A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Tan, Swee Jin ^a   Phan, Huan ^b   Gerry, Benjamin Michael ^b   Kuhn, Alexandre ^a   Hong, Lewis Zuocheng ^a   Min Ong, Yao ^a   Poon, Polly Suk Yean ^a   Unger, Marc Alexander ^b   Jones, Robert C ^b   Quake, Stephen R ^a,c   Burkholder, William F ^a  

^a INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

^b FLUIDIGM CORPORATION   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; CLINICAL PROTOCOL; COLUMN CHROMATOGRAPHY; CONTROLLED STUDY; DNA DETERMINATION; DNA LIBRARY; DNA MICROARRAY; DNA SEQUENCE; EQUIPMENT DESIGN; ESCHERICHIA COLI; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; LABORATORY AUTOMATION; MICROFLUIDIC ANALYSIS; MICROFLUIDICS; NONHUMAN; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; ROBOTICS; SEQUENCE ANALYSIS; TEMPERATURE CONTROLLER;

EID: 84880784583     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0064084     Document Type: Article

References (52)

1. Mitchell P, (2001) Microfluidics--downsizing large-scale biology. Nat Biotechnol 19: 717-721.
2. Hong JW, Studer V, Hang G, Anderson WF, Quake SR, (2004) A nanoliter-scale nucleic acid processor with parallel architecture. Nat Biotechnol 22: 435-439.
3. Marcus JS, Anderson WF, Quake SR, (2006) Microfluidic single-cell mRNA isolation and analysis. Anal Chem 78: 3084-3089.
4. Hong JW, Chen Y, Anderson WF, Quake SR, (2006) Molecular biology on a microfluidic chip. J Phys Condens Matter 18: S691.
5. Zhong JF, Chen Y, Marcus JS, Scherer A, Quake SR, et al. (2008) A microfluidic processor for gene expression profiling of single human embryonic stem cells. Lab Chip 8: 68-74.
6. Dittrich PS, Manz A, (2006) Lab-on-a-chip: microfluidics in drug discovery. Nat Rev Drug Discov 5: 210-218.
7. El-Ali J, Sorger PK, Jensen KF, (2006) Cells on chips. Nature 442: 403-411.
8. Jiang G, Harrison DJ, (2000) mRNA isolation in a microfluidic device for eventual integration of cDNA library construction. Analyst 125: 2176-2179.
9. Kim J, Johnson M, Hill P, Gale BK, (2009) Microfluidic sample preparation: cell lysis and nucleic acid purification. Integr Biol (Camb) 1: 574-586.
10. Schuster SC, (2008) Next-generation sequencing transforms today's biology. Nat Methods 5: 16-18.
11. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328: 636-639.
12. Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133-141.
13. Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, et al. (2010) Clinical assessment incorporating a personal genome. Lancet 375: 1525-1535.
14. Mardis ER, (2008) Next-Generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9: 387-402.
15. Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46.
16. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
17. Lam HY, Clark MJ, Chen R, Natsoulis G, O'Huallachain M, et al. (2012) Performance comparison of whole-genome sequencing platforms. Nat Biotechnol 30: 562.
18. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, et al. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30: 562.
19. Unger MA, Chou HP, Thorsen T, Scherer A, Quake SR, (2000) Monolithic microfabricated valves and pumps by multilayer soft lithography. Science 288: 113-116.
20. Melin J, Quake SR, (2007) Microfluidic large-scale integration: the evolution of design rules for biological automation. Annu Rev Biophys Biomol Struct 36: 213-231.
21. Pontén J, Saksela E, (1967) Two established in vitro cell lines from human mesenchymal tumours. Int J Cancer 2: 434-447.
22. Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
23. Giordano C, (2000) Minutes of the September 7 2000 Meeting of the SBS Microplate Standards Discussion Group. J Biomol Screen 5: 406-411.
24. Spurgeon SL, Jones RC, Ramakrishnan R, (2008) High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLOS ONE 3: e1662.
25. Breadmore MC, Wolfe KA, Arcibal IG, Leung WK, Dickson D, et al. (2003) Microchip-based purification of DNA from biological samples. Anal Chem 75: 1880-1886.
26. Wen J, Legendre LA, Bienvenue JM, Landers JP, (2008) Purification of nucleic acids in microfluidic devices. Anal Chem 80: 6472-6479.
27. Wolfe KA, Breadmore MC, Ferrance JP, Power ME, Conroy JF, et al. (2002) Toward a microchip-based solid-phase extraction method for isolation of nucleic acids. Electrophoresis 23: 727-733.
28. Huft J, Haynes CA, Hansen CL, (2013) Fabrication of high-quality microfluidic solid-phase chromatography columns. Anal Chem 85: 1797-1802.
29. Huft J, Haynes CA, Hansen CL, (2013) Microfluidic integration of parallel solid-phase liquid chromatography. Anal Chem 85: 2999-3005.
30. Kutter JP, (2012) Liquid phase chromatography on microchips. J Chromatogr A 1221: 72-82.
31. Lavrik NV, Taylor LT, Sepaniak MJ, (2011) Nanotechnology and chip level systems for pressure driven liquid chromatography and emerging analytical separation techniques: a review. Anal Chim Acta 694: 6-20.
32. Rahman MM, Elaissari A, (2012) Nucleic acid sample preparation for in vitro molecular diagnosis: from conventional techniques to biotechnology. Drug Discov Today 17: 1199-1207.
33. Gomez FA, (2011) Microfluidics in protein chromatography. Methods Mol Biol 681: 137-150.
34. Hawkins TL, O'Connor-Morin T, Roy A, Santillan C, (1994) DNA purification and isolation using a solid-phase. Nucleic Acids Res 22: 4543-4544.
35. Lundin S, Stranneheim H, Pettersson E, Klevebring D, Lundeberg J, (2010) Increased throughput by parallelization of library preparation for massive sequencing. PLOS ONE 5: e10029.
36. Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, et al. (2010) Unlocking short read sequencing for metagenomics. PLOS ONE 5: e11840.
37. Fisher S, Barry A, Abreu J, Minie B, Nolan J, et al. (2011) A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol 12: R1.
38. Farias-Hesson E, Erikson J, Atkins A, Shen P, Davis RW, et al. (2010) Semi-automated library preparation for high-throughput DNA sequencing platforms. J Biomed Biotechnol, 2010(2010).
39. Borgström E, Lundin S, Lundeberg J, (2011) Large scale library generation for high throughput sequencing. PLOS ONE 6: e19119.
40. Lennon NJ, Lintner RE, Anderson S, Alvarez P, Barry A, et al. (2010) A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biol 11: R15.
41. Frieder M, Jean-Christophe B, (2005) Electrowetting: from basics to applications. J Phys Condens Matter 17: R705.
42. Sung Kwon C, Hyejin M, Chang-Jin K, (2003) Creating, transporting, cutting, and merging liquid droplets by electrowetting-based actuation for digital microfluidic circuits. J Microelectromech S 12: 70-80.
43. Fair R, (2007) Digital microfluidics: is a true lab-on-a-chip possible? Microfluid Nanofluid 3: 245-281.
44. Christel LA, Petersen K, McMillan W, Northrup MA, (1999) Rapid, automated nucleic acid probe assays using silicon microstructures for nucleic acid concentration. J Biomech Eng 121: 22-27.
45. Cady NC, Stelick S, Batt CA, (2003) Nucleic acid purification using microfabricated silicon structures. Biosens Bioelectron 19: 59-66.
46. Hindson BJ, Gutierrez DM, Ness KD, Makarewicz AJ, Metz TR, et al. (2008) Development of an automated DNA purification module using a micro-fabricated pillar chip. Analyst 133: 248-255.
47. Chung YC, Jan MS, Lin YC, Lin JH, Cheng WC, et al. (2004) Microfluidic chip for high efficiency DNA extraction. Lab Chip 4: 141-147.
48. Quail MA, Gu Y, Swerdlow H, Mayho M, (2012) Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation. Electrophoresis 33: 3521-3528.
49. Harrison DJ, Fluri K, Seiler K, Fan Z, Effenhauser CS, et al. (1993) Micromachining a miniaturized capillary electrophoresis-based chemical analysis system on a chip. Science 261: 895-897.
50. Chou CF, Bakajin O, Turner SW, Duke TA, Chan SS, et al. (1999) Sorting by diffusion: an asymmetric obstacle course for continuous molecular separation. Proc Natl Acad Sci U S A 96: 13762-13765.
51. Huang LR, Cox EC, Austin RH, Sturm JC, (2004) Continuous particle separation through deterministic lateral displacement. Science 304: 987-990.
52. Wu AR, Hiatt JB, Lu R, Attema JL, Lobo NA, et al. (2009) Automated microfluidic chromatin immunoprecipitation from 2,000 cells. Lab Chip 9: 1365-1370.