72 7O 76 68
US008778849B2
(12) United States Patent
(10) Patent N0.: (45) Date of Patent:
Bowen et al. (54)
MICROARRAY FABRICATION SYSTEM AND
(58)
CPC ........... .. 130112219/00529; 130112219/00608;
C40B 40/06; C40B 50/00; C40B 50/14;
(71) Applicant: Illumina, Inc., San Diego, CA (US)
C4013 50/18 USPC ........................................ .. 506/16, 23,30, 32
(72) Inventors: M. Shane Bowen, La Jolla, CA (US); Kevin L. Gunderson, Encinitas, CA
(US); Shengrong Lin, Fremont, CA (US); Maria Candelaria Rogert Bacigalupo, Cardiff by the Sea, CA
See application ?le for complete search history. (56)
5,324,633 A 5,429,807 A
Albany, CA (US); Bala Murali Venkatesan, San Diego, CA (US); James Tsay, San Diego, CA (US); John
M. Beierle, Laguna Niguel, CA (US); Lorenzo Berti, San Diego, CA (US);
Sang Ryul Park, San Diego, CA (US)
References Cited U.S. PATENT DOCUMENTS
(US); Kandaswamy Vijayan, San Diego, CA (US); Yir-Shyuan Wu,
FOREIGN PATENT DOCUMENTS EP EP
0868530 Bl 2302028 Al
(Continued) Barbee et al., “Fabrication of DNA Polymer Brush Arrays by
Destructive Micropatterning and Rolling-Circle Ampli?cation,” Macromol. Biosci. 2011, 11:607-617, published online on Feb. 8, 2011*
Oct. 26, 2012
(Continued)
Prior Publication Data
US 2013/0116153 A1
Primary Examiner * Samuel WoolWine
Assistant Examiner * Kaijiang Zhang
May 9, 2013
(74) Attorney, Agent, or Firm * Fletcher, Yoder, PC.
Related US. Application Data
(51)
(52)
OTHER PUBLICATIONS
U.S.C. 154(b) by 0 days.
(65)
(60)
4/2003 3/2011
Subject to any disclaimer, the term of this patent is extended or adjusted under 35
(21) App1.No.: 13/661,524 (22) Filed:
6/1994 Fodor et a1. 7/1995 Matson et al.
(Continued)
(73) Assignee: Illumina, Inc., San Diego, CA (US) Notice:
Jul. 15, 2014
Field of Classi?cation Search
METHOD
(*)
US 8,778,849 B2
Provisional application No. 61/552,712, ?led on Oct. 28, 2011.
Int. Cl. C403 50/18 C403 40/06 C403 50/00 C403 50/14 US. Cl.
(57)
ABSTRACT
A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites
comprise base pads, such as polymer base pads, that promote (2006.01) (2006.01) (2006.01) (2006.01)
the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create
a layout of base pads in a desired pattern. Further, the microar rays may include features to encourage clonality at the sites.
USPC .................. .. 506/32; 506/16; 506/23; 506/30
72 74
7O
18 Claims, 29 Drawing Sheets
76 68
US 8,778,849 B2 Page 2 (56)
References Cited
7,375,234 B2 B2 B2 B2 B2 B1 B2 B2 B2
7/2008 9/2008 6/2009 9/2009 9/2009 10/2009 12/2009 8/2010
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7,785,790 7,813,013 7,837,921 2002/0012930
B1 B2 B2 A1
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A A A A A A A A A
5,744,305 5,750,341 5,772,905 5,795,716 5,831,070 5,837,858 5,856,101
A A A A A A A A
7/1995 9/1995 1/1996 2/1996 10/1996
Southern et 31‘ Barrett et 31' Barrett et al‘ Aldwin et 31' Hollenberg et 31.
12/1996 Coassin et 31. 2/1997 Brenner 4/1997 Sundberg et 31' 6/199'7 8/199'7 4/1998 57998 6/1998 8/1998 11/1998 11/1998 1/1999
Adams et al‘ Brock et al‘ Fodor et 31' Macevicz chou Chee et al' Pease et al‘ Brennan Hubbell et al'
5/2008 Sharpless et 31.
7,405,281 7,427,678 7,547,504 7,582,420 7,595,883 7,597,932 7,635,445 7,785,526
5,858,659 A
1/1999 Sapolsky et al'
2004/0096853 A1
5/2004 Mayer
5,871,921 5,874,219 5,919,523 A
2/1999 7/1999 Landegren Rava Sundberg et etet31‘al‘
2005/0053980 2005/0181394 2005/0181440 A1
3/2005 8/2005 GUIICIGISOII Chee Steemers et 31.6t 6t
5,968,740 5,974,164 5,981,185 5,981,956 6,022,963 6,025,601 6,033,860 6,083,697
A A A A A A A A 6,090,555 A 6,124,120 A 6,136,269 A
6,210,891 B1 6,258,568 B1 6,266,459 6,274,320 6,287,768 6,288,220 6,291,183 6,291,193
B1 B1 B1 B1 B1 B1
10/1999 10/1999 11/1999 11/1999 2/2000 2/2000 3/2000 7/2000
Fodor et 31‘ Chee Matson et 31‘ Stern MCGall et a1, Trulson et al‘ LOCkhaI-t et al‘ Beecher et 31'
2005/0191698 2005/0227252 2006/0006327 2006/0023310 2006/0071075 2006/0102471 2006/0119913 2007/0099208
A1 A1 A1 A1 A1 A1 A1 A1
7/2000 9/2000 10/2000 4/2001 7/2001 7/2001 8/2001 9/2001 9/2001 9/2001 9/2001
Fiekowsky et a1, Lizardi Winkler et al‘ Nyren et al‘ Nyren Walt et al‘ Rothberg et a1, Chenchik et al‘ Kambara et 31‘ Pin.qu et 31' Khodadoust
2007/0128624 2008/0009420 2008/0038718 2008/0108082 2009/0026082 2009/0111169 2009/0127589 2009/0186349 2010/0111768 2010/0137143 2010/0282617
A1 A1 A1 A1 A1 A1 A1 A1 A1 A1 A1
6,297,006 B1
10/2001 Dnmmac et 31‘
6,309,831 6,355,431 B1
10/2001 3/2002 Goldberg Chee et al‘et al‘
6,416,949 B1 6,428,752 B1 6,432,360 B1
7/2002 Dower et al‘ 8/2002 Montagu 8/2002 Church
2011/0059865 A1
9/2005 10/2005 1/2006 2/2006 4/2006 5/2006 6/2006 5/2007 6/2007 1/2008 2/2008
5/2008 1/2009 4/2009
5/2009 7/2009 5/2010
Chee et 31. Moon et a1. Donaldson et 31. Putnam et 31. Moon et a1. Maurer et 31. Moon Drmanac et a1.
Gormley et a1. Schroth et 31. Fischer Rank 6[ 31. Rothberg et 31. Kim et 31. Rothberg et a1. Gunderson et 31. Banerjee et 31. Rothberg et a1. Rothberg et a1.
6/2010 11/2010 3/2011 Smith et 31.
2011/0105366 2011/0111984 A1
5/2011 N3k3t3nl Leb1 et 6t 31.
2011/0220775 A1 2012/0020537 A1
9/2011 Triener et 31. 1/2012 Garcia et 31.
2012/0152742 A1 *
6/2012
Gor?nkel et a1. ........... .. 204/452
6,465,178 B2
10/2002 Chappa et al‘
2012/0270305 A1
10/2012 Reed et 31.
6,482,591 6,489,606 6,514,751 6,737,236 6,770,441 6,859,570
B2 B1 B2 B1 B2 B2
11/2002 12/2002 2/ 2003 5/2004 8/2004 2/2005
2012/0316086 A1
12/2012 L111
6,890,741 6,913,884 6,932,934 6,986,989 7,001,792 7,019,835 7,057,026 7,106,513 7,115,400 7,122,482 7,126,755 7,140,861 7,164,533
B2 B2 B2 B2 B2 B2 B2 B2 B1 B2 B2 B2 B2
5/2005 7/2005 8/2005 1/2006 2/2006 3/2006 6/2006 9/2006 10/2006 10/2006 10/2006 11/2006 1/2007
7,186,656 B2
7,205,244 7,211,414 7,244,559 7,259,258 7,279,113 7,315,019 7,329,492 7,329,860
B2 B2 B2 B2 B2 B2 B2 B2
Lockhart et al. Kersey et a1. Johann et a1. Pieken et a1. Dickinson et a1. Walt et a1.
Fan et a1. Stuelpnagel et a1. Choi et a1. Mirkin et 31. Sauer et a1. McMackin et a1. Barnes et a1. Moon et a1. Adessi et a1. Xu et a1. Moon et a1. Warts et 31. Moon er a1. 3/2007 Sreenivasan
4/2007 5/ 2007 7/2007 8/2007 10/2007 1/2008 2/2008 2/2008
Stacey et al. Hardin et a1. Rothberg et al. Kozlov et al, Watts et al.
Turner et al. Hardin et al. Feng et al.
FOREIGN PATENT DOCUMENTS W0 W0 W0 W0 W0 W0 W0 WO WO W0 WO W0 W0 W0 W0 W0
WO WO WO WO WO WO WO WO
39/10977 91/06678 93/17126 95/35505 00/31148 00/53812 00/63437 01/01143 0162982 A2 W0 03/014392 03049677 A2 W0 2004/018497 WO 2004/024323 W0 2005/033681 W0 2007/123744 W0 2008157640 A2 *
11/1939 5/1991 9/1993 12/1995 6/2000 9/2000 10/2000 1/2001 55/2001 2/2003 6/2003 3/2004 3/2004 4/2005 11/2007 12/2008
OTHER PUBLICATIONS
US. Appl. No. 61/438,486, ?led Feb. 1, 2011, Mark Reed. US Appl. No. 13/267,565, ?led Oct. 6, 2011, Jason Harris. US. Appl. No. 61/657,508, ?led Jun. 8, 2012, Wayne N. George. US. Appl. No. 61/660,487, ?led Jun. 15, 2012, Min-Jui Richard Shen.
US 8,778,849 B2 Page 3 (56)
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Pyrophosphate Release”, Analytical Biochemistry 242(1), 84-9 OTHER PUBLICATIONS
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(2008). Levene et al., “Zero -Mode Waveguides for Single-Molecule Analysis at High Concentrations,” Science 299, 682-686 (2003). Lizardi et al., “Mutation detection and single-molecule counting using isothermal rolling-circle ampli?cation,” Nat. Genet. 19:225 232 (1998). Lundquist et al., “Parallel confocal detection of single molecules in real time”, Opt. Lett. 33, 1026-1028 (2008).
Pyrophosphate”, Science 281(5375), 363 (1998). Ronaghi, “Pyrosequencing Sheds Light on DNA Sequencing”, Genome Res. 11(1), 3-11 (2001). Shendure et al., “Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome,” Science 309: 1728-1732 (2005). Soni & Meller, “Progress toward Ultrafast DNA Sequencing Using Solid-State Nanopores”, Clin. Chem. 53, 1996-2001 (2007). Thornton, “High Rate Thick Film Growth”, Ann. Rev. Mater. Sci.
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* cited by examiner
US. Patent
Jul. 15, 2014
Sheet 1 0f 29
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US 8,778,849 B2
(12) United States Patent
(10) Patent N0.: (45) Date of Patent:
Bowen et al. (54)
MICROARRAY FABRICATION SYSTEM AND
(58)
CPC ........... .. 130112219/00529; 130112219/00608;
C40B 40/06; C40B 50/00; C40B 50/14;
(71) Applicant: Illumina, Inc., San Diego, CA (US)
C4013 50/18 USPC ........................................ .. 506/16, 23,30, 32
(72) Inventors: M. Shane Bowen, La Jolla, CA (US); Kevin L. Gunderson, Encinitas, CA
(US); Shengrong Lin, Fremont, CA (US); Maria Candelaria Rogert Bacigalupo, Cardiff by the Sea, CA
See application ?le for complete search history. (56)
5,324,633 A 5,429,807 A
Albany, CA (US); Bala Murali Venkatesan, San Diego, CA (US); James Tsay, San Diego, CA (US); John
M. Beierle, Laguna Niguel, CA (US); Lorenzo Berti, San Diego, CA (US);
Sang Ryul Park, San Diego, CA (US)
References Cited U.S. PATENT DOCUMENTS
(US); Kandaswamy Vijayan, San Diego, CA (US); Yir-Shyuan Wu,
FOREIGN PATENT DOCUMENTS EP EP
0868530 Bl 2302028 Al
(Continued) Barbee et al., “Fabrication of DNA Polymer Brush Arrays by
Destructive Micropatterning and Rolling-Circle Ampli?cation,” Macromol. Biosci. 2011, 11:607-617, published online on Feb. 8, 2011*
Oct. 26, 2012
(Continued)
Prior Publication Data
US 2013/0116153 A1
Primary Examiner * Samuel WoolWine
Assistant Examiner * Kaijiang Zhang
May 9, 2013
(74) Attorney, Agent, or Firm * Fletcher, Yoder, PC.
Related US. Application Data
(51)
(52)
OTHER PUBLICATIONS
U.S.C. 154(b) by 0 days.
(65)
(60)
4/2003 3/2011
Subject to any disclaimer, the term of this patent is extended or adjusted under 35
(21) App1.No.: 13/661,524 (22) Filed:
6/1994 Fodor et a1. 7/1995 Matson et al.
(Continued)
(73) Assignee: Illumina, Inc., San Diego, CA (US) Notice:
Jul. 15, 2014
Field of Classi?cation Search
METHOD
(*)
US 8,778,849 B2
Provisional application No. 61/552,712, ?led on Oct. 28, 2011.
Int. Cl. C403 50/18 C403 40/06 C403 50/00 C403 50/14 US. Cl.
(57)
ABSTRACT
A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites
comprise base pads, such as polymer base pads, that promote (2006.01) (2006.01) (2006.01) (2006.01)
the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create
a layout of base pads in a desired pattern. Further, the microar rays may include features to encourage clonality at the sites.
USPC .................. .. 506/32; 506/16; 506/23; 506/30
72 74
7O
18 Claims, 29 Drawing Sheets
76 68
US 8,778,849 B2 Page 2 (56)
References Cited
7,375,234 B2 B2 B2 B2 B2 B1 B2 B2 B2
7/2008 9/2008 6/2009 9/2009 9/2009 10/2009 12/2009 8/2010
Xu et al. Pieken et a1. Sreenivasan Oliphant et 31. E1 Gamal et a1. Kl‘OtZ 6t 31. Choi et a1. VOISIII
7,785,790 7,813,013 7,837,921 2002/0012930
B1 B2 B2 A1
8/2010 10/2010 11/2010 1/2002
ChPICh 81 31~ K9111 Xu et a1. Rothberg 6t 31.
2002/0055100 2003/0059929 2003/0108867 2003/0108900 2003/0170684 2003/0207295 2003/0215937 2004/0002090
A1 A1 A1 A1 A1 A1 A1 A1
5/2002 3/2003 6/2003 6/2003 9/2003 11/2003 11/2003 1/2004
K3W3ShlIIl3 6t 31. Heller et a1. Chee et a1. 6t 31. Fan Gunderson et a1. M3tSOI1 Mayer et a1.
US PATENT DOCUMENTS 5,436,327 5,451,683 5,482,867 5,491,074 5,561,071 5,583,211 5,599,675 5,624,711 5 641 658
A A A A A A A A A
5,744,305 5,750,341 5,772,905 5,795,716 5,831,070 5,837,858 5,856,101
A A A A A A A A
7/1995 9/1995 1/1996 2/1996 10/1996
Southern et 31‘ Barrett et 31' Barrett et al‘ Aldwin et 31' Hollenberg et 31.
12/1996 Coassin et 31. 2/1997 Brenner 4/1997 Sundberg et 31' 6/199'7 8/199'7 4/1998 57998 6/1998 8/1998 11/1998 11/1998 1/1999
Adams et al‘ Brock et al‘ Fodor et 31' Macevicz chou Chee et al' Pease et al‘ Brennan Hubbell et al'
5/2008 Sharpless et 31.
7,405,281 7,427,678 7,547,504 7,582,420 7,595,883 7,597,932 7,635,445 7,785,526
5,858,659 A
1/1999 Sapolsky et al'
2004/0096853 A1
5/2004 Mayer
5,871,921 5,874,219 5,919,523 A
2/1999 7/1999 Landegren Rava Sundberg et etet31‘al‘
2005/0053980 2005/0181394 2005/0181440 A1
3/2005 8/2005 GUIICIGISOII Chee Steemers et 31.6t 6t
5,968,740 5,974,164 5,981,185 5,981,956 6,022,963 6,025,601 6,033,860 6,083,697
A A A A A A A A 6,090,555 A 6,124,120 A 6,136,269 A
6,210,891 B1 6,258,568 B1 6,266,459 6,274,320 6,287,768 6,288,220 6,291,183 6,291,193
B1 B1 B1 B1 B1 B1
10/1999 10/1999 11/1999 11/1999 2/2000 2/2000 3/2000 7/2000
Fodor et 31‘ Chee Matson et 31‘ Stern MCGall et a1, Trulson et al‘ LOCkhaI-t et al‘ Beecher et 31'
2005/0191698 2005/0227252 2006/0006327 2006/0023310 2006/0071075 2006/0102471 2006/0119913 2007/0099208
A1 A1 A1 A1 A1 A1 A1 A1
7/2000 9/2000 10/2000 4/2001 7/2001 7/2001 8/2001 9/2001 9/2001 9/2001 9/2001
Fiekowsky et a1, Lizardi Winkler et al‘ Nyren et al‘ Nyren Walt et al‘ Rothberg et a1, Chenchik et al‘ Kambara et 31‘ Pin.qu et 31' Khodadoust
2007/0128624 2008/0009420 2008/0038718 2008/0108082 2009/0026082 2009/0111169 2009/0127589 2009/0186349 2010/0111768 2010/0137143 2010/0282617
A1 A1 A1 A1 A1 A1 A1 A1 A1 A1 A1
6,297,006 B1
10/2001 Dnmmac et 31‘
6,309,831 6,355,431 B1
10/2001 3/2002 Goldberg Chee et al‘et al‘
6,416,949 B1 6,428,752 B1 6,432,360 B1
7/2002 Dower et al‘ 8/2002 Montagu 8/2002 Church
2011/0059865 A1
9/2005 10/2005 1/2006 2/2006 4/2006 5/2006 6/2006 5/2007 6/2007 1/2008 2/2008
5/2008 1/2009 4/2009
5/2009 7/2009 5/2010
Chee et 31. Moon et a1. Donaldson et 31. Putnam et 31. Moon et a1. Maurer et 31. Moon Drmanac et a1.
Gormley et a1. Schroth et 31. Fischer Rank 6[ 31. Rothberg et 31. Kim et 31. Rothberg et a1. Gunderson et 31. Banerjee et 31. Rothberg et a1. Rothberg et a1.
6/2010 11/2010 3/2011 Smith et 31.
2011/0105366 2011/0111984 A1
5/2011 N3k3t3nl Leb1 et 6t 31.
2011/0220775 A1 2012/0020537 A1
9/2011 Triener et 31. 1/2012 Garcia et 31.
2012/0152742 A1 *
6/2012
Gor?nkel et a1. ........... .. 204/452
6,465,178 B2
10/2002 Chappa et al‘
2012/0270305 A1
10/2012 Reed et 31.
6,482,591 6,489,606 6,514,751 6,737,236 6,770,441 6,859,570
B2 B1 B2 B1 B2 B2
11/2002 12/2002 2/ 2003 5/2004 8/2004 2/2005
2012/0316086 A1
12/2012 L111
6,890,741 6,913,884 6,932,934 6,986,989 7,001,792 7,019,835 7,057,026 7,106,513 7,115,400 7,122,482 7,126,755 7,140,861 7,164,533
B2 B2 B2 B2 B2 B2 B2 B2 B1 B2 B2 B2 B2
5/2005 7/2005 8/2005 1/2006 2/2006 3/2006 6/2006 9/2006 10/2006 10/2006 10/2006 11/2006 1/2007
7,186,656 B2
7,205,244 7,211,414 7,244,559 7,259,258 7,279,113 7,315,019 7,329,492 7,329,860
B2 B2 B2 B2 B2 B2 B2 B2
Lockhart et al. Kersey et a1. Johann et a1. Pieken et a1. Dickinson et a1. Walt et a1.
Fan et a1. Stuelpnagel et a1. Choi et a1. Mirkin et 31. Sauer et a1. McMackin et a1. Barnes et a1. Moon et a1. Adessi et a1. Xu et a1. Moon et a1. Warts et 31. Moon er a1. 3/2007 Sreenivasan
4/2007 5/ 2007 7/2007 8/2007 10/2007 1/2008 2/2008 2/2008
Stacey et al. Hardin et a1. Rothberg et al. Kozlov et al, Watts et al.
Turner et al. Hardin et al. Feng et al.
FOREIGN PATENT DOCUMENTS W0 W0 W0 W0 W0 W0 W0 WO WO W0 WO W0 W0 W0 W0 W0
WO WO WO WO WO WO WO WO
39/10977 91/06678 93/17126 95/35505 00/31148 00/53812 00/63437 01/01143 0162982 A2 W0 03/014392 03049677 A2 W0 2004/018497 WO 2004/024323 W0 2005/033681 W0 2007/123744 W0 2008157640 A2 *
11/1939 5/1991 9/1993 12/1995 6/2000 9/2000 10/2000 1/2001 55/2001 2/2003 6/2003 3/2004 3/2004 4/2005 11/2007 12/2008
OTHER PUBLICATIONS
US. Appl. No. 61/438,486, ?led Feb. 1, 2011, Mark Reed. US Appl. No. 13/267,565, ?led Oct. 6, 2011, Jason Harris. US. Appl. No. 61/657,508, ?led Jun. 8, 2012, Wayne N. George. US. Appl. No. 61/660,487, ?led Jun. 15, 2012, Min-Jui Richard Shen.
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