Sequencing genomes from single cells by polymerase cloning (original) (raw)

• Shendure, J., Mitra, R.D., Varma, C. & Church, G.M. Advanced sequencing technologies: methods and goals. Nat. Rev. Genet. 5, 335–344 (2004).
  Article CAS Google Scholar
• Kyrpides, N.C. Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics 15, 773–774 (1999).
  Article CAS Google Scholar
• Moreira, D. & Lopez-Garcia, P. The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol. 10, 31–38 (2002).
  Article CAS Google Scholar
• Falkowski, P.G. & de Vargas, C. Genomics and evolution. Shotgun sequencing in the sea: a blast from the past? Science 304, 58–60 (2004).
  Article Google Scholar
• Tyson, G.W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004).
  Article CAS Google Scholar
• Venter, J.C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004).
  Article CAS Google Scholar
• DeLong, E.F. Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3, 459–469 (2005).
  Article CAS Google Scholar
• Beja, O. et al. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68, 335–345 (2002).
  Article CAS Google Scholar
• Tringe, S.G. et al. Comparative metagenomics of microbial communities. Science 308, 554–557 (2005).
  Article CAS Google Scholar
• Riesenfeld, C.S., Schloss, P.D. & Handelsman, J. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38, 525–552 (2004).
  Article CAS Google Scholar
• Rodriguez-Valera, F. Environmental genomics, the big picture? FEMS Microbiol. Lett. 231, 153–158 (2004).
  Article CAS Google Scholar
• Dean, F.B. et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA 99, 5261–5266 (2002).
  Article CAS Google Scholar
• Hosono, S. et al. Unbiased whole-genome amplification directly from clinical samples. Genome Res. 13, 954–964 (2003).
  Article CAS Google Scholar
• Paez, J.G. et al. Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res. 32, e71 (2004).
  Article Google Scholar
• Telenius, H. et al. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13, 718–725 (1992).
  Article CAS Google Scholar
• Zhang, L. et al. Whole genome amplification from a single cell: implications for genetic analysis. Proc. Natl. Acad. Sci. USA 89, 5847–5851 (1992).
  Article CAS Google Scholar
• Dietmaier, W. et al. Multiple mutation analyses in single tumor cells with improved whole genome amplification. Am. J. Pathol. 154, 83–95 (1999).
  Article CAS Google Scholar
• Nelson, J.R. et al. TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. Biotechniques Suppl., 44–47 (2002).
• Lage, J.M. et al. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res. 13, 294–307 (2003).
  Article CAS Google Scholar
• Handyside, A.H. et al. Isothermal whole genome amplification from single and small numbers of cells: a new era for preimplantation genetic diagnosis of inherited disease. Mol. Hum. Reprod. 10, 767–772 (2004).
  Article CAS Google Scholar
• Hellani, A. et al. Multiple displacement amplification on single cell and possible PGD applications. Mol. Hum. Reprod. 10, 847–852 (2004).
  Article CAS Google Scholar
• Sorensen, K.J., Turteltaub, K., Vrankovich, G., Williams, J. & Christian, A.T. Whole-genome amplification of DNA from residual cells left by incidental contact. Anal. Biochem. 324, 312–314 (2004).
  Article CAS Google Scholar
• Jiang, Z., Zhang, X., Deka, R. & Jin, L. Genome amplification of single sperm using multiple displacement amplification. Nucleic Acids Res. 33, e91 (2005).
  Article Google Scholar
• Detter, J.C. et al. Isothermal strand-displacement amplification applications for high-throughput genomics. Genomics 80, 691–698 (2002).
  Article CAS Google Scholar
• Raghunathan, A. et al. Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol. 71, 3342–3347 (2005).
  Article CAS Google Scholar
• Hutchison, C.A., III, Smith, H.O., Pfannkoch, C. & Venter, J.C. Cell-free cloning using {phi}29 DNA polymerase. Proc. Natl. Acad. Sci. USA 102, 17332–17336 (2005).
  Article CAS Google Scholar
• Hafner, G.J., Yang, I.C., Wolter, L.C., Stafford, M.R. & Giffard, P.M. Isothermal amplification and multimerization of DNA by Bst DNA polymerase. Biotechniques 30, 852–856, 858, 860 passim (2001).
  Article CAS Google Scholar
• Gray, J.W. et al. High-speed chromosome sorting. Science 238, 323–329 (1987).
  Article CAS Google Scholar
• Chisholm, S.W., Olson, R.J., Zettler, E.R. & Goericke, R. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334, 340–343 (1988).
  Article Google Scholar
• Partensky, F., Hess, W.R. & Vaulot, D. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63, 106–127 (1999).
  CAS PubMed PubMed Central Google Scholar
• Rocap, G. et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042–1047 (2003).
  Article CAS Google Scholar
• Dufresne, A. et al. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc. Natl. Acad. Sci. USA 100, 10020–10025 (2003).
  Article CAS Google Scholar
• Urbach, E. & Chisholm, S.W. Genetic diversity in Prochlorococcus Populations flow-cytometrically sorted from the Sargasso Sea and Gulf Stream. Limnol. Oceanogr. 43, 1615–1630 (1998).
  Article CAS Google Scholar
• Panelli, S., Damiani, G., Espen, L. & Sgaramella, V. Ligation overcomes terminal underrepresentation in multiple displacement amplification of linear DNA. Biotechniques 39 174, 176, 178 passim (2005).
  Article CAS Google Scholar
• Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732 (2005).
  Article CAS Google Scholar
• Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005).
  Article CAS Google Scholar
• Thompson, J.R. et al. Genotypic diversity within a natural coastal bacterioplankton population. Science 307, 1311–1313 (2005).
  Article CAS Google Scholar
• Acinas, S.G. et al. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430, 551–554 (2004).
  Article CAS Google Scholar
• Dean, F.B., Nelson, J.R., Giesler, T.L. & Lasken, R.S. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 11, 1095–1099 (2001).
  Article CAS Google Scholar
• Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA 97, 5978–5983 (2000).
  Article CAS Google Scholar