Titration-free massively parallel pyrosequencing using trace amounts of starting material

Nucleic Acids Research

Volumn 38, Issue 13, 2010, Pages

  Zheng, Zongli ^a   Advani, Abdolreza ^b   Melefors, Öjar ^a,b   Glavas, Steve ^b   Nordström, Henrik ^a,b   Ye, Weimin ^a   Engstrand, Lars ^a,b   Andersson, Anders F ^b,c  

^a KAROLINSKA INSTITUTE   (Sweden)

^b SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DOUBLE STRANDED DNA; TRACE METAL; TRANSCRIPTOME;

ARTICLE; BIOMASS; DNA LIBRARY; DNA PROBE; EMULSION; METAGENOMICS; MOLECULAR CLONING; POISSON DISTRIBUTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; STATISTICS;

GENE LIBRARY; OLIGONUCLEOTIDE PROBES; POISSON DISTRIBUTION; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 77955264391     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq332     Document Type: Article

References (19)

1. Harris, T.D., Buzby, P.R., Babcock, H., Beer, E., Bowers, J., Braslavsky, I., Causey, M., Colonell, J., Dimeo, J., Efcavitch, J.W. et al. (2008) Single-molecule DNA sequencing of a viral genome. Science, 320, 106-109.
2. Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., Smith, G.P., Milton, J., Brown, C.G., Hall, K.P., Evers, D.J., Barnes, C.L., Bignell, H.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
3. Shendure, J., Porreca, G.J., Reppas, N.B., Lin, X., McCutcheon, J.P., Rosenbaum, A.M., Wang, M.D., Zhang, K., Mitra, R.D. and Church, G.M. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728-1732.
4. 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. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
5. Clarke, J., Wu, H.C., Jayasinghe, L., Patel, A., Reid, S. and Bayley, H. (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol., 4, 265-270.
6. Meyer, M., Briggs, A.W., Maricic, T., Hober, B., Hoffner, B., Krause, J., Weihmann, A., Paabo, S. and Hofreiter, M. (2008) From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res., 36, e5.
7. White, R.A. 3rd, Blainey, P.C., Fan, H.C. and Quake, S.R. (2009) Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics, 10, 116.
8. Linnarsson, S. (2010) Recent advances in DNA sequencing methods-general principles of sample preparation. Exp. Cell Res., doi:101016/j.physletb.2003.10.071.
9. Wiley, G., Macmil, S., Qu, C., Wang, P., Xing, Y., White, D., Li, J., White, J.D., Domingo, A. and Roe, B.A. (2009) Methods for generating shotgun and mixed shotgun/paired-end libraries for the 454 DNA sequencer. Curr. Protoc. Hum. Genet., Chapter 18, Unit181.
10. R Development Core Team. (2009) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
11. Oh, J.D., Kling-Backhed, H., Giannakis, M., Xu, J., Fulton, R.S., Fulton, L.A., Cordum, H.S., Wang, C., Elliott, G., Edwards, J. et al. (2006) The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression. Proc. Natl Acad. Sci. USA, 103, 9999-10004.
12. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
13. Blow, M.J., Zhang, T., Woyke, T., Speller, C.F., Krivoshapkin, A., Yang, D.Y., Derevianko, A. and Rubin, E.M. (2008) Identification of ancient remains through genomic sequencing. Genome Res., 18, 1347-1353.
14. Pinard, R., de Winter, A., Sarkis, G.J., Gerstein, M.B., Tartaro, K.R., Plant, R.N., Egholm, M., Rothberg, J.M. and Leamon, J.H. (2006) Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics, 7, 216.
15. Maricic, T. and Paabo, S. (2009) Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands. Biotechniques, 46, 51-52, 54-57.
16. Kutyavin, I.V., Afonina, I.A., Mills, A., Gorn, V.V., Lukhtanov, E.A., Belousov, E.S., Singer, M.J., Walburger, D.K., Lokhov, S.G., Gall, A.A. et al. (2000) 3'-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res., 28, 655-661.
17. Sandberg, J., Stahl, P.L., Ahmadian, A., Bjursell, M.K. and Lundeberg, J. (2009) Flow cytometry for enrichment and titration in massively parallel DNA sequencing. Nucleic Acids Res., 37, e63.
18. Roche Diagnostics GmbH. (2008) GS FLX Titanium emPCR Method Manual. Roche Diagnostics, Roche Applied Science, 68298 Mannheim, Germany.
19. Syed, F., Grunenwald, H. and Caruccio, N. (2009) Optimized library preparation method for next-generation sequencing [advertising feature]. Nat. Methods, 6, i-ii.