A method for counting PCR template molecules with application to next-generation sequencing

Nucleic Acids Research

Volumn 39, Issue 12, 2011, Pages

  Casbon, James A ^a   Osborne, Robert J ^a   Brenner, Sydney ^a,b   Lichtenstein, Conrad P ^a  

^a BABRAHAM INSTITUTE   (United Kingdom)

^b KING'S COLLEGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE;

ARTICLE; DNA SEQUENCE; DNA STRUCTURE; DNA TEMPLATE; ERROR; FALSE POSITIVE RESULT; GENE AMPLIFICATION; GENOTYPE; HUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

ALLELES; GENE LIBRARY; GENOTYPE; HUMANS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; TEMPLATES, GENETIC;

EID: 79960226263     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr217     Document Type: Article

References (28)

1. Kozarewa, I., Ning, Z., Quail, M.A., Sanders, M.J., Berriman, M. and Turner, D.J. (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods, 6, 291-295.
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. Korbel, J.O., Urban, A.E., Affourtit, J.P., Godwin, B., Grubert, F., Simons, J.F., Kim, P.M., Palejev, D., Carriero, N.J., Du, L. et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science, 318, 420-426. (Pubitemid 47614521)
4. Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C. et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol., 27, 182-189.
5. Johnson, D.S., Mortazavi, A., Myers, R.M. and Wold, B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502. (Pubitemid 46906620)
6. Chiu, R.W., Chan, K.C., Gao, Y., Lau, V.Y., Zheng, W., Leung, T.Y., Foo, C.H., Xie, B., Tsui, N.B., Lun, F.M. et al. (2008) Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc. Natl Acad. Sci. USA, 105, 20458-20463.
7. Fan, H.C., Blumenfeld, Y.J., Chitkara, U., Hudgins, L. and Quake, S.R. (2008) Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc. Natl Acad. Sci. USA, 105, 16266-16271.
8. Bainbridge, M.N., Wang, M., Burgess, D.L., Kovar, C., Rodesch, M.J., D'Ascenzo, M., Kitzman, J., Wu, Y.Q., Newsham, I., Richmond, T.A. et al. (2010) Whole exome capture in solution with 3 Gbp of data. Genome Biol., 11, R62.
9. Cornish-Bowden, A. (1985) Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res., 13, 3021-3030.
10. Charalambides, C.A. and Charalambides, C.A. (2005) Combinatorial Methods in Discrete Distributions. John Wiley and Sons.
11. McKinney, E.H. (1966) Generalized Birthday Problem. Am. Math. Monthly, 73, 385-387.
12. R Development Core Team (2008) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
13. Wickham, H. (2009) ggplot2: Elegant Graphics for Data Analysis. Springer, New York.
14. Nejentsev, S., Walker, N., Riches, D., Egholm, M. and Todd, J.A. (2009) Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science, 324, 387-389.
15. Valouev, A., Ichikawa, J., Tonthat, T., Stuart, J., Ranade, S., Peckham, H., Zeng, K., Malek, J.A., Costa, G., McKernan, K. et al. (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res., 18, 1051-1063. (Pubitemid 351931156)
16. 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. (Pubitemid 41613494)
17. Lin, Z., Cui, X. and Li, H. (1996) Multiplex genotype determination at a large number of gene loci. Proc. Natl Acad. Sci. USA, 93, 2582-2587. (Pubitemid 26104390)
18. Brownie, J., Shawcross, S., Theaker, J., Whitcombe, D., Ferrie, R., Newton, C. and Little, S. (1997) The elimination of primer-dimer accumulation in PCR. Nucleic Acids Res., 25, 3235-3241. (Pubitemid 27338681)
19. Hamady, M., Walker, J.J., Harris, J.K., Gold, N.J. and Knight, R. (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods, 5, 235-237. (Pubitemid 351325646)
20. Chiang, D.Y., Getz, G., Jaffe, D.B., O'Kelly, M.J., Zhao, X., Carter, S.L., Russ, C., Nusbaum, C., Meyerson, M. and Lander, E.S. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6, 99-103.
21. Levin, J.Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D.A., Friedman, N., Gnirke, A. and Regev, A. (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods, 7, 709-715.
22. Wilhelm, B.T., Marguerat, S., Watt, S., Schubert, F., Wood, V., Goodhead, I., Penkett, C.J., Rogers, J. and Bahler, J. (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature, 453, 1239-1243. (Pubitemid 351913597)
23. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628. (Pubitemid 351911867)
24. Sultan, M., Schulz, M.H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D. et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 321, 956-960.
25. Zagordi, O., Klein, R., Daumer, M. and Beerenwinkel, N. (2010) Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res., 38, 7400-7409.
26. Hanage, W.P., Fraser, C., Tang, J., Connor, T.R. and Corander, J. (2009) Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science, 324, 1454-1457.
27. Yooseph, S., Sutton, G., Rusch, D.B., Halpern, A.L., Williamson, S.J., Remington, K., Eisen, J.A., Heidelberg, K.B., Manning, G., Li, W. et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol., 5, e16.
28. Ley, T.J., Mardis, E.R., Ding, L., Fulton, B., McLellan, M.D., Chen, K., Dooling, D., Dunford-Shore, B.H., McGrath, S., Hickenbotham, M. et al. (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456, 66-72.