Optimization of high-speed DNA sequencing on microfabricated capillary electrophoresis channels

Analytical Chemistry

Volumn 71, Issue 3, 1999, Pages 566-573

  Liu, Shaorong ^a,b   Shi, Yining ^a   Ja, William W ^a   Mathies, Richard A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Molecular Dynamics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; AUTOANALYZER; CAPILLARY ELECTROPHORESIS; DNA SEQUENCE; MICROANALYSIS;

BASE SEQUENCE; DNA; ELECTROPHORESIS, CAPILLARY; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA;

EID: 0033083477     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac980783v     Document Type: Article

References (49)

1. Smith, L. M.; Sanders, J. Z.; Kaiser, R. J.; Hughes, P.; Dodd, C.; Connell, C. R.; Heiner, C.; Kent, S. B. H.; Hood, L. E. Nature 1986, 321, 674-679.
2. Cohen, A. S.; Najarian, D. R.; Paulus, A.; Guttman, A.; Smith, J. A.; Karger, B. L. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 9660-9663.
3. Kasper, T. J.; Melera, M.; Gozel, P.; Brownlee, R. G. J. Chromatogr. 1988, 458, 303-312.
4. Drossman, H.; Luckey, J. A.; Kostichka, A. J.; D'Cunha, J.; Smith, L. M. Anal. Chem. 1990, 62, 900-903.
5. Cohen, A. S.; Najarian, D. R.; Karger, B. L. J. Chromatogr. 1990, 516, 49-60.
6. Swerdlow, H.; Wu, S.; Harke, H.; Dovichi, N. J. J. Chromatogr. 1990, 516, 61-67.
7. Zhang, J. Z.; Fang, Y.; Hou, J. Y.; Ren, H. J.; Jiang, R.; Roos, P.; Dovichi, N. J. Anal. Chem. 1995, 67, 4589-4593.
8. Ju, J.; Kheterpal, I.; Scherer, J. R.; Ruan, C.; Fuller, C. W.; Glazer, A. N.; Mathies, R. A. Anal. Biochem. 1995, 231, 131-140.
9. Carrilho, E.; Ruiz-Martinez, M. C.; Berka, J.; Smirnov, I.; Goetzinger, W.; Miller, A. W.; Brady, D.; Karger, B. L. Anal. Chem. 1996, 68, 3305-3313.
10. Kim, Y.; Yeung, E. S. J. Chromatogr., A 1997, 781, 315-325.
11. Huang, X. C.; Quesada, M. A.; Mathies, R. A. Anal. Chem. 1992, 64, 967-972.
12. Huang, X. C.; Quesada, M. A.; Mathies, R. A. Anal. Chem. 1992, 64, 2149-2154.
13. Mathies, R. A.; Huang, X. C. Nature (London) 1992, 359, 167-169.
14. Kheterpal, I.; Scherer, J. R.; Clark, S. M.; Radhakrishnan, A.; Ju, J.; Ginther, C. L.; Sensabaugh, G. F.; Mathies, R. Electrophoresis 1996, 17, 1852-1859.
15. Takahashi, S.; Murakami, K.; Anazawa, T.; Kambara, H. Anal. Chem. 1994, 66, 1021-1026.
16. Quesada, M. A.; Zhang, S. Electrophoresis 1996, 17, 1841-1851.
17. Ueno, K.; Yeung, E. S. Anal. Chem. 1994, 66, 1424-1431.
18. Mansfield, E. S.; Vainer, M.; Harris, D. W.; Gasparini, P.; Estivill, X.; Surrey, S.; Fortina, P. J. Chromatogr., A 1997, 781, 295-305.
19. Bashkin, J.; Marsh, M.; Barker, D.; Johnston, R. Appl. Theor. Electrophor. 1996, 6, 23-28.
20. Woolley, A. T.; Mathies, R. A. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 11348-11352.
21. Woolley, A. T.; Mathies, R. A. Proc. Int. Soc. Opt. Eng.-SPIE 1995, 2386, 36-44.
22. Woolley, A. T.; Mathies, R. A. Anal. Chem. 1995, 67, 3676-3680.
23. Woolley, A. T.; Sensabaugh, G. F.; Mathies, R. A. Anal. Chem. 1997, 69, 2181-2186.
24. Simpson, P. C.; Roach, D.; Woolley, A. T.; Thorsen, T.; Johnston, R.; Sensabaugh, G. F.; Mathies, R. A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 2256-2261.
25. Harrison, D. J.; Fluri, K.; Seiler, K.; Fan, Z.; Effenhauser, C. S.; Manz, A. Science 1993, 261, 895-897.
26. Jacobson, S. C.; Hergenroeder, R.; Koutny, L. B.; Warmack, R. J.; Ramsey, J. M. Anal. Chem. 1994, 66, 1107-1113.
27. Manz, A.; Harrison, D. J.; Verpoorte, E. M. J.; Fettinger, J. C.; Paulus, A.; Ludi, H.; Widmer, H. M. J. Chromatogr. 1992, 593, 253-258.
28. Effenhauser, C. S.; Manz, A.; Widmer, H. M. Anal. Chem. 1993, 65, 2637-2642.
29. Jacobson, S. C.; Hergenroeder, R.; Koutny, L. B.; Ramsey, J. M. Anal. Chem. 1994, 66, 1114-1118.
30. Effenhauser, C. S.; Paulus, A.; Manz, A.; Widmer, H. M. Anal. Chem. 1994, 66, 2949-2953.
31. Woolley, A. T.; Hadley, D.; Landre, P.; deMello, A. J.; Mathies, R. A.; Northrup, M. A. Anal. Chem. 1996, 68, 4081-4086.
32. Waters, L. C.; Jacobson, S. C.; Kroutuchinina, N.; Khandurina, J.; Foote, R. S.; Ramsey, J. M. Anal. Chem. 1998, 70, 158-162.
33. Schmalzing, D.; Adourian, A.; Koutny, L.; Ziaugara, L.; Matsudaira, P.; Ehrlich, D. Anal. Chem. 1998, 70, 2303-2310.
34. Simpson, P. C.; Woolley, A. T.; Mathies, R. A. Biomed. Microdevices 1998, 1, 7-26.
35. Hjerten, S. J. Chromatogr. 1985, 347, 191-198.
36. Hung, S.; Mathies, R. A.; Glazer, A. N. Anal. Biochem. 1997, 252, 78-88.
37. Giddings, M. C.; Severin, J. S.; Westphall, M.; Wu, J. Z., Smith, L. M. Genome Res. 1998, 8, 644-665.
38. Yin, Z. B.; Severin, J.; Giddings, M. C.; Huang, W. A.; Westphall, M. S.; Smith, L. M. Electrophoresis 1996, 17, 1143-1150.
39. Giddings, M. C.; Brumley, R. L.; Haker, M.; Smith, L. M. Nucleic Acids Res. 1993, 21, 4530-4540.
40. The script steps included the following: primer peak deletion; baseline subtraction (calculated over regions of 75 s or 750 data points); spectral separation to remove cross-talk due to spectral overlap of the four dye primers (BaseFinder allows formulation of the matrix by simply selecting four isolated peaks, one for each base); two rounds of successive noise filtering (first round, window width M = 10, Gaussian width σ = 2; second round, M = 10, σ = 1.8) and deconvolution (four iterations with the default spread function and α = 0.25); a final noise filtering (M = 5, σ = 1); preliminary base-calling to allow for sequence-adjusted normalization of the four channels (default values except for maximum iterations, 3); normalization of the signal intensities; histogram equalization (to cut off high, spurious peaks); mobility shift correction; and base-calling. The final base-calling module used parameters that evenly weighted base spacing, peak widths, and peak heights. A maximum of 10 iterations was allowed, and beginning and end width tolerances were set at 1.70 and 1.35, respectively. Spacing tolerance was set at 1.45.
41. Dear, S.; Staden, R. DNA Sequence 1992, 3, 107-110.
42. Ewing, B.; Hillier, L.; Wendl, M. C.; Green, P. Genome Res. 1998, 8, 175-194.
43. Ruiz-Martinez, M. C.; Berka, J.; Belenkii, A.; Foret, F.; Miller, A. M.; Karger, B. L. Anal. Chem. 1993, 65, 2851-2858.
44. Kleparnik, K.; Foret, F.; Berka, J.; Goetzinger, W.; Miller A. W.; Karger, B. L. Electrophoresis 1996, 17, 1860-1866.
45. Wang, Y.; Wallin, J. M.; Ju, J.; Sensabaugh, G. F.; Mathies, R. A. Electrophoresis 1996, 17, 1485-1490.
46. Wang, Y.; Hung, S. H.; Linn, J. F.; Steiner, G.; Glazer, A. N.; Sidransky, D.; Mathies, R. A. Electrophoresis 1997, 18, 1742-1749.
47. Schmalzing, D.; Koutny, L.; Adourian, A.; Belgrader, P.; Matsudaira, P.; Ehrlich, D. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 10273-10278.
48. Sunada, T. M.; Blanch, H. W. Electrophoresis 1997, 18, 2243-2254.
49. Luckey, J. A.; Norris, T. B.; Smith, L. M. J. Phys. Chem. 1993, 97, 3067-3075.