Methods for generating shotgun and mixed shotgun/paired-end libraries for the 454 DNA sequencer

Current Protocols in Human Genetics

Volumn , Issue SUPPL. 61, 2009, Pages

  Wiley, Graham ^a   Macmil, Simone ^a   Qu, Chunmei ^a   Wang, Ping ^a   Xing, Yanbo ^a   White, Doug ^a   Li, Jianfeng ^a   White, James D ^a   Domingo, Alexander ^b   Roe, Bruce A ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b Roche Diagnostics Corporation   (United States)

Author keywords

DNA Library; Paired end; Pyrosequencing; Shotgun

Indexed keywords

DIDEOXYNUCLEOTIDE; DNA; DNA FRAGMENT;

DNA DETERMINATION; DNA LIBRARY; DNA PURIFICATION; DNA SEQUENCE; DNA SEQUENCER; FLUORESCENCE; GENE AMPLIFICATION; GENE TECHNOLOGY; HIGH THROUGHPUT SCREENING; HUMAN; LABORATORY AUTOMATION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; REVIEW;

DNA; GENE LIBRARY; GENOMICS; MODELS, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 65249153474     PISSN: 19348266     EISSN: 19348258     Source Type: Journal    
DOI: 10.1002/0471142905.hg1801s61     Document Type: Review

References (13)

1. Dahl, F., Stenberg, J., Fredriksson, S., Welch, K., Zhang, M., Nilsson, M., Bicknell, D., Bodmer, W.F., Davis, R.W., and Ji, H. 2007. Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc. Natl. Acad. Sci. U.S.A. 104:9387-9392.
2. Hawkins, T.L., O'Connor-Morin, T., Roy, A., and Santillan, C. 1994. DNA purification and isolation using a solid-phase. Nucleic Acids Res. 22:4543-4544.
3. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., Dewell, S.B., Du, L., Fierro, J.M., Gomes, X.V., Godwin, B.C., He, W., Helgesen, S., Ho, C.H., Irzyk, G.P., Jando, S.C., Alenquer, M.L., Jarvie, T.P., Jirage, K.B., Kim, J.B., Knight, J.R., Lanza, J.R., Leamon, J.H., Lefkowitz, S.M., Lei, M., Li, J., Lohman, K.L., Lu, H., Makhijani, V.B., McDade, K.E., McKenna, M.P., Myers, E.W., Nickerson, E., Nobile, J.R., Plant, R., Puc, B.P., Ronan, M.T., Roth, G.T., Sarkis, G.J., Simons, J.F., Simpson, J.W., Srinivasan, M., Tartaro, K.R., Tomasz, A., Vogt, K.A., Volkmer, G.A., Wang, S.H., Wang, Y., Weiner, M.P., Yu, P., Begley, R.F., and Rothberg, J.M. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
4. Meyer, M., Briggs, A.W., Maricic, T., Höber, B., Höffner, B., Krause, J., Weihmann, A., Pääbo, S., and Hofreiter, M. 2008. From micrograms to picograms: Quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res. 36:e5.
5. Nakano, M., Komatsu, J., Matsuura, S., Takashima, K., Katsura, S., and Mizuno, A. 2003. Singlemolecule PCR using water-in-oil emulsion. J. Biotechnol. 102:117-124.
6. Ng, P., Tan, J.J., Ooi, H.S., Lee, Y.L., Chiu, K.P., Fullwood, M.J., Srinivasan, K.G., Perbost, C., Du, L., Sung, W.K., Wei, C.L., and Ruan, Y. 2006. Multiplex sequencing of pairedend ditags (MS-PET): A strategy for the ultrahigh- throughput analysis of transcriptomes and genomes. Nucleic Acids Res. 34:e84.
7. Nyrén, P. and Lundin, A. 1985. Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis. Anal. Biochem. 151:504-509.
8. Nyrén, P. 1987. Enzymatic method for continuous monitoring of DNA polymerase activity. Anal. Biochem. 167:235-238.
9. Nyrén, P., Pettersson, B., and Uhlén, M. 1993. Solid phase DNAminisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. Anal. Biochem. 208:171-175.
10. Oefner, P.J., Hunicke-Smith, S.P., Chiang, L., Dietrich, F., Mulligan, J., and Davis, R.W. 1996. Efficient random subcloning of DNA sheared in a recirculating point-sink flow system. Nucleic Acids Res. 24:3879-3886.
11. Roe, B. 2004. Shotgun library construction for DNA sequencing In Methods in Molecular Biology, vol 255: Bacterial Artificial Chromosomes, Volume 1: Library Construction, Physical Mapping, and Sequencing (S. Zhao and M. Stodolsky, eds.) pp. 171-187. Humana Press, Totowa, New Jersey.
12. Roe, B.A., Crabtree, J.S., and Khan, A.S. 1996. DNA Isolation and Sequencing (Essential Techniques Series). John Wiley & Sons, New York.
13. Ronaghi, M., Uhlén, M. and Nyrén, P. 1998. DNA Sequencing: A sequencing method based on real-time pyrophosphate. Science 281:363-365