`US010457984B2
`
`c12) United States Patent
`Ju et al.
`
`US 10,457,984 B2
`(IO) Patent No.:
`(45) Date of Patent:
`*Oct. 29, 2019
`
`(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 ........... C12Q 116869 (2013.01); C07H 19110
`(2013.01); C07H 19114 (2013.01); C07H
`21100 (2013.01); C12Q 1168 (2013.01); C12Q
`11686 (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 .............................. C12Q 1/6869; C07H 19/14
`USPC ............................................. 536/4.1; 435/6.1
`See application file for complete search history.
`
`(56)
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`
`(21) Appl. No.: 16/150,180
`
`(22) Filed:
`
`Oct. 2, 2018
`
`(65)
`
`Prior Publication Data
`
`US 2019/0085015 Al Mar. 21, 2019
`
`Related U.S. Application Data
`
`(60) 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.
`C12Q 1168
`C07H 19114
`C12Q 116869
`C07H 21100
`C12Q 11686
`C12Q 116874
`C12Q 116872
`C07H 19110
`
`(2018.01)
`(2006.01)
`(2018.01)
`(2006.01)
`(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
`5,242,796 A
`
`12/1987 Ward et al.
`9/1988 Herman
`2/1989 Seela
`4/1989 Dattagupta et al.
`9/1989 Melamede
`12/1989 Radding et al.
`8/1991 Hartley
`9/1991 Hobbs, Jr. et al.
`6/1992 Urdea
`9/1992 Hobbs, Jr. et al.
`12/1992 Brennan
`12/1992 Stavrianopoulos
`9/1993 Prober et al.
`(Continued)
`
`FOREIGN PATENT DOCUMENTS
`
`CA
`CA
`
`4/2002
`2425112
`11/2002
`2408143
`(Continued)
`
`OTHER PUBLICATIONS
`
`U.S. Pat. No. 09/266,187, filed Mar. 10, 1999, Stemple et al.
`(Continued)
`
`Primary Examiner -
`Jezia Riley
`(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 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.
`
`Page 1
`
`Illumina Ex. 1003
`IPR Petition - USP 10,435,742
`
`
`
`US 10,457,984 B2
`Page 2
`
`(56)
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`
`5,302,509 A
`5,308,990 A
`5,328,824 A
`5,332,666 A
`5,383,858 A
`5,424,186 A
`5,436,143 A
`5,437,975 A
`5,449,767 A
`5,476,928 A
`5,516,664 A
`5,534,424 A
`5,547,839 A
`5,547,859 A
`5,556,748 A
`5,599,675 A
`5,602,000 A
`5,614,365 A
`5,637,469 A
`5,654,419 A
`5,658,736 A
`5,709,999 A
`5,714,330 A
`5,728,528 A
`5,763,594 A
`5,770,365 A
`5,770,367 A
`5,789,167 A
`5,798,210 A
`5,804,386 A
`5,808,045 A
`5,814,454 A
`5,821,356 A
`5,834,203 A
`5,844,106 A
`5,849,542 A
`5,853,992 A
`5,856,104 A
`5,858,671 A
`5,869,255 A
`5,872,244 A
`5,876,936 A
`5,885,775 A
`5,885,813 A
`5,908,755 A
`5,945,283 A
`5,948,648 A
`5,952,180 A
`5,959,089 A
`5,962,228 A
`6,001,566 A
`6,001,611 A
`6,008,379 A
`6,013,445 A
`6,028,190 A
`6,046,005 A
`6,074,823 A
`6,087,095 A
`6,111,116 A
`6,136,543 A
`6,175,107 Bl
`6,197,557 Bl
`6,207,831 Bl
`6,210,891 Bl
`6,214,987 Bl
`6,218,118 Bl
`6,218,530 Bl
`6,221,592 Bl
`6,232,465 Bl
`6,242,193 Bl
`6,245,507 Bl
`6,248,884 Bl
`6,255,083 Bl
`6,255,475 Bl
`6,274,320 Bl
`
`4/1994 Cheeseman
`5/1994 Takahashi et al.
`7/1994 Ward et al.
`7/1994 Prober et al.
`1/1995 Reilly et al.
`6/1995 Fodor et al.
`7/1995 Hyman
`8/1995 McClelland et al.
`9/1995 Ward et al.
`12/1995 Ward et al.
`5/1996 Hyman
`7/1996 Uhlen et al.
`8/1996 Dower et al.
`8/1996 Goodman et al.
`9/1996 Douglas
`2/1997 Brenner
`2/1997 Hyman
`3/1997 Tabor et al.
`6/1997 Wilding et al.
`8/1997 Mathies et al.
`8/1997 Wong
`1/1998 Shattuck-Eidens et al.
`2/1998 Brenner et al.
`3/1998 Mathies et al.
`6/1998 Hiatt et al.
`6/1998 Lane et al.
`6/1998 Southern et al.
`8/1998 Konrad
`8/1998 Canard et al.
`9/1998 Ju
`9/1998 Hiatt et al.
`9/1998 Ju
`10/1998 Khan et al.
`11/1998 Katzir et al.
`12/1998 Seela et al.
`12/1998 Reeve et al.
`12/1998 Glazer et al.
`1/1999 Chee et al.
`1/1999 Jones
`2/1999 Mathies et al.
`2/1999 Hiatt et al.
`3/1999 Ju
`3/1999 Haff et al.
`3/1999 Davis et al.
`6/1999 Kumar et al.
`8/1999 Kwok et al.
`9/1999 Khan et al.
`9/1999 Ju
`9/1999 Hannessian
`10/1999 Brenner
`12/1999 Canard et al.
`12/1999 Will
`12/1999 Benson et al.
`1/2000 Albrecht et al.
`2/2000 Mathies et al.
`4/2000 Ju et al.
`6/2000 Koster
`7/2000 Rosenthal et al.
`8/2000 Benson et al.
`10/2000 Anazawa et al.
`1/2001 Juvinall
`3/2001 Makarov et al.
`3/2001 Auer et al.
`4/2001 Nyren et al.
`4/2001 Hiatt et al.
`4/2001 Sampson et al.
`4/2001 Rothschild et al.
`4/2001 Schwartz et al.
`5/2001 Hiatt et al.
`6/2001 Anazawa et al.
`6/2001 Bogdanov
`6/2001 Lam et al.
`7/2001 Williams
`7/2001 Kwiatkowski
`8/2001 Rothberg et al.
`
`6,277,607 Bl
`6,287,821 Bl
`6,294,324 Bl
`6,309,829 Bl
`6,309,836 Bl
`6,312,893 Bl
`6,316,230 Bl
`6,335,155 Bl
`6,361,940 Bl
`6,380,378 Bl
`6,432,360 Bl
`6,495,680 Bl
`6,524,829 Bl
`6,555,349 Bl
`6,613,508 Bl
`6,613,513 Bl
`6,627,436 B2
`6,627,748 Bl
`6,632,655 Bl
`6,639,088 B2
`6,664,079 B2
`6,664,399 Bl
`6,713,255 Bl
`6,780,591 B2
`6,787,308 B2
`6,818,395 Bl
`6,833,246 B2
`6,858,393 Bl
`6,864,052 Bl
`6,911,345 B2
`6,934,636 Bl
`6,982,146 Bl
`7,037,687 B2
`7,056,661 B2
`7,056,666 B2
`7,057,026 B2
`7,057,031 B2
`7,074,597 B2
`7,078,499 B2
`7,105,300 B2
`7,270,951 Bl
`7,279,563 B2
`7,329,496 B2
`7,345,159 B2
`7,393,533 Bl
`7,414,116 B2
`7,427,673 B2
`7,459,275 B2
`7,541,444 B2
`7,566,537 B2
`7,622,279 B2
`7,635,578 B2
`7,713,698 B2
`7,771,973 B2
`7,785,790 Bl
`7,790,869 B2
`7,883,869 B2
`7,982,029 B2
`8,088,575 B2
`8,158,346 B2
`8,298,792 B2
`8,399,188 B2
`8,796,432 B2
`8,889,348 B2
`9,115,163 B2
`9,133,511 B2
`9,159,610 B2
`9,175,342 B2
`9,255,292 B2
`9,297,042 B2
`9,708,358 B2
`9,718,852 B2
`9,719,139 B2
`9,725,480 B2
`9,868,985 B2
`2002/0012966 Al
`2002/0168642 Al
`2003/0008285 Al
`2003/0022225 Al
`
`8/2001 Tyagi et al.
`9/2001 Shi et al.
`9/2001 Bensimon et al.
`10/2001 Livak et al.
`10/2001 Kwiatkowski
`11/2001 Van Ness et al.
`11/2001 Egholm et al.
`1/2002 Wells et al.
`3/2002 Van Ness et al.
`4/2002 Kitamura et al.
`8/2002 Church
`12/2002 Gong
`2/2003 Seeger
`4/2003 O'Donnell
`9/2003 Ness et al.
`9/2003 Paree et al.
`9/2003 Sorge et al.
`9/2003 Ju et al.
`10/2003 Mehta et al.
`10/2003 Kwiatkowski
`12/2003 Ju et al.
`12/2003 Sabesan
`3/2004 Makino et al.
`8/2004 Williams et al.
`9/2004 Balasubramanian et al.
`11/2004 Quake et al.
`12/2004 Balasubramanian
`2/2005 Anderson et al.
`3/2005 Drmanac et al.
`6/2005 Quake et al.
`8/2005 Skierczynski et al.
`1/2006 Schneider et al.
`5/2006 Williams et al.
`6/2006 Korlach et al.
`6/2006 Dower et al.
`6/2006 Barnes et al.
`6/2006 Olejnik et al.
`7/2006 Ju
`7/2006 Odedra et al.
`9/2006 Paree et al.
`9/2007 Stemple et al.
`10/2007 Kwiatkowski
`2/2008 Dower et al.
`3/2008 Ju et al.
`7/2008 Crotty et al.
`8/2008 Milton et al.
`9/2008 Balasubramanian et al.
`12/2008 Dower et al.
`6/2009 Milton et al.
`7/2009 Balasubramanian et al.
`11/2009 Ju
`12/2009 Ju et al.
`5/2010 Ju et al.
`8/2010 Milton et al.
`8/2010 Church et al.
`9/2010 Ju et al.
`2/2011 Ju et al.
`7/2011 Ju et al.
`1/2012 Ju et al.
`4/2012 Balasubramanian et al.
`10/2012 Ju et al.
`3/2013 Zhao et al.
`8/2014 Ju et al.
`11/2014 Ju
`8/2015 Ju et al.
`9/2015 Ju et al.
`10/2015 Zhang et al.
`11/2015 Ju et al.
`2/2016 Ju et al.
`3/2016 Ju et al.
`7/2017 Ju et al.
`8/2017 Ju et al.
`8/2017 Ju et al.
`8/2017 Ju et al.
`1/2018 Ju et al.
`1/2002 Shi et al.
`11/2002 Drukier
`1/2003 Fischer
`1/2003 Monforte et al.
`
`Page 2
`
`
`
`US 10,457,984 B2
`Page 3
`
`(56)
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`
`2003/0027140 Al
`2003/0044871 Al
`2003/0054360 Al
`2003/0099972 Al
`2003/0166282 Al
`2003/0180769 Al
`2003/0186256 Al
`2003/0190680 Al
`2003/0198982 Al
`2004/0014096 Al
`2004/0096825 Al
`2005/0032081 Al
`2005/0170367 Al
`2005/0239134 Al
`2006/0003352 Al
`2006/0057565 Al
`2006/0105461 Al
`2006/0160081 Al
`2006/0160113 Al
`2006/0240439 Al
`2006/0252038 Al
`2007/0166705 Al
`2009/0088332 Al
`2009/0240030 Al
`2010/0159531 Al
`2010/0323350 Al
`2011/0014611 Al
`2011/0124054 Al
`2012/0052489 Al
`2012/0142006 Al
`2013/0264207 Al
`2014/0315191 Al
`2015/0037788 Al
`2015/0080232 Al
`2015/0111759 Al
`2015/0119259 Al
`2015/0197800 Al
`2015/0368710 Al
`2016/0024570 Al
`2016/0024574 Al
`2016/0041179 Al
`2016/0090621 Al
`2016/0264612 Al
`2017 /0088574 Al
`2017/0088575 Al
`2017 /0088891 Al
`2017 /0313737 Al
`2018/0201642 Al
`
`2/2003 Ju et al.
`3/2003 Cutsforth et al.
`3/2003 Gold et al.
`5/2003 Olejnik et al.
`9/2003 Brown et al.
`9/2003 Metzker
`10/2003 Fischer
`10/2003 Rothschild et al.
`10/2003 Seela et al.
`1/2004 Anderson et al.
`5/2004 Chenna et al.
`2/2005 Ju et al.
`8/2005 Quake et al.
`10/2005 Gorenstein et al.
`1/2006 Lipkin et al.
`3/2006 Ju et al.
`5/2006 Tom-Moy et al.
`7/2006 Milton et al.
`7/2006 Korlach et al.
`10/2006 Smith et al.
`11/2006 Ju
`7/2007 Milton et al.
`4/2009 Ju et al.
`9/2009 Ju et al.
`6/2010 Gordon et al.
`12/2010 Gordon et al.
`1/2011 Ju et al.
`5/2011 Olejnik et al.
`3/2012 Gordon et al.
`6/2012 Ju et al.
`10/2013 Ju et al.
`10/2014 Ju et al.
`2/2015 Ju
`3/2015 Ju et al.
`4/2015 Ju et al.
`4/2015 Ju et al.
`7/2015 Ju et al.
`12/2015 Fuller et al.
`1/2016 Ju et al.
`1/2016 Ju et al.
`2/2016 Ju et al.
`3/2016 Ju et al.
`9/2016 Ju et al.
`3/2017 Ju et al.
`3/2017 Ju et al.
`3/2017 Ju et al.
`11/2017 Ju et al.
`7/2018 Ju et al.
`
`FOREIGN PATENT DOCUMENTS
`
`DE
`DE
`DE
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`EP
`GB
`GB
`GB
`GB
`GB
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`
`4141178
`20122767
`112007002932.3
`0251786 Bl
`0995804
`1182267
`1291354
`0808320
`1337541 Bl
`1218391
`0992511
`2209911 Bl
`2000 0013276
`2001 0029012
`2446083
`2446084
`2457402
`WO 1989/09282
`WO 89/10977
`WO 1989/11548
`WO 1990/13666
`WO 91/06678
`WO 1991/06678
`WO1992/10587
`
`6/1993
`8/2007
`8/2015
`11/1994
`4/2000
`2/2002
`3/2003
`4/2003
`3/2007
`4/2007
`3/2009
`10/2013
`6/2000
`12/2001
`3/2011
`3/2011
`9/2011
`10/1989
`11/1989
`11/1989
`11/1990
`5/1991
`5/1991
`6/1992
`
`WO
`WO 1993/05183
`WO
`WO 93/12340
`WO
`WO 1993/21340
`WO
`WO 1994/14972
`WO
`WO 1996/07669
`WO
`WO 96/23807
`WO
`WO 1996/23807
`WO
`WO 96/27025
`WO
`WO 1996/27025
`WO
`WO 1997/08183
`WO
`WO 1997/27317
`WO
`WO 1997/35033
`WO
`WO 1998/30720
`WO
`WO 98/33939
`WO
`WO 1998/33939
`WO
`WO 1998/44151
`WO
`WO 98/53300
`WO
`WO 1999/05315
`WO
`WO 1999/49082
`WO
`WO 1999/57321
`WO
`WO 2000/02895
`WO
`WO 2000/06770
`WO
`WO 2000/09753
`WO
`WO 2000/15844
`WO
`WO 2000/18956
`WO
`WO 2000/21974
`WO
`WO 2000/50172
`WO
`WO 2000/50642
`WO
`WO 00/53812
`WO
`WO 2000/53805
`WO
`WO 2000/53812
`WO
`WO 2000/70073
`WO
`WO 2001/16375
`WO
`WO 2001/23610
`WO
`WO 2001/25247
`WO
`WO 2001/27625
`WO
`WO 2001/32930
`WO
`WO 2001/57248
`WO
`WO 2001/57249
`WO
`WO 01/92284
`WO
`WO 2001/92284
`WO
`WO 2002/02813
`WO
`WO 02/21098
`WO
`WO 2002/22883
`WO
`WO 02/29003
`WO
`WO 2002/29003
`WO
`WO 2002/72892
`WO WO 2002/079519
`WO
`WO 2002/88381
`WO
`WO 2002/88382
`WO
`WO 2003/02767
`WO
`WO 2003/20968
`WO
`WO 2003/48178
`WO
`WO 2003/48387
`WO
`WO 2003/85135
`WO
`WO 04/18493
`WO
`WO 04/18497
`WO
`WO 2004/18493
`WO WO 2004/018493
`WO
`WO 2004/18497
`WO WO 2004/018497
`WO WO 2004/055160
`WO WO 2005/084367
`WO
`WO 2006/73436
`WO WO 2007 /002204
`WO
`WO 2007/62105
`WO WO 2008/069973
`WO WO 2012/083249
`WO WO 2012/162429
`WO WO 2013/154999
`WO WO 2013/191793
`WO WO 2014/144883
`WO WO 2014/144898
`WO WO 2015/123430
`
`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
`
`
`
`US 10,457,984 B2
`Page 4
`
`(56)
`
`References Cited
`
`FOREIGN PATENT DOCUMENTS
`
`WO
`WO
`
`WO 2015/148402
`WO 2015/179284
`
`10/2015
`11/2015
`
`OTHER PUBLICATIONS
`
`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(cid:173)
`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(cid:173)
`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. ยง1.132 (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 Yorkv. 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 IPR2012-00006).
`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(cid:173)
`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).
`Rarnzaeva 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).
`Rarnzaeva et al., "88. ?-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
`?-Substituted 7-Deaza- and 8-Aza-7-Deazapurine Nucleosides,"
`Nucleosides & Nucleotides, 16(7-9), pp. 963-966, 1997 (Exhibit
`1044, filed Sep. 27, 2013 in connection with IPR2012-00006).
`Burgess et al., "Syntheses ofNucleosides Designed for Combinato(cid:173)
`rial DNA Sequencing," Chemistry-A European Journal, vol. 5,
`No. 3, pp. 951-960, 1999 (Exhibit 1045, filed Sep. 27, 2013 in
`connection with IPR2012-00006).
`Jan. 28, 2013 Declaration of Dr. Bruce P. Branchaud in Support of
`Petition for Inter Partes Review of U.S. Pat. No. 7,057,026 (Exhibit
`1049, filed Sep. 27, 2013 in connection with IPR2012-00006).
`Lee et al., "DNA sequencing with dye-labeled terminators and T7
`DNA polymerase: effect of dyes and dNTPs on incorporation of
`dye-terminators and probability analysis of termination fragments,"
`Nucleic Acids Research, vol. 20, No. 10, pp. 2471-2483, 1992
`(Exhibit 1050, filed Sep. 27, 2013 in connection with IPR2012-
`00006).
`http://www.answers.com/topic/incubate, Accessed Sep. 27, 2013
`(Exhibit 1051, filed Sep. 27, 2013 in connection with IPR2012-
`00006).
`http:// en. wikipedia. org/wiki/Fluorenylmethyloxycarbonyl_
`chloride, Accessed Sep. 27, 2013 (Exhibit 1052, filed Sep. 27, 2013
`in connection with IPR2012-00006).
`Sep. 27, 2013 Declaration of Kevin Burgess (Exhibit 1053, filed
`Sep. 27, 2013 in connection with IPR2012-00006).
`Fuji, et al., "An Improved Method for Methoxymethylation of
`Alcohols under Mild Acidic Conditions," Synthesis-The Journal
`of Synthetic Organic Chemistry, pp. 276-277, Apr. 1975 (Exhibit
`1054, filed Sep. 27, 2013 in connection with IPR2012-00006).
`Dower patent with highlights (Exhibit 2006, filed Apr. 26, 2013 in
`connection with IPR2012-00006).
`U.S. Pat. No. 7,713,698 (filed Aug. 20, 2007, issued May 11, 2010)
`(Exhibit 1001 in IPR2012-00006)(Exhibit 2011, filed Jun. 24, 2013
`in connection with IPR2012-00006).
`U.S. Pat. No. 7,790,869 (filed Jun. 5, 2007, issued Sep. 7, 2010)
`(Exhibit 1001 in IPR2012-00007) (Exhibit 2012, filed Jun. 24, 2013
`in connection with IPR2012-00006).
`Oct. 2, 2012 Declaration of George Weinstock Under 37 CFR 1.132
`(Exhibit 1021 in IPR2013-00011 )(Exhibit 2013, filed Jun. 24, 2013
`in connection with IPR2012-00006).
`Petition for Inter Partes Review of U.S. Pat. No. 8,088,575 (Paper
`4 in IPR2013-00011) (Exhibit 2014, filed Jun. 24, 2013 in connec(cid:173)
`tion with IPR2012-00006).
`Metzker et al. (1994) Termination of DNA synthesis by novel
`3'-modified-deoxyribonucleoside 5'-triphosphates. Nucleic Acids
`Res. 22:4259-4267 (Exhibit 2015, filed Jun. 24, 2013 in connection
`with IPR2012-00006).
`Wu et al. (2007) Termination of DNA synthesis by N6-alkylated, not
`3' -O-alkylated, photocleavable 2' -deoxyadenosine triphosphates. Nucleic
`Acids Res. 35:6339-6349 (Exhibit 2016, filed Jun. 24, 2013 in
`connection with IPR2012-00006).
`Sep. 15, 2012 Declaration of George Weinstock Under 37 CFR
`1.132 (Exhibit 1021 in IPR2012-00007) (Exhibit 2017, filed Jun.
`24, 2013 in connection with IPR2012-00006).
`Sep. 15, 2012 Declaration of George Weinstock Under 37 CFR
`1.132 (Exhibit 1021 in IPR2012-00006) (Exhibit 2018, filed Jun.
`24, 2013 in connection with IPR2012-00006).
`Definition of "DN Amicroarray." http://en/wikipedia.org/wiki/DN A_
`microarray (Exhibit 2019, filed Jun. 24, 2013 in connection with
`IPR2012-00006).
`Brettin et al. (2005) Expression capable library for studies of
`Neisseria gonorrhoeae, version 1.0 BMC Microbiology. 5:50 (Exhibit
`2020, filed Jun. 24, 2013 in connection with IPR2012-00006).
`George M. Weinstock, Handbook of Molecular Microbial Ecology,
`vol. 1----Chapter 18: The Impact of Next-Generation Sequencing
`Technologies on Metagenomics 141-147 Frans J. de Bruijn ed.,
`John Wiley & Sons, Inc. (2011) (Exhibit 2021, filed Jun. 24, 2013
`in connection with IPR2012-00006).
`Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
`7,713,698 (Paper 3 in IPR2012-00006) (Exhibit 2022, filed Jun. 24,
`2013 in connection with IPR2012-00006).
`
`Page 4
`
`
`
`US 10,457,984 B2
`Page 5
`
`(56)
`
`References Cited
`
`OTHER PUBLICATIONS
`
`Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
`7,790,869 (Paper 5 in IPR2012-00007) (Exhibit 2023, filed Jun. 24,
`2013 in connection with IPR2012-00006).
`Maxam and Gilbert (1977) A new method for sequencing DNA,
`Proc. Natl. Acad. Sci. USA. 74:560-564 (Exhibit 2024, filed Jun. 24,
`2013 in connection with IPR2012-00006).
`Sanger et al. ( 1977) DNA sequencing with chain-terminating inhibi(cid:173)
`tors, Proc. Natl. Acad. Sci. USA. 74:5463-5467 (Exhibit 2025, filed
`Jun. 24, 2013 in connection with IPR2012-00006).
`Pennisi (2000) DOE Team Sequences Three Chromosomes, Sci(cid:173)
`ence. 288:417-419 (Exhibit 2026, filed Jun. 24, 2013 in connection
`with IPR2012-00006).
`Welch and Burgess (1999) Synthesis of Fluorescent, Photolabile
`3'-O-Protected nucleoside Triphosphates for the Base Addition
`Sequencing Scheme, nucleosides & Nucleotides. 18: 197-201 (Exhibit
`2027, filed Jun. 24, 2013 in connection with IPR2012-00006).
`Hyman (1998) A New Method of Sequencing DNA, Analytical
`Biochemistry 174:423-436 (Exhibit 2028, filed Jun. 24, 2013 in
`connection with IPR2012-00006).
`Canard and Sarfati (1994) DNA polymerase fluorescent substrates
`with reversible 3'-tags, Gene. 148:1-6 (Exhibit 2030, filed Jun. 24,
`2013 in connection with IPR2012-00006).
`Sarfati et al. ( 1987) Synthesis of Fluorescent or Biotinylated Nucleoside
`Compounds, Tetrahedron Letters. 43:3491-3497 (Exhibit 2032,
`filed Jun. 24, 2013 in connection with IPR2012-00006).
`Jun. 25, 2013 Substitute Declaration of Dr. George. L. Trainor
`[redacted] (Exhibit 2033, filed Aug. 30, 2013 in connection with
`IPR2012-00006).
`Jingyue Ju et. al. (2006) Four-color DNA sequencing by synthesis
`using/cleavable fluorescent nucleotide reversible terminators, Pro(cid:173)
`ceedings of the National Academy of Sciences. 103: 19635-19640
`(Exhibit 2034, 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 2035, filed Jun. 25, 2013 in connection with
`IPR2012-00006).
`Form 7 Review Context and Analysis, Biomedical Engineering and
`Research to Aid Persons with Disabilities Programs Dec. 19-20,
`2000 Panel Review, Fluorescence Imaging Chip System for Mas(cid:173)
`sive Parallel DNA Sequencing. Proposal No. BES-0097793 (Exhibit
`2036, 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
`2037, filed Jun. 25, 2013 in connection with IPR2012-00006).
`Correspondence between George Rupp, Chancellor, Columbia Uni(cid:173)
`versity and Richard T. Schlossberg, President, The David and Lucile
`Packard Foundation (2001) (Exhibit 2038, filed Jun. 25, 2013 in
`connection with IPR2012-00006).
`The David and Lucile Packard Foundation, Packard Fellowships for
`Science and Engineering, http://www.packard.org/what-wefund/
`con serv ati on -and-sci enc e/packard-fellowships-for-science(cid:173)
`andengineering/ (last visited Jun. 25, 2013) (Exhibit 2039, filed Jun.
`25, 2013 in connection with IPR2012-00006).
`"Chemistry for Next-Generation Sequencing." http:/ /www.illumina.
`corn/technology/sequencing_technology.ilrnn (Exhibit 2040, filed
`Jun. 25, 2013 in connection with IPR2012-00006).
`Chiang et al. (2010) Mammalian microRNAs: experimental evalu(cid:173)
`ation of novel and previously annotated genes, Genes & Dev.
`24:992, 993 (Exhibit 2041, 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 chem(cid:173)
`istry, Proc. Natl Acad. Sci. 101(15):5488-5493 (Exhibit 2042, filed
`Jun. 25, 2013 in connection with IPR2012-00006).
`Curriculum vitae of Mr. Raymond S. Sims (Exhibit 2043, filed Jun.
`25, 2013 in connection with IPR2012-00006).
`Prior Testimony of Mr. Raymond S. Sims (Exhibit 2044, filed Jun.
`25, 2013 in connection with IPR2012-00006).
`
`Documents reviewed by Mr. Raymond S. Sims in this Proceeding
`(Exhibit 2045, filed Jun. 25, 2013 in connection with IPR2012-
`00006).
`Gary Schroth Proof of Chiang Paper (Exhibit 2052, filed Jun. 25,
`2013 in connection with IPR2012-00006).
`Information about Dr. Ju's intellectual property sent to Illumina
`(Exhibit 2074, filed Jun. 25, 2013 in connection with IPR2012-
`00006).
`IPR Default Protective Order (Exhibit 2090, filed Jun. 26, 2013 in
`connection with IPR2012-00006).
`Declaration of Raymond S. Sims (Exhibit 2091, filed Jun. 26, 2013
`in connection with IPR2012-00006).
`Rough Transcript of the Sep. 4, 2013 deposition of Dr. George L.
`Trainor (Exhibit 2092, filed Oct. 10, 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 2093, filed Oct. 1, 2013 in connection with
`IPR2012-00006).
`Final transcript of the Sep. 4-6, 2013 deposition of Dr. George L.
`Trainor (Exhibit 2094, filed Oct. 1, 2013 in connection with
`IPR2012-00006).
`Final transcript of the Sep. 3, 2013, deposition of Raymond S. Sims
`(Exhibit 2095, filed Oct. 1, 2013 in connection with IPR2012-
`00006).
`Nov. 12, 2013 Petitioner Motion to Exclude Evidence in connection
`with IPR2012-00006.
`Videotaped Deposition Transcript of Kevin Burgess, Ph.D., Oct. 28,
`2013, signed with errata----(Exhibit 1056, filed Nov. 19, 2013 in
`connection with IPR2012-00006).
`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.
`Welch, M., et al (2005) Corrigenda to Syntheses of Nucleosides
`Designed for Combinatorial DNA Sequencing Chem. Eur.J., 1999,
`951-960. Published in Chem. Eur. J, 2005, 11, 7136-7145 (Exhibit
`2099, filed Nov. 12, 2013 in connection with IPR2012-00006).
`Welch, M (1999) "Base Additions Sequencing Scheme (BASS) and
`Studies Toward New Sequencing Methodologies." PhD. Disserta(cid:173)
`tion, Texas A&M University (Exhibit 2100, filed Nov. 12, 2013 in
`connection with IPR2012-00006).
`Lu and Burgess (2006) "A Diversity Oriented Synthesis of 3'-O(cid:173)
`modified nucleoside triphosphates for DNA 'Sequencing by Syn(cid:173)
`thesis'." Bioorganic & Medicinal Chemistry Letters, 16, 3902-3905
`(Exhibit 2101, filed Nov. 12, 2013 in connection with IPR2012-
`00006).
`Advanced Sequencing Technology Awards 2004. http://www.genome.
`gov/12513162 (accessed Oct. 14, 2013) (Exhibit 2102, filed Nov.
`12, 2013 in connection with IPR2012-00006).
`Welch and Burgess (2006) Erratum to Synthesis of Fluorescent,
`Photolabile 3'-O-Protected Nucleoside Triphosphates for the Base
`Addition Sequencing Scheme, Nucleosides & Nucleotides,18:197-
`201. Published in Nucleosides, Nucleotides and Nucleic Acids,
`25:1, 119 (Exhibit 2103, filed Nov. 12, 2013 in connection with
`IPR2012-00006).
`Nov. 26, 2013 Petitioner Response to Motion for Observations in
`connection with IPR2012-00006.
`Nov. 26, 2013 Patent Owner Opposition to Petitioner's Motion to
`Exclude in connection with IPR2012-00006.
`Nov. 26, 2013 Petitioner Opposition to Motion to Exclude in
`connection with IPR2012-00006.
`Dec. 3, 2013 Petitioner Reply to Patent Owner's Opposition to
`Motion to Exclude in connection with IPR2012-00006.
`Dec. 3, 2013 Patent Owner Reply on Motion to Exclude in con(cid:173)
`nection with IPR2012-00006.
`Columbia's Demonstratives Under 42.70(b) for Dec. 17, 2013 Oral
`Hearing in connection with IPR2012-00006, IPR2012-00007, and
`IPR2013-00011 (Exhibit 21025, filed Dec. 15, 2013 in connection
`with IPR2012-00006).
`
`Page 5
`
`
`
`US 10,457,984 B2
`Page 6
`
`(56)
`
`References Cited
`
`OTHER PUBLICATIONS
`
`Ilumina's Invalidity Demonstratives for Final Hearing Dec. 17,
`2013 in connection with IPR2012-00006, IPR2012-00007, and
`IPR2013-00011 (Exhibit 1057, filed Dec. 16, 2013 in connection
`with IPR2012-00006).
`Feb. 10, 2014 Record of Dec. 17, 2013 Oral Hearing in connection
`with IPR2012-00006, IPR2012-00007, and IPR2013-00011.
`Mar. 6, 2014 Final Written Decision in connection with IPR2012-
`00006.
`Patent Owner Preliminary Response filed by The Trustees of
`Columbia University in the City of New York Mar. 27, 2018, in
`connection with Case No. IPR2018-00291.
`Patent Owner Preliminary Response filed by The Trustees of
`Columbia University in the City of New York Apr. 9, 2018, in
`connection with Case No. IPR2018-00318.
`Patent Owner Preliminary Response filed by The Trustees of
`Columbia University in the City of New York Apr. 9, 2018, in
`connection with Case No. IPR2018-00322.
`Patent Owner Preliminary Response filed by The Trustees of
`Columbia University in the City of New York May 4, 2018, in
`connection with Case No. IPR2018-00385.
`Patent Owner Preliminary Response filed by The Trustees of
`Columbia University in the City of New York Jul. 6, 2018, in
`connection with Case No. IPR2018-00797.
`Excerpts from the Prosecution History of U.S. Pat. No. 9,718,852
`not included in Ex-1009 (Exhibit 2005 filed by The Trustees of
`Columbia University in the City of New York with the Patent Owner
`Preliminary Response, in connection with Case No. IPR2018-
`00291).
`Excerpts from the Prosecution History of U.S. Pat. No. 9,725,480
`not included in Ex-1038 (Exhibit 2006 filed by The Trustees of
`Columbia University in the City of New York with the Patent Owner
`Preliminary Response, in connection with Case Nos. IPR2018-
`00291, IPR2018-00318, and IPR2018-00322).
`IPR2013-00517, Ex. 2011, Declaration of Floyd Romesberg, Ph.D.
`(May 5, 2014) (Exhibit 2007 filed by The Trustees of Columbia
`University in the City of New York with the Patent Owner Prelimi(cid:173)
`nary Response, in connection with Case Nos. IPR2018-00291,
`IPR2018-00318, IPR2018-00322, IPR2018-00385, and IPR2018-
`00797).
`IPR2013-00 517, Paper 3 2, Illumina' s Patent Owner Response (May
`5, 2014) (Exhibit 2008 filed by The Trustees of Columbia Univer(cid:173)
`sity in the City of New York with the Patent Owner Preliminary
`Response, in connection with Case Nos. IPR2018- 00291, IPR2018-
`00318, IPR2018-00322, IPR2018-00385, and IPR2018-00797).
`Excerpts from the Ex Parte Reexamination History of U.S. Pat. No.
`5,808,045 (Exhibit 2009 filed by The Trustees of Columbia Uni(cid:173)
`versity in the City of New York with the Patent Owner Preliminary
`Response, in connection with Case Nos. IPR2018-00291, IPR2018-
`00318, IPR2018-00322, IPR2018-00385, and IPR2018-00797).
`Assignment data in connection with U.S. Pat. No. 5,808,045 (Exhibit
`2010 filed by The