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Computational and Mathematical Methods in Medicine
Volume 2013 (2013), Article ID 491612, 13 pages
http://dx.doi.org/10.1155/2013/491612
Research Article

Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2

Received 6 May 2013; Accepted 30 July 2013

Academic Editor: Yanxin Huang

Copyright © 2013 Wadim L. Matochko and Ratmir Derda. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. K. Scott and G. P. Smith, “Searching for peptide ligands with an epitope library,” Science, vol. 249, no. 4967, pp. 386–390, 1990. View at Google Scholar · View at Scopus
  2. G. P. Smith and V. A. Petrenko, “Phage display,” Chemical Reviews, vol. 97, no. 2, pp. 391–410, 1997. View at Google Scholar · View at Scopus
  3. A. D. Ellington and J. W. Szostak, “In vitro selection of RNA molecules that bind specific ligands,” Nature, vol. 346, no. 6287, pp. 818–822, 1990. View at Publisher · View at Google Scholar · View at Scopus
  4. C. Tuerk and L. Gold, “Systemic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase,” Science, vol. 249, no. 4968, pp. 505–510, 1990. View at Google Scholar · View at Scopus
  5. E. Dias-Neto, D. N. Nunes, R. J. Giordano et al., “Next-generation phage display: integrating and comparing available molecular tools to enable costeffective high-throughput analysis,” PLoS ONE, vol. 4, no. 12, Article ID e8338, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. W. L. Matochko, K. Chu, B. Jin, S. W. Lee, G. M. Whitesides, and R. Derda, “Deep sequencing analysis of phage libraries using Illumina platform,” Methods, vol. 58, pp. 47–55, 2012. View at Google Scholar
  7. A. Ernst, D. Gfeller, Z. Kan et al., “Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing,” Molecular BioSystems, vol. 6, no. 10, pp. 1782–1790, 2010. View at Publisher · View at Google Scholar · View at Scopus
  8. G. V. Kupakuwana, J. E. Crill, M. P. McPike, and P. N. Borer, “Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing,” PLoS ONE, vol. 6, no. 5, Article ID e19395, 2011. View at Publisher · View at Google Scholar · View at Scopus
  9. P. A. C. 'T Hoen, S. M. G. Jirka, B. R. Ten Broeke et al., “Phage display screening without repetitious selection rounds,” Analytical Biochemistry, vol. 421, no. 2, pp. 622–631, 2012. View at Publisher · View at Google Scholar · View at Scopus
  10. H. Zhang, A. Torkamani, T. M. Jones, D. I. Ruiz, J. Pons, and R. A. Lerner, “Phenotype-information-phenotype cycle for deconvolution of combinatorial antibody libraries selected against complex systems,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 33, pp. 13456–13461, 2011. View at Publisher · View at Google Scholar · View at Scopus
  11. R. Derda, S. K. Y. Tang, S. C. Li, S. Ng, W. Matochko, and M. R. Jafari, “Diversity of phage-displayed libraries of peptides during panning and amplification,” Molecules, vol. 16, no. 2, pp. 1776–1803, 2011. View at Publisher · View at Google Scholar · View at Scopus
  12. R. W. Hamming, “Error detecting and error correcting codes,” Bell System Technical Journal, vol. 29, pp. 147–160, 1950. View at Google Scholar
  13. D. J. Rodi, A. S. Soares, and L. Makowski, “Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries,” Journal of Molecular Biology, vol. 322, no. 5, pp. 1039–1052, 2002. View at Publisher · View at Google Scholar · View at Scopus
  14. L. Makowski, “Quantitative analysis of peptide libraries,” in Phage Nanobiotechnology, chapter 3, 2011. View at Publisher · View at Google Scholar
  15. C. E. Shannon, “A mathematical theory of communication,” Bell System Technical Journal, vol. 27, pp. 379–423, 1948. View at Google Scholar
  16. U. Ravn, F. Gueneau, L. Baerlocher et al., “By-passing in vitro screening: next generation sequencing technologies applied to antibody display and in silico candidate selection,” Nucleic Acids Research, vol. 38, no. 21, 2010. View at Publisher · View at Google Scholar · View at Scopus
  17. T. Kim, M. S. Tyndel, H. Huang et al., “MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets,” Nucleic Acids Research, vol. 40, no. 6, article e47, 2012. View at Publisher · View at Google Scholar · View at Scopus
  18. J. A. Weinstein, N. Jiang, R. A. White III, D. S. Fisher, and S. R. Quake, “High-throughput sequencing of the zebrafish antibody repertoire,” Science, vol. 324, no. 5928, pp. 807–810, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. B. J. DeKosky, G. C. Ippolito, R. P. Deschner et al. et al., “High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire,” Nature Biotechnology, vol. 31, pp. 166–169, 2013. View at Google Scholar
  20. B. Levitan, “Stochastic modeling and optimization of phage display,” Journal of Molecular Biology, vol. 277, no. 4, pp. 893–916, 1998. View at Publisher · View at Google Scholar · View at Scopus
  21. C. S. Riesenfeld, P. D. Schloss, and J. Handelsman, “Metagenomics: genomic analysis of microbial communities,” Annual Review of Genetics, vol. 38, pp. 525–552, 2004. View at Publisher · View at Google Scholar · View at Scopus
  22. M. L. Sogin, H. G. Morrison, J. A. Huber et al., “Microbial diversity in the deep sea and the underexplored ‘rare biosphere’,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 32, pp. 12115–12120, 2006. View at Publisher · View at Google Scholar · View at Scopus
  23. F. Bäckhed, R. E. Ley, J. L. Sonnenburg, D. A. Peterson, and J. I. Gordon, “Host-bacterial mutualism in the human intestine,” Science, vol. 307, no. 5717, pp. 1915–1920, 2005. View at Publisher · View at Google Scholar · View at Scopus
  24. N. Beerenwinkel and O. Zagordi, “Ultra-deep sequencing for the analysis of viral populations,” Current Opinion in Virology, vol. 1, no. 5, pp. 413–418, 2011. View at Publisher · View at Google Scholar · View at Scopus
  25. J. A. Huber, D. B. Mark Welch, H. G. Morrison et al., “Microbial population structures in the deep marine biosphere,” Science, vol. 318, no. 5847, pp. 97–100, 2007. View at Publisher · View at Google Scholar · View at Scopus
  26. A. Wilm, P. P. K. Aw, D. Bertrand et al., “LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets,” Nucleic Acids Research, vol. 40, pp. 11189–11201, 2012. View at Google Scholar
  27. P. J. Turnbaugh, C. Quince, J. J. Faith et al., “Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 16, pp. 7503–7508, 2010. View at Publisher · View at Google Scholar · View at Scopus
  28. C. Quince, A. Lanzén, T. P. Curtis et al., “Accurate determination of microbial diversity from 454 pyrosequencing data,” Nature Methods, vol. 6, no. 9, pp. 639–641, 2009. View at Publisher · View at Google Scholar · View at Scopus
  29. S. J. Watson, M. R. A. Welkers, D. P. Depledge et al., “Viral population analysis and minority-variant detection using short read next-generation sequencing,” Philosophical Transactions of the Royal Society B, vol. 368, no. 1614, Article ID 20120205, 2013. View at Publisher · View at Google Scholar
  30. D. R. Bentley, S. Balasubramanian, H. P. Swerdlow et al. et al., “Accurate whole human genome sequencing using reversible terminator chemistry,” Nature, vol. 456, pp. 53–59, 2008. View at Google Scholar
  31. K. Nakamura, T. Oshima, T. Morimoto et al., “Sequence-specific error profile of Illumina sequencers,” Nucleic Acids Research, vol. 39, no. 13, 2011. View at Publisher · View at Google Scholar · View at Scopus
  32. M. A. Quail, I. Kozarewa, F. Smith et al., “A large genome center's improvements to the Illumina sequencing system,” Nature Methods, vol. 5, no. 12, pp. 1005–1010, 2008. View at Publisher · View at Google Scholar · View at Scopus
  33. O. Zagordi, R. Klein, M. Däumer, and N. Beerenwinkel, “Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies,” Nucleic Acids Research, vol. 38, no. 21, pp. 7400–7409, 2010. View at Publisher · View at Google Scholar · View at Scopus
  34. M. W. Schmitt, S. R. Kennedy, J. J. Salk, E. J. Fox, J. B. Hiatt, and L. A. Loeb, “Detection of ultra-rare mutations by next-generation sequencing,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, pp. 14508–14513, 2012. View at Google Scholar
  35. A. Syropoulos, “Mathematics of multisets,” in Proceedings of the Workshop on Multiset Processing: Multiset Processing, Mathematical, Computer Science, and Molecular Computing Points of View, pp. 347–358, Springer, 2001.
  36. W. Arap, M. G. Kolonin, M. Trepel et al., “Steps toward mapping the human vasculature by phage display,” Nature Medicine, vol. 8, no. 2, pp. 121–127, 2002. View at Publisher · View at Google Scholar · View at Scopus
  37. S. Blond-Elguindi, S. E. Cwirla, W. J. Dower et al., “Affinity panning of a library of peptides displayed on bacteriophages reveals the binding specificity of BiP,” Cell, vol. 75, no. 4, pp. 717–728, 1993. View at Publisher · View at Google Scholar · View at Scopus
  38. S. Cox, E. Rosten, J. Monypenny et al., “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nature Methods, vol. 9, no. 2, pp. 195–200, 2012. View at Publisher · View at Google Scholar · View at Scopus
  39. E. Rosten, G. E. Jones, and S. Cox, “Image plug-in for Bayesian analysis of blinking and bleaching,” Nature Methods, vol. 10, pp. 97–98, 2013. View at Google Scholar
  40. W. L. Matochko, S. Ng, M. R. Jafari, J. Romaniuk, S. K. Y. Tang, and R. Derda, “Uniform amplification of phage display libraries in monodisperse emulsions,” Methods, vol. 58, pp. 18–27, 2012. View at Google Scholar
  41. E. A. Peters, P. J. Schatz, S. S. Johnson, and W. J. Dower, “Membrane insertion defects caused by positive charges in the early mature region of protein pIII of filamentous phage fd can be corrected by prlA suppressors,” Journal of Bacteriology, vol. 176, no. 14, pp. 4296–4305, 1994. View at Google Scholar · View at Scopus
  42. L. A. Brammer, B. Bolduc, J. L. Kass, K. M. Felice, C. J. Noren, and M. F. Hall, “A target-unrelated peptide in an M13 phage display library traced to an advantageous mutation in the gene II ribosome-binding site,” Analytical Biochemistry, vol. 373, no. 1, pp. 88–98, 2008. View at Publisher · View at Google Scholar · View at Scopus
  43. G. A. Kuzmicheva, P. K. Jayanna, I. B. Sorokulova, and V. A. Petrenko, “Diversity and censoring of landscape phage libraries,” Protein Engineering, Design and Selection, vol. 22, no. 1, pp. 9–18, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. D. R. Wilson and B. B. Finlay, “Phage display: applications, innovations, and issues in phage and host biology,” Canadian Journal of Microbiology, vol. 44, no. 4, pp. 313–329, 1998. View at Publisher · View at Google Scholar · View at Scopus
  45. R. Derda, S. K. Y. Tang, and G. M. Whitesides, “Uniform amplification of phage with different growth characteristics in individual compartments consisting of monodisperse droplets,” Angewandte Chemie, vol. 49, no. 31, pp. 5301–5304, 2010. View at Publisher · View at Google Scholar · View at Scopus
  46. J. C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer, “Substantial biases in ultra-short read data sets from high-throughput DNA sequencing,” Nucleic Acids Research, vol. 36, no. 16, article e105, 2008. View at Publisher · View at Google Scholar · View at Scopus
  47. W. L. Matochko, S. C. Li, S. K. Y. Tang, and R. Derda, “Prospective identification of parasitic sequences in phage display screens,” Nucleic Acids Research, 2013. View at Publisher · View at Google Scholar