Single-molecule emulsion PCR in microfluidic droplets

Analytical and Bioanalytical Chemistry

Volumn 403, Issue 8, 2012, Pages 2127-2143

  Zhu, Zhi ^a   Jenkins, Gareth ^a   Zhang, Wenhua ^a   Zhang, Mingxia ^a   Guan, Zhichao ^a   Yang, Chaoyong James ^a  

^a XIAMEN UNIVERSITY   (China)

Author keywords

Emulsion PCR; High throughput screening; Microfluidic droplets; Next generation DNA sequencing; Rare mutation detection; Single molecule amplification

Indexed keywords

CROSS CONTAMINATION; DISCRETE VOLUMES; DNA SEQUENCING; HIGH-THROUGHPUT SCREENING; MONODISPERSE DROPLETS; MUTATION DETECTION; NOVEL SOLUTIONS; PARALLEL REACTIONS; QUANTITATIVE DETECTION; SINGLE-MOLECULE;

BIOMEDICAL ENGINEERING; DNA SEQUENCES; DROPS; EMULSIFICATION; MICROFLUIDICS; MOLECULES;

POLYMERASE CHAIN REACTION;

DNA;

ANIMAL; CHEMISTRY; EMULSION; EQUIPMENT DESIGN; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INSTRUMENTATION; METHODOLOGY; MICROFLUIDICS; POLYMERASE CHAIN REACTION; REVIEW;

ANIMALS; DNA; EMULSIONS; EQUIPMENT DESIGN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICROFLUIDICS; POLYMERASE CHAIN REACTION;

EID: 84863715597     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-012-5914-x     Document Type: Review

References (111)

1. Xie XS, Yu J, Yang WY (2006) Science 312:228-230
2. Sims CE, Allbritton NL (2007) Lab Chip 7:423-440
3. Li GW, Xie XS (2011) Nature 475:308-315
4. Funatsu T, Harada Y, Tokunaga M, Saito K, Yanagida T (1995) Nature 374:555-559
5. Wang MD, Schnitzer MJ, Yin H, Landick R, Gelles J, Block SM (1998) Science 282:902-907
6. Weiss S (1999) Science 283:1676-1683
7. Check E (2005) Nature 437:1084-1086
8. Raser JM, O'Shea EK (2005) Science 309:2010-2013
9. Misteli T, Soutoglou E (2009) Nat Rev Mol Cell Biol 10:243-254
10. Stratton MR, Campbell PJ, Futreal PA (2009) Nature 458:719-724
11. Burkhart DL, Sage J (2008) Nat Rev Cancer 8:671-682
12. Jeffreys AJ, Wilson V, Neumann R, Keyte J (1988) Nucleic Acids Res 16:10953-10971
13. Jeffreys AJ, Neumann R, Wilson V (1990) Cell 60:473-485
14. Li HH, Gyllensten UB, Cui XF, Saiki RK, Erlich HA, Arnheim N (1988) Nature 335:414-417
15. Ruano G, Kidd KK, Stephens JC (1990) Proc Natl Acad Sci U S A 87:6296-6300
16. Song H, Chen DL, Ismagilov RF (2006) Angew Chem Int Ed Engl 45:7336-7356
17. Dittrich PS, Manz A (2006) Nat Rev Drug Discovery 5:210-218
18. Price AK, Culbertson CT (2007) Anal Chem 79:2614-2621
19. Chiu DT, Lorenz RM (2009) Acc Chem Res 42:649-658
20. Lindstrom S, Andersson-Svahn H (2010) Lab Chip 10:3363-3372
21. Teh SY, Lin R, Hung LH, Lee AP (2008) Lab Chip 8:198-220
22. Huebner A, Sharma S, Srisa-Art M, Hollfelder F, Edel JB, Demello AJ (2008) Lab Chip 8:1244-1254
23. Theberge AB, Courtois F, Schaerli Y, Fischlechner M, Abell C, Hollfelder F, Huck WTS (2010) Angew Chem Int Edit 49:5846-5868
24. Baroud CN, Gallaire F, Dangla R (2010) Lab Chip 10:2032-2045
25. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N (1985) Science 230:1350-1354
26. Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Cold Spring Harbor Symp Quant Biol 51:263-273
27. Zhang C, Da X (2010) Chem Rev (Washington, DC, U S) 110:4910-4947
28. Kemp DJ, Smith DB, Foote SJ, Samaras N, Peterson MG (1989) Proc Natl Acad Sci U S A 86:2423-2427
29. Porterjordan K, Rosenberg EI, Keiser JF, Gross JD, Ross AM, Nasim S, Garrett CT (1990) J Med Virol 30:85-91
30. Kalinina O, Lebedeva I, Brown J, Silver J (1997) Nucleic Acids Res 25:1999-2004
31. Lagally ET, Medintz I, Mathies RA (2001) Anal Chem 73:565-570
32. Nakano M, Komatsu J, Matsuura S, Takashima K, Katsura S, Mizuno A (2003) J Biotechnol 102:117-124
33. Shao KK, Ding WF, Wang F, Li HQ, Ma D, Wang HM (2011) PLoS One 6
34. Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B (2003) Proc Natl Acad Sci U S A 100:8817-8822
35. Diehl F, Li M, He YP, Kinzler KW, Vogelstein B, Dressman D (2006) Nat Methods 3:551-559
36. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Science 309:1728-1732
37. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Nature 437:376-380
38. Kumaresan P, Yang CJ, Cronier SA, Blazej RG, Mathies RA (2008) Anal Chem 80:3522-3529
39. Thorsen T, Roberts RW, Arnold FH, Quake SR (2001) Phys Rev Lett 86:4163-4166
40. Nisisako T, Torii T, Higuchi T (2002) Lab Chip 2:24-26
41. Zagnoni M, Anderson J, Cooper JM (2010) Langmuir 26:9416-9422
42. Gupta A, Kumar R (2010) Microfluid Nanofluid 8:799-812
43. van Steijn V, Kleijn CR, Kreutzer MT (2010) Lab Chip 10:2513-2518
44. Schneider T, Burnham DR, VanOrden J, Chiu DT (2011) Lab Chip 11:2055-2059
45. Sivasamy J, Wong TN, Nguyen NT, Kao LTH (2011) Microfluid Nanofluid 11:1-10
46. Liu HH, Zhang YH (2009) J Appl Phys 106
47. Anna SL, Bontoux N, Stone HA (2003) Appl Phys Lett 82:364-366
48. Ward T, Faivre M, Abkarian M, Stone HA (2005) Electrophoresis 26:3716-3724
49. Nie ZH, Seo MS, Xu SQ, Lewis PC, Mok M, Kumacheva E, Whitesides GM, Garstecki P, Stone HA (2008) Microfluid Nanofluid 5:585-594
50. Yobas L, Martens S, Ong WL, Ranganathan N (2006) Lab Chip 6:1073-1079
51. Peng L, Yang M, Guo SS, Liu W, Zhao XZ (2011) Biomed Microdevices 13:559-564
52. Takeuchi S, Garstecki P, Weibel DB, Whitesides GM (2005) Adv Mater (Weinheim, Ger) 17:1067
53. Utada AS, Lorenceau E, Link DR, Kaplan PD, Stone HA, Weitz DA (2005) Science 308:537-541
54. Tan YC, Fisher JS, Lee AI, Cristini V, Lee AP (2004) Lab Chip 4:292-298
55. Link DR, Anna SL, Weitz DA, Stone HA (2004) Phys Rev Lett 92:054503
56. Hatch AC, Fisher JS, Tovar AR, Hsieh AT, Lin R, Pentoney SL, Yang DL, Lee AP (2011) Lab Chip 11:3838-3845
57. Link DR, Grasland-Mongrain E, Duri A, Sarrazin F, Cheng Z, Cristobal G, Marquez M, Weitz DA (2006) Angew Chem Int Ed Engl 45:2556-2560
58. Cho SK, Moon HJ, Kim CJ (2003) JMicroelectromech S 12:70-80
59. Song H, Tice JD, Ismagilov RF (2003) Angew Chem Int Edit 42:768-772
60. Hung LH, Choi KM, Tseng WY, Tan YC, Shea KJ, Lee AP (2006) Lab Chip 6:174-178
61. Kohler JM, Henkel T, Grodrian A, Kirner T, Roth M, Martin K, Metze J (2004) Chem Eng J (Lausanne) 101:201-216
62. Fidalgo LM, Abell C, Huck WTS (2007) Lab Chip 7:984-986
63. Mazutis L, Araghi AF, Miller OJ, Baret JC, Frenz L, Janoshazi A, Taly V, Miller BJ, Hutchison JB, Link D, Griffiths AD, Ryckelynck M (2009) Anal Chem 81:4813-4821
64. Tresset G, Takeuchi S (2005) Anal Chem 77:2795-2801
65. Tan WH, Takeuchi S (2006) Lab Chip 6:757-763
66. Stroock AD, Dertinger SKW, Ajdari A, Mezic I, Stone HA, Whitesides GM (2002) Science 295:647-651
67. Bringer MR, Gerdts CJ, Song H, Tice JD, Ismagilov RF (2004) Philos T Roy Soc A 362:1087-1104
68. Liau A, Karnik R, Majumdar A, Cate JHD (2005) Anal Chem 77:7618-7625
69. Cabral JT, Hudson SD (2006) Lab Chip 6:427-436
70. Paik P, Pamula VK, Pollack MG, Fair RB (2003) Lab Chip 3:28-33
71. Chatterjee D, Hetayothin B, Wheeler AR, King DJ, Garrell RL (2006) Lab Chip 6:199-206
72. Tan YC, Ho YL, Lee AP (2008) Microfluid Nanofluid 4:343-348
73. Huh D, Bahng JH, Ling YB, Wei HH, Kripfgans OD, Fowlkes JB, Grotberg JB, Takayama S (2007) Anal Chem 79:1369-1376
74. Baret JC, Miller OJ, Taly V, Ryckelynck M, El-Harrak A, Frenz L, Rick C, Samuels ML, Hutchison JB, Agresti JJ, Link DR, Weitz DA, Griffiths AD (2009) Lab Chip 9:1850-1858
75. Boukellal H, Selimovic S, Jia YW, Cristobal G, Fraden S (2009) Lab Chip 9:331-338
76. Edgar JS, Milne G, Zhao YQ, Pabbati CP, Lim DSW, Chiu DT (2009) Angew Chem Int Edit 48:2719-2722
77. Wang W, Yang C, Li CM (2009) Lab Chip 9:1504-1506
78. Bai YP, He XM, Liu DS, Patil SN, Bratton D, Huebner A, Hollfelder F, Abell C, Huck WTS (2010) Lab Chip 10:1281-1285
79. Huebner A, Bratton D, Whyte G, Yang M, deMello AJ, Abell C, Hollfelder F (2009) Lab Chip 9:692-698
80. Frenz L, Blank K, Brouzes E, Griffiths AD (2009) Lab Chip 9:1344-1348
81. Mary P, Abate AR, Agresti JJ, Weitz DA (2011) Biomicrofluidics 5
82. Hettiarachchi K, Talu E, Longo ML, Dayton PA, Lee AP (2007) Lab Chip 7:463-468
83. Malic L, Veres T, Tabrizian M (2009) Lab Chip 9:473-475
84. Marz A, Henkel T, Cialla D, Schmitt M, Popp J (2011) Lab Chip 11:3584-3592
85. Beer NR, Hindson BJ, Wheeler EK, Hall SB, Rose KA, Kennedy IM, Colston BW (2007) Anal Chem 79:8471-8475
86. Beer NR, Wheeler EK, Lee-Houghton L, Watkins N, Nasarabadi S, Hebert N, Leung P, Arnold DW, Bailey CG, Colston BW (2008) Anal Chem 80:1854-1858
87. Kiss MM, Ortoleva-Donnelly L, Beer NR, Warner J, Bailey CG, Colston BW, Rothberg JM, Link DR, Leamon JH (2008) Anal Chem 80:8975-8981
88. Schaerli Y, Wootton RC, Robinson T, Stein V, Dunsby C, Neil MAA, French PMW, deMello AJ, Abell C, Hollfelder F (2009) Anal Chem 81:302-306
89. Zeng Y, Novak R, Shuga J, Smith MT, Mathies RA (2010) Anal Chem 82:3183-3190
90. Leng XF, Zhang WH, Wang CM, Cui LA, Yang CJ (2010) Lab Chip 10:2841-2843
91. Novak R, Zeng Y, Shuga J, Venugopalan G, Fletcher DA, Smith MT, Mathies RA (2011) Angew Chem Int Edit 50:390-395
92. Hua ZS, Rouse JL, Eckhardt AE, Srinivasan V, Pamula VK, Schell WA, Benton JL, Mitchell TG, Pollack MG (2010) Anal Chem 82:2310-2316
93. Zhong Q, Bhattacharya S, Kotsopoulos S, Olson J, Taly V, Griffiths AD, Link DR, Larson JW (2011) Lab Chip 11:2167-2174
94. Pekin D, Skhiri Y, Baret JC, Le Corre D, Mazutis L, Ben Salem C, Millot F, El Harrak A, Hutchison JB, Larson JW, Link DR, Laurent-Puig P, Griffiths AD, Taly V (2011) Lab Chip 11:2156-2166
95. Reetz MT, Jaeger KE (1999) Biocatalysis - from Discovery to Application 200:31-57
96. Pluckthun A, Schaffitzel C, Hanes J, Jermutus L (2001) Advances in Protein Chemistry 55(55):367-403
97. Paegel BM (2010) Curr Opin Chem Biol 14:568-573
98. Ellington AD, Szostak JW (1990) Nature 346:818-822
99. Tuerk C, Gold L (1990) Science 249:505-510
100. Robertson DL, Joyce GF (1990) Nature 344:467-468
101. Nutiu R, Li Y (2005) Angew Chemie Int Ed 44:1061-1065
102. Fang X, Tan W (2010) Acc Chem Res 43:48-57
103. Zhang WY, Zhang WH, Liu ZY, Li C, Zhu Z, Yang CJ (2012) Anal Chem 84:350-355
104. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Dontin MJ, D'Souza CA, Fox DS, Grinberg V, Fu JM, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJM, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW (2005) Science 307:1321-1324
105. Zhao SY, Shetty J, Hou LH, Delcher A, Zhu BL, Osoegawa K, de Jong P, Nierman WC, Strausberg RL, Fraser CM (2004) Genome Res 14:1851-1860
106. Blazej RG, Kumaresan P, Cronier SA, Mathies RA (2007) Anal Chem 79:4499-4506
107. Ronaghi M, Uhlen M, Nyren P (1998) Science 281:363-365
108. Goldberg SMD, Johnson J, Busam D, Feldblyum T, Ferriera S, Friedman R, Halpern A, Khouri H, Kravitz SA, Lauro FM, Li K, Rogers YH, Strausberg R, Sutton G, Tallon L, Thomas T, Venter E, Frazier M, Venter JC (2006) Proc Natl Acad Sci U S A 103:11240-11245
109. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM (2008) Nature 452:U872-U875
110. Vogelstein B, Kinzler KW (2004) Nat Med (N Y, NY, U S) 10:789-799
111. Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, Kitano TK, Hodel MR, Petersen JF, Wyatt PW, Steenblock ER, Shah PH, Bousse LJ, Troup CB, Mellen JC, Wittmann DK, Erndt NG, Cauley TH, Koehler RT, So AP, Dube S, Rose KA, Montesclaros L, Wang SL, Stumbo DP, Hodges SP, Romine S, Milanovich FP, White HE, Regan JF, Karlin-Neumann GA, Hindson CM, Saxonov S, Colston BW (2011) Anal Chem 83:8604-8610