`US009708358B2
`
`c12) United States Patent
`Ju et al.
`
`(IO) Patent No.:
`(45) Date of Patent:
`
`US 9,708,358 B2
`*Jul. 18, 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.: 15/380,284
`
`(22)
`
`Filed:
`
`Dec. 15, 2016
`
`(65)
`
`Prior Publication Data
`
`US 2017/0088574 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 19110
`C12Q 1168
`U.S. Cl.
`CPC .......... . C07H 19110 (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
`
`U.S. PATENT DOCUMENTS
`
`4,711,955 A
`4,772,691 A
`4,804,748 A
`4,824,775 A
`4,863,849 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
`5,302,509 A
`5,308,990 A
`5,328,824 A
`5,332,666 A
`5,383,858 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
`
`12/1987 Ward et al.
`9/1988 Herman
`2/1989 Seela
`4/1989 Dattagupta et al.
`9/1989 Melamede
`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.
`4/1994 Cheeseman
`5/1994 Takahashi et al.
`7/1994 Ward et al.
`7/1994 Prober et al.
`1/1995 Reilly 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
`(Continued)
`
`FOREIGN PATENT DOCUMENTS
`
`CA
`CA
`
`4/2002
`2425112
`11/2002
`2408143
`(Continued)
`
`OTHER PUBLICATIONS
`
`Office Action issued Sep. 21, 2007 in connection with U.S. Appl.
`No. 10/380,256.
`Office Action issued Oct. 25, 2002 in connection with U.S. Appl.
`No. 09/972,364.
`Office Action issued Mar. 14, 2003 in connection with U.S. Appl.
`No. 09/972,364.
`Office Action issued Dec. 20, 2006 in connection with U.S. Appl.
`No. 10/702,203.
`Amendment filed May 21, 2007 in response to Office Action issued
`Dec. 20, 2006 in connection with U.S. Appl. No. 10/702,203.
`Notice of Allowance issued Sep. 6, 2007 in connection with U.S.
`Appl. No. 10/702,203.
`Office Action issued Jun. 24, 2008 in connection with U.S. Appl.
`No. 11/894,690.
`
`(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. 1018
`IPR Petition - USP 10,435,742
`
`
`
`US 9,708,358 B2
`Page 2
`
`(56)
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`
`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
`5,869,255 A
`5,872,244 A
`5,876,936 A
`5,885,775 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
`6,136,543 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
`6,255,083 Bl
`6,255,475 Bl
`6,274,320 Bl
`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
`6,495,680 Bl
`6,524,829 Bl
`6,555,349 Bl
`6,613,508 Bl
`6,613,513 Bl
`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
`
`6/1997 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.
`2/1999 Mathies et al.
`2/1999 Hiatt et al.
`3/1999 Ju
`3/1999 Haff 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.
`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
`7/2001 Williams
`7/2001 Kwiatkowski
`8/2001 Rothberg et 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.
`12/2002 Gong
`2/2003 Seeger
`4/2003 O'Donnell
`9/2003 Ness et al.
`9/2003 Paree 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.
`
`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
`7,414,116 B2
`7,427,673 B2
`7,459,275 B2
`7,566,537 B2
`7,622,279 B2
`7,635,578 B2
`7,713,698 B2
`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
`2002/0012966 Al
`2002/0168642 Al
`2003/0008285 Al
`2003/0022225 Al
`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
`2011/0014611 Al
`2011/0124054 Al
`2012/0052489 Al
`2012/0142006 Al
`2013/0264207 Al
`2014/0315191 Al
`2015/0037788 Al
`2015/0080232 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.
`8/2008 Milton et al.
`9/2008 Balasubramanian et al.
`12/2008 Dower et al.
`7/2009 Balasubramanian et al.
`11/2009 Ju
`12/2009 Ju et al.
`5/2010 Ju 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.
`1/2002 Shi et al.
`11/2002 Drukier
`1/2003 Fischer
`1/2003 Monforte et 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.
`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.
`
`Page 2
`
`
`
`(56)
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`
`2015/0111759 Al
`2015/0119259 Al
`2015/0197800 Al
`2015/0368710 Al
`2016/0024570 Al
`2016/0024574 Al
`2016/0041179 Al
`2016/0090621 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.
`
`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
`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
`
`4141178
`20122767
`112007002932.3
`0251786 Bl
`0995804
`1182267
`1291354
`0808320
`1337541 Bl
`1218391
`0992511
`2209911 Bl
`2000 0013276
`2001 0029012
`2446083
`2446084
`2457402
`WO 89/09282
`WO 89/11548
`WO 90/13666
`WO 91/06678
`WO92/10587
`WO 93/05183
`WO 93/12340
`WO 93/21340
`WO 94/14972
`WO 96/07669
`WO 96/23807
`WO 96/27025
`WO 97/08183
`WO 97/27317
`WO 97/35033
`WO 98/30720
`WO 98/33939
`WO 98/44151
`WO 99/05315
`WO 99/49082
`WO 99/57321
`WO 00/02895
`WO 00/06770
`WO 00/09753
`WO 00/15844
`WO 00/18956
`WO 00/21974
`WO 00/50172
`WO 00/50642
`WO 00/53805
`WO 00/53812
`WO 00/70073
`WO 01/16375
`WO 01/23610
`WO 01/25247
`WO 01/27625
`WO 01/32930
`WO 01/57248
`WO 01/57249
`WO 01/92284
`WO 02/02813
`WO 02/21098
`WO 02/022883
`WO 02/029003
`WO 02/72892
`WO 02/079519
`WO 02/88381
`
`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
`11/1990
`5/1991
`6/1992
`3/1993
`10/1993
`10/1993
`7 /1994
`3/1996
`8/1996
`9/1996
`3/1997
`7 /1997
`9/1997
`7 /1998
`8/1998
`10/1998
`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
`11/2000
`3/2001
`4/2001
`4/2001
`4/2001
`5/2001
`8/2001
`8/2001
`12/2001
`1/2002
`3/2002
`3/2002
`4/2002
`9/2002
`10/2002
`11/2002
`
`US 9,708,358 B2
`Page 3
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`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`
`WO 02/88382
`WO 03/002767
`WO 03/020968
`WO 03/048178
`WO 03/048387
`WO 03/085135
`WO 2004/018493
`WO 2004/018497
`WO 2004/055160
`WO 2005/084367
`WO 2006/073436
`WO 2007 /002204
`WO 2007/062105
`WO 2008/069973
`WO 2012/083249
`WO 2012/162429
`WO 2013/154999
`WO 2013/191793
`WO 2014/144883
`WO 2014/144898
`WO 2015/123430
`WO 2015/148402
`WO 2015/179284
`
`11/2002
`1/2003
`3/2003
`6/2003
`6/2003
`10/2003
`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
`10/2015
`11/2015
`
`OTHER PUBLICATIONS
`
`Amendment filed Oct. 16, 2008 in response to Office Action issued
`Jun. 24, 2008 in connection with U.S. Appl. No. 11/894,690.
`Supplemental Amendment filed Jan. 16, 2009 in connection with
`U.S. Appl. No. 11/894,690.
`Notice of Allowance issued Feb. 24, 2009 in connection with U.S.
`Appl. No. 11/894,690.
`Office Action issued Jun. 5, 2009 in connection with U.S. Appl. No.
`11/894,690.
`Nov. 5, 2009 Amendment in response to Office Action issued Jun.
`5, 2009 in connection with U.S. Appl. No. 11/894,690.
`Office Action issued Sep. 3, 2008 in connection with U.S. Appl. No.
`11/894,808.
`Dec. 19, 2008 Amendment in response to Office Action issued Sep.
`3, 2008 in connection with U.S. Appl. No. 11/894,808.
`Amendment after Notice of Allowance filed Jun. 23, 2009 in
`connection with U.S. Appl. No. 11/894,808.
`Office Action issued Jul. 10, 2009 in connection with U.S. Appl. No.
`11/810,509.
`Jan. 11, 2010 Amendment in response to Office Action issued Jul.
`10, 2009 in connection with U.S. Appl. No. 11/810,509.
`Jan. 26, 2010 Supplemental Amendment in connection with U.S.
`Appl. No. 11/810,509.
`Notice of Allowance and Fee(s) Due issued Apr. 2, 2010 in
`connection with U.S. Appl. No. 11/810,509.
`Office Action issued Oct. 28, 2010 in connection with U.S. Appl.
`No. 12/804,284.
`Office Action issued Feb. 4, 2011 in connection with U.S. Appl. No.
`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.
`Office Action issued May 8, 2012 in connection with U.S. Appl. No.
`13/339,089.
`Notice of Abandonment issued Sep. 13, 2013 in connection with
`U.S. Appl. No. 13/672,437.
`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.
`Official Action issued Mar. 17, 2009 in connection with Canadian
`Patent Application No. CA 2425112 OA.
`Sep. 17, 2009 Response to Official Action issued Mar. 17, 2009 in
`connection with Canadian Patent Application No. CA 2425112 OA.
`Official Action issued Mar. 16, 2010 in connection with Canadian
`Patent Application No. CA 2425112 OA.
`
`Page 3
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`
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`US 9,708,358 B2
`Page 4
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`(56)
`
`References Cited
`
`OTHER PUBLICATIONS
`
`Sep. 16, 2010 Response to Official Action issued Mar. 16, 2010 in
`connection with Canadian Patent Application No. CA 2425112 OA.
`Partial European Search Report issued Apr. 26, 2007 in , connection
`with European Patent Application No. 07004522.4.
`Extended European Search Report issued Jul. 18, 2007 in connec(cid:173)
`tion with European Patent Application No. 07004522.4.
`Official Action issued Mar. 14, 2008 in connection with European
`Patent Application No. 07004522.4.
`Sep. 24, 2008 Response to Official Action issued Mar. 14, 2008 in
`connection with European Patent Application No. 07004522.4.
`Communication Pursuant to Article 94(3) EPC issued Apr. 30, 2009
`in connection with counterpart European Patent Application No.
`07004522.4.
`Nov. 10, 2009 Response to Communication Pursuant to Article
`94(3) EPC issued Apr. 30, 2009 in connection with counterpart
`European Patent Application No. 07004522.4.
`Communication Pursuant to Article 94(3) EPC issued Jun. 10, 2012
`in connection with counterpart European Patent Application No.
`07004522.4.
`Oct. 20, 2010 Response to Communication Pursuant to Article 94(3)
`EPC issued Jun. 10, 2012 in connection with counterpart European
`Patent Application No. 07004522.4.
`Communication Pursuant to Article 94(3) EPC issued Apr. 1, 2011
`in connection with counterpart European Patent Application No.
`07004522.4.
`Oct. 11, 2011 Response to Communication Pursuant to Article 94(3)
`EPC issued Apr. 1, 2011 in connection with counterpart European
`Patent Application No. 07004522.4.
`Communication Pursuant to Article 94(3) EPC issued May 24, 2012
`in connection with counterpart European Patent Application No.
`07004522.4.
`Nov. 30, 2012 Response to Communication Pursuant to Article
`94(3) EPC issued May 24, 2012 in connection with counterpart
`European Patent Application No. 07004522.4.
`Communication Pursuant to Article 94(3) EPC issued Jun. 12, 2013
`in connection with counterpart European Patent Application No.
`07004522.4.
`Dec. 31, 2013 Response to Communication Pursuant to Article
`94(3) EPC issued Jun. 12, 2013 in connection with counterpart
`European Patent Application No. 07004522.4.
`Jul. 9, 2014 Communication accompanying Summons to Attend
`Oral Proceedings in connection with counterpart European Patent
`Application No. 07004522.4.
`Jan. 2, 2015 Written Submission in connection with counterpart
`European Patent Application No. 07004522.4.
`Jan. 15, 2015 Communication in connection with counterpart Euro(cid:173)
`pean Patent Application No. 07004522.4.
`Jan. 29, 2015 Written Submission in connection with counterpart
`European Patent Application No. 07004522.4.
`Feb. 5, 2015 Communication in connection with counterpart Euro(cid:173)
`pean Patent Application No. 07004522.4.
`Mar. 23, 2015 Decision of Refusal in connection with counterpart
`European Patent Application No. 07004522.4.
`Jun. 1, 2015 Notice of Appeal in connection with counterpart
`European Patent Application No. 07004522.4.
`Aug. 3, 2015 Statement of Grounds of Appeal in connection with
`counterpart European Patent Application No. 07004522.4.
`International Search Report issued May 13, 2002 in connection with
`PCT/US0l/31243.
`European Search Report issued Feb. 27, 2004 in connection with
`European Patent Application No. 01977533.7
`Supplementary European Search Report issued Feb. 16, 2004 in
`connection with European Patent Application No. 01977533.
`Communication Pursuant to Article 94(3) EPC issued Mar. 30, 2005
`in connection with European Patent Application No. 01977533.7.
`Oct. 10, 2005 Response to Communication Pursuant to Article 94(3)
`EPC issued Mar. 30, 2005 in connection with European Patent
`Application No. 01977533.7.
`
`Communication Pursuant to Article 94(3) EPC issued Nov. 16, 2005
`in connection with European Patent Application No. 01977533.7.
`Mar. 22, 2006 Response to Communication Pursuant to Article
`94(3) EPC issued Nov. 16, 2005 in connection with European Patent
`Application No. 01977533.7.
`International Preliminary Examination Report issued on Jun. 13,
`2003 in connection with PCT/US0l/31243.
`Official Action issued Mar. 31, 2006 in connection with European
`Patent Application No. 01968905.8.
`Official Action issued May 21, 2007 in connection with European
`Patent Application No. 01968905.8.
`International Preliminary Examination Report issued on Feb. 25,
`2003 in connection with PCT/US0l/28967.
`Supplementary European Search Report issued Jun. 7, 2005 in
`connection with European Patent Application No. 01968905.
`International Search Report issued Jan. 23, 2002 in connection with
`PCT/US0l/28967.
`European Search Report issued May 18, 2016 in connection with
`European Patent Application No. EP15195765.l, Ju et al.
`Notification of Transmittal of International Search Report and the
`Written Opinion of the International Searching Authority, or the
`Declaration issued Sep. 9, 2008 in connection with International
`Application No. PCT/US06/24157.
`Notification of Transmittal of International Search Report and
`Written Opinion, issued Feb. 6, 2008 in connection with Interna(cid:173)
`tional Application No. PCT/06/042739.
`Notification Concerning Transmittal of International Preliminary
`Report on Patentability issued May 15, 2008 in connection with
`International Application No. PCT/US2006/042698.
`Notification of Transmittal of the International Search Report and
`Written Opinion, issued Aug. 12, 2008 in connection with Interna(cid:173)
`tional Application No. PCT/US07/24646.
`Office Action issued Nov. 14, 2007 in connection with U.S. Appl.
`No. 10/735,081.
`Office Action issued Jul. 8, 2008 in connection with U.S. Appl. No.
`10/591,520.
`Restriction Requirement issued Oct. 1, 2007 in connection with
`U.S. Appl. No. 10/521,206.
`U.S. Application for a Method for Direct Nucleic Acid Sequencing;
`U.S. Appl. No. 09/266,187, filed Mar. 10, 1999.
`U.S. Appl. No. 90/008,149, filed Aug. 4, 2006, Girten.
`U.S. Appl. No. 90/008,152, filed Aug. 3, 2006, Girten.
`International Search Report issued Sep. 26, 2003 in connection with
`PCT/US03/21818.
`International Preliminary Examination Report issued on Mar. 18,
`2005 in connection with PCT/US03/21818.
`Notification of Transmittal of International Search Report and
`Written Opinion, issued May 22, 2008 in connection with Interna(cid:173)
`tional Application No. PCT/US06/45180.
`International Preliminary Report on Patentability issued on Sep. 5,
`2006 in connection with PCT/US05/06960.
`International Search Report issued Oct. 29, 2007 in connection with
`PCT International Application No. PCT/US07/13559.
`Supplementary European Search Report issued Feb. 9, 2007 m
`connection with European Patent Application No. 03764568.6.
`Supplementary European Search Report issued Sep. 9, 2008 in
`connection with PCT International Application No. PCT/US05/
`06960.
`International Search Report issued Sep. 18, 2002 in connection with
`PCT/US02/09752.
`International Preliminary Examination Report issued on Mar. 17,
`2003 in connection with PCT/US02/09752.
`Supplementary European Search Report issued May 25, 2005 in
`connection with European Patent Application No. 02728606.1.
`Written Opinion of the International Searching Authority issued
`Oct. 27, 2005 in connection with PCT/US05/06960.
`Written Opinion of the International Searching Authority issued
`Dec. 15, 2006 in connection with PCT/US05/13883.
`International Search Report issued Jun. 8, 2004 in connection with
`PCT/US03/39354.
`International Search Report issued Nov. 4, 2005 in connection with
`PCT/US05/06960.
`
`Page 4
`
`
`
`US 9,708,358 B2
`Page 5
`
`(56)
`
`References Cited
`
`OTHER PUBLICATIONS
`
`International Search Report issued Dec. 15, 2006 in connection with
`PCT/US05/13883.
`Arbo et al. ( 1993) "Solid Phase Synthesis of Protected Peptides
`Using New Cobalt (III) Amine Linkers," Int. J. Peptide Protein Res.
`42: 138-154.
`Axelrod, V.D. et al. (1978) "Specific termination of RNA poly(cid:173)
`merase synthesis as a method of RNA and DNA sequencing,"
`Nucleic Acids Res. 5(10):3549-3563.
`Badman, E. R. et al. (2000) "A Parallel Miniature Cylindrical Ion
`Trap Array," Anal. Chem (2000) 72:3291-3297.
`Badman, E. R. et al. (2000) "Cylindrical Ion Trap Array with Mass
`Selection by Variation in Trap Dimensions," Anal. Chem. 72: 5079-
`5086.
`Bai et al. (2003) "Photocleavage of a 2-nitrobenzyl Linker Bridging
`a Fluorophore to the 5' end of DNA," PNAS, vol. 100, No. 2, pp.
`409-413.
`Bai, X., Kim, S., Li, Z., Turro, N.J. and Ju, J. (2004) "Design and
`Synthesis of a Photocleavable Biotinylated Nucleotide for DNA
`Analysis by Mass Spectrometry," Nucleic Acids Research,
`32(2):534-541.
`(1993)
`and Glazer, A.N.
`Benson, S.C., Mathies, R.A.,
`"Heterodimeric DNA-binding dyes designed for energy transfer:
`stability and applications of the DNA complexes," Nucleic Acids
`Res. 21 :5720-5726.
`Benson, S.C., Singh, P., and Glazer, A.N. (1993) "Heterodimeric
`DNA-binding dyes designed for energy transfer: synthesis and
`spectroscopic properties," Nucleic Acids Res. 21:5727-5735.
`Bergmann et al. (1995) "Ally! As Internucleotide Protecting Group
`in DNA Synthesis to be Cleaved Off by Ammonia," Tetrahedron,
`51:6971-6976.
`Bergseid M., Baytan A.R., Wiley J.P., Ankener W.M., Stolowitz,
`Hughs K.A., and Chestnut J.D. (2000) "Small-molecule base
`the purification of proteins,"
`chemical affinity system for
`Bio Techniques 29: 1126-1133.
`Bi, L., Kim D.H., and Ju, J. (2006) "Design and Synthesis of a
`Chemically Cleavable Fluorescent Nucleotide, 3'-O-Allyl-dGTP(cid:173)
`allyl-Bodipy-FL-510, as a Reversible Terminator for DNA Sequenc(cid:173)
`ing by Synthesis" J. Arn. Chem. Soc., 128:2542-2543.
`Braslavsky I.; Hebert, B.; Kartalov, E.; et al. (2003) "Sequence
`information can be obtained from single DNA molecules." Proc.
`Natl. Acad. Sci. 100(7):3960-3964.
`Brunckova, J. et al. (1994) "Intramolecular Hydrogen AtomAbstrc(cid:173)
`tion in Carbohydrates and Nucleosides: Inversion of an a-to 13-Man(cid:173)
`nopyranoside and Generation of Thymidine C-4' Radicals." Tetra(cid:173)
`hedron Letters, vol. 35, pp. 6619-6622.
`Buck, G.A. et al. (1999) "Design Strategies and Performance of
`Custom DNA Sequencing Primers," Bio Techniques 27(3):528-536.
`Burgess, K. et al. ( 1997) "Photolytic Mass Laddering for Fast
`Characterization of Oligomers on Single Resin Beads,"J. Org.
`Chem. 62:5662-5663.
`"The Complex Formation of
`(1999)
`Buschmann et al.
`alpha,omega-Dicarboxylic Acids and alpha,omega-Diols with
`Cucurbituril and alpha-Cyclodextrin," Acta Chim. Slov. 46(3):405-
`411.
`Buschmann et al. (2003) "Spectroscopic Study and Evaluation of
`Red-Absorbing Fluorescent Dyes," Bioconjugate Chem., 14:195-
`204.
`Canard B. et al. (1994) "DNA polymerase fluorescent substrates
`with reversible 3'-tags," Gene, 148: 1-6.
`Canard, B. et al. (1995) "Catalytic editing properties of DNA
`polymerases," Proc. Natl. Acad. Sci. USA 92:10859-10863.
`Caetano-Anolies (1994) "DNA Amplification Fingerprinting Using
`Arbitrary Mini-hairpin Oligonucleotide Primers." Nature Biotech(cid:173)
`nology, 12:619-623.
`Caruthers, M.H. ( 1985) "Gene synthesis machines: DNA chemistry
`and its uses," Science 230:281-285.
`Chee, M. et al. (1996) "Accessing genetic information with high
`density DNA arrays," Science 274:610-614.
`
`Chen X. and Kwok, P.-Y. (1997) "Template-directed dye-terminator
`incorporation (TDI) assay: a homogeneous DNA diagnostic method
`based on fluorescence resonance energy transfer," Nucleic Acids
`Res. 25:347-353.
`Chiu, N.H., Tang, K., Yip, P., Braun, A., Koster, H., and Cantor, C.R.
`(2000) "Mass spectrometry of single-stranded restriction fragments
`captured by an undigested complementary sequence," Nucleic
`Acids Res. 28:E31.
`Collins, F. S.; Morgan, M.; Patrinos, A. (2003) "The Human
`Genome Project: Lessons from Large-Scale Biology." Science, 300,
`pp. 286-290.
`Crespo-Hernandez et al., (2000) "Part 1. Photochemical and
`Photophysical Studies of Guanine Derivatives: Intermediates Con(cid:173)
`tributing to its Photodestruction Mechanism in Aqueous Solution
`and the Participation of the Electron Adduct," Photochemistry and
`Photobiology, 71(5):534-543.
`Drmanac, S.; Kita, D.; Labat, I.; et al. (1998) "Accurate sequencing
`by hybridization for DNA diagnostics and individual genomics."
`Nat. Biotech., 16:54-58.
`Edwards, J. et al. (2001) "DNA sequencing using biotinylated
`dideoxynucleotides and mass spectrometry," Nucleic Acids Res.
`29(21): 1041-1046.
`Elango, N. et al. (1983) "Amino Acid Sequence of Human Respi(cid:173)
`ratory Syncytial Virus Nucleocapsid Protein," Nucleic Acids
`Research 11(17) : 5941-5951.
`Fallahpour, R.A. (2000) "Photochemical and Thermal reactions of
`Azido-Oligopyridines: Diazepinones, a New Class of Metal-Com(cid:173)
`plex Ligands," Helvetica Chimica Acta. 83:384-393.
`Fei, Z. et al. (1998) "MALDI-TOF mass spectrometric typing of
`single nucleotide polymorphisms with mass-tagged ddNTPs,"
`Nucleic Acids Research 26(11):2827-2828.
`Finzi, L. et al. (1995) "Measurement of Lactose Repressor-Medi(cid:173)
`ated Loop Formation and Breakdown in Single DNA Molecules."
`Science, 267:378-380.
`Fu, D.J., Tang, K., Braun, A., Reuter, D., Darnhofer-Demar, B.,
`Little, D.P., O'Donnell, M.J., Cantor, C.R., and Koster, H. (1998)
`"Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass
`spectrometry," Nat. Biotechnol. 16:381-384.
`Gibson, K.J. et al. ( 1987) "Synthesis and Application of Derivatiz(cid:173)
`able Oligonucleotides," Nucleic Acids Research, 15(16): 6455-
`6467.
`(1999) "5-[3-(E)-(4-Azido-2,3,5,6,(cid:173)
`Godovikova, T.S. et al.
`tetrafluorobenzamido )propenyl- l ]-2'deoxyuridine-5' -triphosphate
`Substitutes for Thymidine-5'triphosphate in the Polymerase Chain
`Reaction," Bioconjugate Chem., 10: 529-537.
`Green, T.W. et al. and Wuts, P.G.M. "Protective Groups in Organic
`Synthesis" 3rd ed. New York: John Wiley & Sons, Inc., 1999. 96-99,
`190-191, 260-261, 542-543, and 750-751.
`Griffin, T.J. et al. (1999) "Direct Genetic Analysis by Matrix(cid:173)
`Assisted Laser Desorption/Ionization Mass Spectrometry," Proc.
`Nat. Acad. Sci. USA 96:6301-6306.
`Guibe (1997) "Allylic Protecting Groups and Their Use in a
`Complex Environment Part I: Allylic Protection of Alcohols,"
`Tetrahedron, 53:13509-13556.
`Guibe (1998) "Allylic Protecting Groups and Their Use in a
`Complex Environment Part II: Allylic Protecting Groups and their
`Removal through Catalytic Palladium n-Allyl Methodology," Tet(cid:173)
`rahedron, 54:2967-3042.
`Hacia J.G., Edgemon K., Sun B., Stern D., Fodor S.A., and Collins
`F.S. (1998) "Two Color Hybridization Analysis Using High Density
`Oligonucleotide Arrays and Energy Transfer Dyes," Nucleic Acids
`Res. 26:3865-6.
`Haff L.A., et al. (1997) "Multiplex Genotyping of PCR Products
`with Mass Tag-Labeled Primers," Nucleic Acids Res. 25(18):3749-
`3750.
`Hafliger, D. et al. (1997) "Seminested RT-PCR Systems for Small
`Round Structured Viruses and Detection of Enteric Viruses in
`Seafood," International Journal of Food Microbiology 37:27-36.
`Hanshaw et al. (2004) "An Indicator Displacement System for
`Fluorescent Detection of Phosphate Oxyanions Under Physiological
`Conditions," Tetrahedron Letters, vol. 45, pp. 8721-8724.
`
`Page 5
`
`
`
`US 9,708,358 B2
`Page 6
`
`(56)
`
`References Cited
`
`OTHER PUBLICATIONS
`
`Hayawaka et al. (1993) "O-Allyl Protection of Guanine and Thy(cid:173)
`mine Residues in Oligodeoxyribonucleotides," J. Org. Chem.,
`58:5551-5555.
`Renner, W.D. et al. (1983) "Enzyme Action at 3' Termini oflonizing
`Radiation-Induced DNA Strand Breaks,"
`J. Biol. Chem.
`258(24): 15198-15205.
`Hovinen et al. (1994) "Synthesis of 3'-O-(m- Aminoalkoxymethyl)
`thymidine 5'-Triphosphates, Terminators of DNA Synthesis that
`Enable 3'-Labelling," J. Chem. Soc. Perkin Trans., 1:211-217.
`Hu et al. (1999) "Optical Mapping of DNA Polymerase I Action and
`Products," BBRC, 254:466-473.
`Huang, B.G. et al. "Synthesis and in vitro Antitumor Activity of
`Some Amino-deoxy 3-hexofuranosylpyrrolo[2,3-d] pyrimidines."
`Carbohydrate Research, 1998, 308(3-4):319-328.
`Huber et al. (1999) "Monitoring Solid Phase Synthesis by Infrared
`Spectroscopic Techniques." Analytica Chimica Acta, 393:213.
`Hultman et al. (1989) "Direct Solid Phase Sequencing of Genomic
`and Plasmid DNA Using Magnetic Beads as Solid Support,"
`Nucleic Acids Research 17(3):4937-4946.
`Hyman, E.D., (1988) "A new method of sequencing DNA," Ana(cid:173)
`lytical Biochemistry 174:423-436.
`Ikeda, K. et al. (1995) "A Non-Radioactive DNA Sequencing
`Method Using Biotinylated Dideoxynucleoside Triphosphates and
`Delta TTH DNA Polymerase," DNA Research 2(31):225-227.
`Ireland, R.E. and Varney, M.D. (1986) "Approach to the total
`synthesis of chlorothricolide: synthesis of (±)-19.20-dihydro-24-O(cid:173)
`methylchlorothricolide, methyl ester, ethyl carbonate," J. Org.
`Chem. 51:635-648.
`Jiang-Baucom, P. et al. (1997) "DNA Typing of Human Leukocyte
`Antigen Sequence Polymorphisms by Peptide Nucleic Acid Probes
`and MALDI-TOF Mass Spectrometry," Anal. Chem. 69:4894-4896.
`Ju, J., Ruan C., Fuller, C.W., Glazer, A.N., and Mathies R.A. (1995)
`"Fluorescence energy transfer dye-labeled primers for DNA
`sequencing and analysis," Proc. Natl. Acad. Sci. USA 92: 4347-
`4351.
`Ju, J.et al. (1996) "Cassette Labeling for Facile Construction of
`Energy Transfer Fluorescent Primers," Nuc. Acids Res. 24(6): 1144-
`1148.
`Ju, J., Glazer, A.N., and Mathies, R.A. (1996) "Energy Transfer
`Primers: Anew Fluorescence Labeling Paradigm for DNA Sequenc(cid:173)
`ing and Analysis," Nature Medicine 2:246-249.
`