Error analysis of idealized nanopore sequencing

Electrophoresis

Volumn 34, Issue 15, 2013, Pages 2137-2144

  O'Donnell, Christopher R ^a   Wang, Hongyun ^a   Dunbar, William B ^a  

^a University of California Santa Cruz   (United States)

Author keywords

DNA sequencing; Error rates; Nanopore; Nucleic acids; Single molecule sequencing

Indexed keywords

DNA; DNA SEQUENCES; ENZYMES; ESCHERICHIA COLI; GENE ENCODING; NANOPORES; NUMERICAL METHODS; RANDOM ERRORS; SYSTEMATIC ERRORS;

CHANNEL ERROR; CURRENT AMPLITUDE; DNA SEQUENCING; ERROR RATE; ESCHERICHIA COLI K12; IONIC CURRENT; SEQUENCING METHOD; SINGLE MOLECULE; SINGLE-MOLECULE SEQUENCING; TRADE-OFF CURVES;

ERROR ANALYSIS;

ENZYME; NUCLEOTIDE; SINGLE STRANDED DNA;

ACCURACY; ALGORITHM; ANALYTICAL ERROR; ARTICLE; COMPUTER SIMULATION; ENZYME METABOLISM; ESCHERICHIA COLI K 12; ION CURRENT; NANOPORE; NOISE;

EID: 84881246791     PISSN: 01730835     EISSN: 15222683     Source Type: Journal    
DOI: 10.1002/elps.201300174     Document Type: Article

References (22)

1. Xuan, J., Yu, Y., Qing, T., Guo, L., Shi, L., Cancer Lett. 2013, DOI: 10.1016/j.canlet.2012.11.025.
2. Myllykangas, S., Buenrostro, J., Ji, H. P., in: Rodríguez-Ezpeleta, N., Hackenberg, M., Aransay, A. M. (Eds.), Bioinformatics for High Throughput Sequencing, Springer, New York 2012, pp. 11-25.
3. Thompson, J., Milos, P., Genome Biol. 2011, 12, 217.
4. Lam, E. T., Hastie, A., Lin, C., Ehrlich, D., Das, S. K., Austin, M. D., Desh- pande, P., Cao, H., Nagarajan, N., Xiao, M., Kwok, P.-Y., Nat. Biotechnol. 2012, 30, 771-776.
5. Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K. W., Vogelstein, B., Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 9530-9535.
6. Branton, D., Deamer, D. W., Marziali, A., Bayley, H., Benner, S. A., Butler, T., Ventra, M. D., Garaj, S., Hibbs, A., Huang, X., Jovanovich, S. B., Krstic, P. S., Lindsay, S., Ling, X. S., Mastrangelo, C. H., Meller, A., Oliver, J. S., Pershin, Y. V., Ramsey, J. M., Riehn, R., Soni, G. V., Tabard-Cossa, V., Wanunu, M., Wiggin, M., Schloss, J. A., Nat. Biotechnol. 2008, 26, 1146-1153.
7. Pollack, A., The New York Times, Feb 17, 2012, pp. B2.
8. Maitra, R. D., Kim, J., Dunbar, W. B., Electrophoresis 2012, 33, 3418-3428.
9. Cherf, G. M., Lieberman, K. R., Rashid, H., Lam, C. E., Karplus, K., Akeson, M., Nat. Biotechnol. 2012, 30, 344-348.
10. Manrao, E. A., Derrington, I. M., Laszlo, A. H., Langford, K. W., Hopper, M. K., Gillgren, N., Pavlenok, M., Niederweis, M., Gundlach, J. H., Nat. Biotechnol. 2012, 30, 349-353.
11. Clarke, J., Wu, H.-C., Jayasinghe, L., Patel, A., Reid, S., Bayley, H., Nat. Nanotechnol. 2009, 4, 265-270.
12. Sanchez-Cespedes, M., Parrella, P., Nomoto, S., Cohen, D., Xiao, Y., Esteller, M., Jeronimo, C., Jordan, R. C. K., Nicol, T., Koch, W. M., Schoenberg, M., Mazzarelli, P., Fazio, V. M., Sidransky, D., Cancer Res. 2001, 61, 7015-7019.
13. Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J. Mau, B., Shao, Y., Science 1997, 277, 1453-1462.
14. Venkataramanan, L., Sigworth, F. J., Biophys. J. 2002, 82, 1930-1942.
15. Qin, F., Auerbach, A., Sachs, F., Biophys. J. 2000, 79, 1928-1944.
16. Sakmann, B., Neher, E. (Eds.), Single-Channel Recording, Plenum Press, New York 1995.
17. Garalde, D. R., O'Donnell, C. R., Maitra, R. D., Wiberg, D. M., Wang, G., Dunbar, W. B., IEEE Trans. Control Syst. Technol. 2013, DOI: 10.1109/TCST.2012.2224349.
18. Loman, N. J., Misra, R. V., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J., Pallen, M. J., Nat. Biotechnol. 2012, 30, 434-439.
19. Loman, N. J., Constantinidou, C., Chan, J. Z., Halachev, M., Sergeant, M., Penn, C. W., Robinson, E. R., Pallen, M. J., Nat. Rev. Microbiol. 2012, 10, 599-606.
20. Brockman, W., Alvarez, P., Young, S., Garber, M., Giannoukos, G., Lee, W., Russ, C., Lander, E., Nusbaum, C., Jaffe, D., Genome Res. 2008, 18, 763-770.
21. Ewing, B., Green, P., Genome Res. 1998, 8, 186-194.
22. Holt, R. A., Jones, S. J. M., Genome Res. 2008, 18, 839-846.