
`Mar . 26 , 2013 Request for Reconsideration in connection with
`IPR2012 - 00006 .
`Apr . 26 , 2013 Opposition to Request for Reconsideration ( Rehear
`ing ) Under 37 C . F . R . 42 . 71 . ( C ) in connection with IPR2012 - 00006 .
`Sep . 27 , 2013 Petitioner Opposition to Motion to Amend in con
`nection with IPR2012 - 00006 .
`Sep . 27 , 2013 Petitioner Reply to Response to Petition in connection
`with IPR2012 - 00006 .
`Nov . 18 , 2013 Substitute Patent Owner Reply on Motion to Amend
`in connection with IPR2012 - 00006 .
`Prober et al . ( 1987 ) , “ A System for Rapid DNA Sequencing with
`Fluorescent Chain - Terminating Dideoxynucleotides ” , Science vol .
`238 , Oct . 16 , 1987 , pp . 336 - 341 ( Exhibit 1003 , filed Sep . 16 , 2012
`in connection with IPR2012 - 00006 ) .
`Sep . 15 , 2012 Declaration of George Weinstock Under Rule 37
`C . F . R . $ 1 . 132 ( Exhibit 1021 , filed Sep . 16 , 2012 in connection with
`IPR2012 - 00006 ) .
`Excerpts of File History of U . S . Pat . No . 7 , 713 , 698 ( Exhibit 1022 ,
`filed Sep . 16 , 2012 in connection with IPR2012 - 00006 ) .
`Columbia ' s Amended Complaint from The Trustees of Columbia
`University in the City of New York v . Illumina , Inc . , D . Del C . A . No .
`12 - 376 ( GMS ) , filed Apr . 11 , 2012 ( Exhibit 1025 , filed Apr . 30 ,
`2013 in connection with IPR2012 - 00006 ) .
`Illumina ' s Answer to Amended Complaint from The Trustees of
`Columbia University in the City of New York v . Illumina , Inc . , D .
`Del C . A . No . 12 - 376 ( GMS ) , filed Dec . 21 , 2012 ( Exhibit 1026 ,
`filed Apr . 30 , 2013 in connection with .
`Rosenblum et al . , “ New Dye - Labeled Terminators for Improved
`DNA Sequencing Patterns , ” Nucleic Acid Research , 1997 , vol . 25 ,
`No . 22 , pp . 4500 - 4504 ( Exhibit 1030 , filed Jun . 18 , 2013 in
`connection with IPR2012 - 00006 ) .
`Jun . 8 , 2013 Videotaped Deposition Transcript of George M .
`Weinstock , Ph . D . ( Exhibit 1034 , filed Jun . 18 , 2013 in connection
`with IPR2012 - 00006 ) .
`“ Next Generation Genomics : World Map of High - throughput Sequenc
`ers , " Sep . 1 , 2013 ( Exhibit 1036 , filed Sep . 27 , 2013 in connection
`with IPR2012 - 00006 ) .
`Videotaped . Deposition Transcript of Dr . Xiaohai Liu , Mar . 20 ,
`2013 ( Exhibit 1039 , filed Sep . 27 , 2013 in connection with IPR2012
`00006 ) .
`Excerpt from videotaped Deposition Transcript of George M . Weinstock ,
`Ph . D . , Jun . 8 , 2013 ( Exhibit 1040 , filed Sep . 27 , 2013 in connection
`with IPR2012 - 00006 ) .
`Seela et al . , “ Oligonucleotide Duplex Stability Controlled by the
`7 - Substituents of 7 - Deazaguanine Bases , " Bioorganic & Medical
`Chemistry Letters , vol . 5 , No . 24 , pp . 3049 - 3052 , 1995 ( Exhibit
`1041 , filed Sep . 27 , 2013 in connection with IPR2012 - 00006 ) .
`Ramzaeva et al . , “ 123 . 7 - Deazaguanine DNA : Oligonucleotides
`with Hydrophobic or Cationic Side Chains , " Helvetica Chimica
`Acta ' , vol . 80 , pp . 1809 - 1822 , 1997 ( Exhibit 1042 , filed Sep . 27 ,
`2013 in connection with IPR2012 - 00006 ) .
`Ramzaeva et al . , “ 88 . 7 - Substituted 7 - Deaza - 2 ' - deoxyguanosines :
`Regioselective Halogenation of Pyrrolo [ 2 , 3 - d ] pyrimidine Nucleosides , "
`Helvetica Chimica Acta , vol . 78 , pp . 1083 - 1090 , 1995 ( Exhibit
`1043 , filed Sep . 27 , 2013 in connection with IPR2012 - 00006 ) .
`Seela et al . , “ Duplex Stability of Oligonucleotides Containing
`7 - Substituted 7 - Deaza - and 8 - Aza - 7 - Deazapurin