Integrated genetic analysis microsystems

Journal of Physics D: Applied Physics

Volumn 37, Issue 23, 2004, Pages

  Lagally, Eric T ^a   Mathies, Richard A ^b  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; ELECTROPHORESIS; EPIDEMIOLOGY; FLUID MECHANICS; GENES; MATERIALS SCIENCE; MICROELECTROMECHANICAL DEVICES; NUCLEIC ACIDS;

BIOWARFARE DETECTION; CAPILLARY ELECTROPHORESIS (CE); FORENSICS; GENETIC ANALYSIS;

GENETIC ENGINEERING;

EID: 10644239267     PISSN: 00223727     EISSN: None     Source Type: Journal    
DOI: 10.1088/0022-3727/37/23/R01     Document Type: Review

References (108)

1. Lander E S et al 2001 Initial sequencing and analysis of the human genome Nature 409 860-921
2. Venter J C et al 2001 The sequence of the human genome Science 291 1304-51
3. US Department of Energy 2000 Microbial Genome Program Report
4. Huang Y et al 2002 MEMS-based sample preparation for molecular diagnostics Anal. Bioanal. Chem. 372 49-65
5. 2003 Handbook of Chemistry and Physics (Boca Raton, FL: CRC Press) 102-15
6. 2000 Modern Plastics Handbook M. Plastics (Harper, CA: McGraw-Hill) 306-400
7. Madou M 2002 Fundamentals of Microfabrication (Boca Raton, FL: CRC Press)
8. Poser S et al 1997 Chip elements for fast thermocycling Sensors Actuator A - Phys. 62 672-5
9. Daniel J H et al 1998 Silicon microchambers for DNA amplification Sensors Actuators A 71 81-8
10. Lagally E T, Simpson P C and Mathies R A 2000 Monolithic integrated microfluidic DNA amplification and capillary electrophoresis analysis system Sensors Actuators B 63 138-46
11. Duffy D C et al 1998 Rapid prototyping of microfluidic systems in poly(dimethylsiloxane) Anal. Chem. 70 4974-84
12. Shoffner M A et al 1996 Chip PCR. 1. Surface passivation of microfabricated silicon-glass chips for PCR Nucleic Acids Res. 24 375-9
13. Ocvirk G et al 2000 Electrokinetic control of fluid flow in native poly(dimethylsiloxane) capillary electrophoresis devices Electrophoresis 21 107-15
14. Hjerten S 1985 High-performance electrophoresis: elimination of electroendosmosis and solute adsorption J. Chramatogr. 347 191-8
15. Handique K et al 2000 Nanoliter liquid metering in microchannels using hydrophobic patterns Anal. Chem. 72 4100-9
16. Hu S W et al 2002 Surface modification of poly(dimethylsiloxane) microfluidic devices by ultraviolet polymer grafting Anal. Chem. 74 4117-23
17. Gillmor S D et al 2002 Low-contact-angle polydimethylsiloxane (PDMS) membranes for fabricating micro-bioarrays 2nd Annual IEEE-EMBS Special Topic Conf. on Microtechnologies in Medicine and Biology (Madison, WI, USA) pp 51-6
18. Fritz J L and Owen M J 1995 Hydrophobic recovery of plasma-treated polydimethylsiloxane J. Adhesives 54 33-45
19. Larsson A and Derand H 2002 Stability of polycarbonate and polystyrene surfaces after hydrophilization with high intensity oxygen RF plasma J. Colloid Interface Sci. 246 214-21
20. Giordano B C, Copeland E R and Landers J P 2001 Towards dynamic coating of glass microchip chambers for amplifying DNA via the polymerase chain reaction Electrophoresis 22 334-40
21. Schena M et al 1995 Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray Science 270 467-70
22. Fodor S P A et al 1991 Light-directed, spatially addressable parallel chemical synthesis Science 251 767-73
23. Gillmor S D et al 2000 Hydrophilic/hydrophobic patterned surfaces as templates for DNA arrays Langmuir 16 7223-8
24. Larson B J, Gillmor S D and Lagally M G 2004 Controlled deposition of picoliter amounts of fluid using an ultrasonically driven micropipette Rev. Sci. Instrum. 75 832-6
25. Sosnowski R G et al 1997 Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control Proc. Natl Acad. Sci. USA 94 1119-23
26. Manz A, Graber N and Widmer HM 1990 Miniaturized total chemical-analysis systems - a novel concept for chemical sensing Sensors Actuators B 1 244-8
27. Harrison D J et al 1992 Micromachining a miniaturized capillary electrophoresis-based chemical analysis system on a chip Science 261 895-7
28. Woolley A T and Mathies R A 1994 Ultra-high-speed DNA fragment separations using microfabricated capillary array electrophoresis chips Proc. Natl Acad. Sci. USA 91 11348-52
29. Woolley A T and Mathies R A 1995 Ultra-high-speed DNA-sequencing using capillary electrophoresis chips Anal. Chem. 67 3676-80
30. Luckey J A, Norris T B and Smith L M 1993 Analysis of resolution in DNA sequencing by capillary gel-electrophoresis J. Phys. Chem. 97 3067-75
31. Paegel B M et al 2002 High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor Proc. Natl Acad. Sci. USA 99 574-9
32. Paegel B M et al 2000 Turn geometry for minimizing band broadening in microfabricated capillary electrophoresis channels Anal. Chem. 72 3030-7
33. Emrich C A et al 2002 Microfabricated 384-lane capillary array electrophoresis bioanalyzer for ultra high-throughput genetic analysis Anal. Chem. 74 5076-83
34. Medintz I et al 2000 High speed single nucleotide polymorphism typing of a hereditary haemochromatosis mutation with capillary array electrophoresis microplates Electrophoresis 21 2352-8
35. Medintz I et al 2001 High-performance multiplex SNP analysis of three haemochromatosis-related mutations with capillary array electrophoresis microplates Genome Res. 11 413-21
36. Medintz I L et al 2001 Genotyping energy-transfer-cassette-labeled short-tandem-repeat amplicons with capillary array electrophoresis microchannel plates Clin. Chem. 47 1614-21
37. Medintz I L et al 2000 Loss of heterozygosity assay for molecular detection of cancer using energy-transfer primers and capillary array electrophoresis Genome Res. 10 1211-18
38. Tian H J et al 2000 Single-strand conformation polymorphism analysis by capillary and microchip electrophoresis: a fast, simple method for detection of common mutations in BRCA1 and BRCA2 Genomics 63 25-34
39. Tao P et al 2004 Fabrication of calcium fluoride capillary electrophoresis microdevices for on-chip infrared detection J. Chromatogr. A 1027 231-5
40. Han J, Turner S W and Craighead H G 1999 Entropic trapping and escape of long DNA molecules at submicron size constriction Phys. Rev. Lett. 83 1688-91
41. Han J and Craighead H G 1999 Entropic trapping and sieving of long DNA molecules in a nanofluidic channel J. Vac. Sci. Technol. A 17 2142-7
42. Cabodi M, Turner S W P and Craighead H G 2002 Entropic recoil separation of long DNA molecules Anal. Chem. 74 5169-74
43. Saiki R K et al 1985 Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle-cell anemia Science 230 1350-4
44. Skidmore M L, Foght J M and Sharp M J 2000 Microbial life beneath a high Arctic glacier Appl. Environ. Microbiol. 66 3214-20
45. Enright M C et al 2000 Molecular typing of bacteria directly from cerebrospinal fluid Eur. J. Clin. Microbiol. Infect. Dis. 19 627-30
46. Higuchi R et al 1988 DNA typing from single hairs Nature 332 543-6
47. Ansari S A, Farrah S R and Chaudhry G R 1992 Presence of human-immunodeficiency-virus nucleic-acids in waste-water and their detection by polymerase chain-reaction Appl. Environ. Microbiol. 58 3984-90
48. Josephson K L et al 1991 Fecal-coliforms in soil detected by polymerase chain-reaction and DNA-DNA hybridizations Soil Sci. Soc. Am. J. 55 1326-32
49. Hecker K H and Roux K H 1996 High and low annealing temperatures increase both specificity and yield in touchdown and stepdown PCR Biotechniques 20 478
50. Held C A et al 1996 Real time quantitative PCR Genome Res. 6 986-94
51. Northrup M A et al 1993 DNA Amplification with a microfabricated reaction chamber Proc. 7th Int. Conf. on Solid-State Sensors and Actuators (Yokohama, Japan) pp 924-6
52. Wilding P, Shoffner M A and Kricka L J 1994 PCR in a silicon microstructure Clin. Chem. 40 1815-8
53. Cheng J et al 1996 Chip PCR. 2. Investigation of different PCR amplification systems in microfabricated silicon-glass chips Nucleic Acids Res. 24 380-5
54. Chaudhari A M et al 1998 Transient liquid crystal thermometry of microfabricated PCR vessel arrays J. Microelectromech. Syst. 7 345-55
55. Taylor T B et al 1998 Process control for optimal PCR performance in glass microstructures J. Biomed. Microdev. 1 65-70
56. Kopp M U, de Mello A J and Manz A 1998 Chemical amplification: continuous-flow PCR on a chip Science 280 1046-8
57. Obeid P J and Christopoulos T K 2003 Continuous-flow DNA and RNA amplification chip combined with laser-induced fluorescence detection Anal. Chim. Acta 494 1-9
58. Shin Y S et al 2003 PDMS-based micro PCR chip with parylene coating J. Micromech. Microeng. 13 768-74
59. Sun K et al 2002 A heater-integrated transparent microchannel chip for continuous-flow PCR Sensors Actuators B 84 283-9
60. Zhang Q T et al 2002 Temperature analysis of continuous-flow micro-PCR based on FEA Sensors Actuators B - Chem. 82 75-81
61. Oda R P et al 1998 Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA Anal. Chem. 70 4361-8
62. Huhmer A F R and Landers J P 2000 Noncontact infrared-mediated thermocycling for effective polymerase chain reaction amplification of DNA in nanoliter volumes Anal. Chem. 72 5507-12
63. Giordano B C et al 2001 Polymerase chain reaction in polymeric microchips: DNA amplification in less than 240 s Anal. Biochem. 291 124-32
64. Liu J, Enzelberger M and Quake S 2002 A nanoliter rotary device for polymerase chain reaction Electrophoresis 23 1531-6
65. Bu M Q et al 2003 Design and theoretical evaluation of a novel microfluidic device to be used for PCR J. Micromech. Microeng. 13 S125-30
66. Heap D M, Herrmann M G and Wittwer C T 2000 PCR amplification using electrolytic resistance for heating and temperature monitoring Biotechniques 29 1006-8
67. Belgrader P et al 1998 Rapid PCR for identity testing using a battery-powered miniature thermal cycler J. Forensic Sci. 43 315-19
68. Belgrader P et al 2001 A battery-powered notebook thermal cycler for rapid multiplex real time PCR analysis Anal. Chem. 73 286-9
69. Higgins J A et al 2003 A handheld real time thermal cycler for bacterial pathogen detection Biosensors Bioelectr. 18 1115-23
70. Pal D and Venkataraman V 2002 A portable battery-operated chip thermocycler based on induction heating Sensors Actuators A 102 151-6
71. Burns M A et al 1998 An integrated nanoliter DNA analysis device Science 282 484-7
72. Cheng J et al 1996 Analysis of ligase chain reaction products amplified in a silicon-glass chip using capillary electrophoresis J. Chromatogr. A 732 151-8
73. Woolley A T et al 1996 Functional integration of PCR amplification and capillary electrophoresis in a microfabricated DNA analysis device Anal. Chem. 68 4081-6
74. Anderson R C et al 1997 Microfluidic biochemical analysis system Proc. 1997 Int. Conf. on Solid-State Sensors and Actuators (Transducers'97) pp 477-80
75. Anderson R C et al 2000 A miniature integrated device for automated multistep genetic assays Nucleic Acids Res. 28 e60
76. Waters L C et al 1998 Microchip device for cell lysis, multiplex PCR amplification, and electrophoretic sizing Anal. Chem. 70 158-62
77. Jacobson S C and Ramsey J M 1996 Integrated microdevice for DNA restriction fragment analysis Anal. Chem. 68 720-3
78. Simpson P C, Woolley A T and Mathies R A 1998 Microfabrication technology for the production of capillary array electrophoresis chips J. Biomed. Microdev. 17-26
79. Lagally E T, Medintz I and Mathies R A 2001 Single-molecule DNA amplification and analysis in an integrated microfluidic device Anal Chem. 73 565-70
80. Lagally E T, Emrich C A and Mathies R A 2001 Fully integrated PCR-capillary electrophoresis microsystem for DNA analysis Lab. Chip. 1 102-7
81. Koh C G et al 2003 Integrating polymerase chain reaction, valving, and electrophoresis in a plastic device for bacterial detection Anal. Chem. 75 4591-8
82. Lagally E T et al 2004 Integrated portable genetic analysis microsystem for pathogen/infectious disease detection Anal. Chem. 76 3162-70
83. Grover W H et al 2003 Monolithic membrane valves and diaphragm pumps for practical large-scale integration into microfluidic devices Sensors Actuators B 89 315-23
84. Stevens D L 2003 Community-acquired Staphylococcus aureus infections: increasing virulence and emerging methicillin resistance in the new millenium Curr. Opin. Infect. Dis. 16 189-91
85. Woolley A T et al 1998 Capillary electrophoresis chips with integrated electrochemical detection Anal. Chem. 70 684-8
86. Ertl P et al 2004 Capillary electrophoresis chips with a sheath-flow supported electrochemical detection system Anal. Chem. 76 3749-55
87. Lee T M H and Hsing I M 2002 Sequence-specific electrochemical detection of asymmetric PCR amplicons of traditional Chinese medicinal plant DNA Anal. Chem. 74 5057-62
88. Cai H et al 2002 Electrochemical detection of DNA hybridization based on silver-enhanced gold nanoparticle label Anal Chim. Acta 469 165-72
89. Wang J, Polsky R and Xu D K 2001 Silver-enhanced colloidal gold electrochemical stripping detection of DNA hybridization Langmuir 17 5739-41
90. Lee T M H, Carles M C and Hsing I M 2003 Microfabricated PCR-electrochemical device for simultaneous DNA amplification and detection Lab. Chip. 3 100-5
91. Chabinyc M L et al 2001 An integrated fluorescence detection system in poly(dimethylsiloxane) for microfluidic applications Anal. Chem. 73 4491-8
92. Namasivayam V et al 2004 Advances in on-chip photodetection for applications in miniaturized genetic analysis systems J. Micromech. Microeng. 14 81-90
93. Roulet J C et al 2002 Performance of an integrated microoptical system for fluorescence detection in microfluidic systems Anal. Chem. 74 3400-07
94. Kamei T et al 2003 Integrated hydrogenated amorphous Si photodiode detector for microfluidic bioanalytical devices Anal. Chem. 75 5300-5
95. Thrush E et al 2004 Integrated semiconductor vertical-cavity surface-emitting lasers and PIN photodetectors for biomedical fluorescence sensing IEEE J. Quantum Electron. 40 491-8
96. Kwon S and Lee L P 2004 Micromachined transmissive scanning confocal microscope Opt. Lett. 29 706-8
97. Cheng J et al 1998 Preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips Nat. Biotechnol. 16 541-6
98. Manaresi N et al 2003 A CMOS chip for individual cell manipulation and detection IEEE J. Solid-State Circuit 38 2297-305
99. Lapizco-Encinas B H et al 2004 Dielectrophoretic concentration and separation of live and dead bacteria in an array of insulators Anal. Chem. 76 1571-9
100. Paegel B M, Yeung S H I and Mathies R A 2002 Microchip bioprocessor for integrated nanovolume sample purification and DNA sequencing Anal. Chem. 74 5092-8
101. Paegel B M, Blazej R G and Mathies R A 2003 Microfluidic devices for DNA sequencing: sample preparation and electrophoretic analysis Curr. Opin. Biotechnol. 14 42-50
102. Unger M A et al 2000 Monolithic microfabricated valves and pumps by multilayer soft lithography Science 288 113-16
103. Thorsen T, Maerkl S J and Quake S R 2002 Microfluidic large-scale integration Science 298 580-4
104. Fu A Y et al 2002 An integrated microfabricated cell sorter Anal. Chem. 74 2451-7
105. Hong J W et al 2004 A nanoliter-scale nucleic acid processor with parallel architecture Nat. Biotechnol. 22 435-9
106. Sen DeWine M 2003 A bill to improve investigation and prosecution of sexual assault cases with DNA evidence, and for other purposes, S.149 US Senate
107. Gray B L et al 1999 Novel interconnection technologies for integrated microfluidic systems Sensors Actuators A 77 57-65
108. Fujii T et al 2003 A plug and play microfluidic device Lab. Chip. 3 193-7