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Volumn 5, Issue , 2015, Pages

Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

Author keywords

[No Author keywords available]

Indexed keywords

CONTROLLED STUDY; DNA BARCODING; EXPERIMENTAL MODEL; GENE AMPLIFICATION; HIGH THROUGHPUT SEQUENCING; POLYMERASE CHAIN REACTION; QUANTITATIVE STUDY; STOCHASTIC MODEL; BIOLOGY; CELL LINE; HUMAN; PROCEDURES; SOFTWARE; STANDARDS;

EID: 84944342666     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep14629     Document Type: Article
Times cited : (64)

References (34)
  • 1
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • Polz, M. F. and Cavanaugh, C. M. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64, 3724-3730 (1998).
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 2
    • 10444268966 scopus 로고    scopus 로고
    • Reevaluation and Reduction of a PCR Bias Caused by Reannealing of Templates
    • Kurata, S. et al. Reevaluation and Reduction of a PCR Bias Caused by Reannealing of Templates. Appl. Environ. Microbiol. 70, 7545-7549 (2004).
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 7545-7549
    • Kurata, S.1
  • 3
    • 84893192555 scopus 로고    scopus 로고
    • DNA polymerase preference determines PCR priming efficiency
    • Pan, W. et al. DNA polymerase preference determines PCR priming efficiency. BMC Biotechnol. 14, 10 (2014).
    • (2014) BMC Biotechnol. , vol.14 , pp. 10
    • Pan, W.1
  • 4
    • 80052520350 scopus 로고    scopus 로고
    • Barcoding bias in high-throughput multiplex sequencing of miRNA
    • Alon, S. et al. Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res. 21, 1506-1511 (2011).
    • (2011) Genome Res. , vol.21 , pp. 1506-1511
    • Alon, S.1
  • 5
    • 0029806142 scopus 로고    scopus 로고
    • Identification of non-amplifying CYP21 genes when using PCR-based diagnosis of 21-hydroxylase deficiency in congenital adrenal hyperplasia (CAH) affected pedigrees
    • Day, D. Identification of non-amplifying CYP21 genes when using PCR-based diagnosis of 21-hydroxylase deficiency in congenital adrenal hyperplasia (CAH) affected pedigrees. Hum. Mol. Genet. 5, 2039-2048 (1996).
    • (1996) Hum. Mol. Genet. , vol.5 , pp. 2039-2048
    • Day, D.1
  • 6
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    • Aird, D. et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12, R18 (2011).
    • (2011) Genome Biol. , vol.12 , pp. R18
    • Aird, D.1
  • 7
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1
  • 8
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-80 (2005).
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1
  • 10
    • 45549088326 scopus 로고    scopus 로고
    • The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
    • Nagalakshmi, U. et al. The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing. Science (80-. ). 320, 1344-1349 (2008).
    • (2008) Science (80-. ) , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1
  • 11
    • 19444379602 scopus 로고    scopus 로고
    • Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR
    • Miner, B. E. Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR. Nucleic Acids Res. 32, e135-e135 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. e135-e135
    • Miner, B.E.1
  • 13
    • 79960226263 scopus 로고    scopus 로고
    • A method for counting PCR template molecules with application to next-generation sequencing
    • Casbon, J. A., Osborne, R. J., Brenner, S. and Lichtenstein, C. P. A method for counting PCR template molecules with application to next-generation sequencing. Nucleic Acids Res. 39, e81-e81 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. e81-e81
    • Casbon, J.A.1    Osborne, R.J.2    Brenner, S.3    Lichtenstein, C.P.4
  • 14
    • 84856484968 scopus 로고    scopus 로고
    • Counting absolute numbers of molecules using unique molecular identifiers
    • Kivioja, T. et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods 9, 72-74 (2011).
    • (2011) Nat. Methods , vol.9 , pp. 72-74
    • Kivioja, T.1
  • 15
    • 84892159495 scopus 로고    scopus 로고
    • Preparing Unbiased T-Cell Receptor and Antibody cDNA Libraries for the Deep Next Generation Sequencing Profiling
    • Mamedov, I. Z. et al. Preparing Unbiased T-Cell Receptor and Antibody cDNA Libraries for the Deep Next Generation Sequencing Profiling. Front. Immunol. 4, 456 (2013).
    • (2013) Front. Immunol. , vol.4 , pp. 456
    • Mamedov, I.Z.1
  • 16
    • 84901857468 scopus 로고    scopus 로고
    • Towards error-free profiling of immune repertoires
    • Shugay, M. et al. Towards error-free profiling of immune repertoires. Nat. Methods 11, 653-5 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 653-655
    • Shugay, M.1
  • 17
    • 0032302901 scopus 로고    scopus 로고
    • Estimation of the parameters of a branching process from migrating binomial observations
    • Jacob, C. and Peccoud, J. Estimation of the parameters of a branching process from migrating binomial observations. Adv. Appl. Probab. 30, 948-967 (1998).
    • (1998) Adv. Appl. Probab. , vol.30 , pp. 948-967
    • Jacob, C.1    Peccoud, J.2
  • 18
    • 3142666986 scopus 로고    scopus 로고
    • Modelling the PCR Amplification Process by a Size-Dependent Branching Process and Estimation of the Efficiency
    • Lalam, N., Jacob, C. and Jagers, P. Modelling the PCR Amplification Process by a Size-Dependent Branching Process and Estimation of the Efficiency. Adv. Appl. Probab. 36, 602-615 (2004).
    • (2004) Adv. Appl. Probab. , vol.36 , pp. 602-615
    • Lalam, N.1    Jacob, C.2    Jagers, P.3
  • 19
    • 79960143568 scopus 로고    scopus 로고
    • Inference for quantitation parameters in polymerase chain reactions via branching processes with random effects
    • Hanlon, B. and Vidyashankar, A. N. Inference for Quantitation Parameters in Polymerase Chain Reactions via Branching Processes With Random Effects. J. Am. Stat. Assoc. 106, 525-533 (2011).
    • (2011) J. Am. Stat. Assoc. , vol.106 , pp. 525-533
    • Hanlon, B.1    Vidyashankar, A.N.2
  • 20
    • 0029826566 scopus 로고    scopus 로고
    • Efficiency of DNA replication in the polymerase chain reaction
    • Stolovitzky, G. and Cecchi, G. Efficiency of DNA replication in the polymerase chain reaction. Proc. Natl. Acad. Sci. USA 93, 12947-12952 (1996).
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 12947-12952
    • Stolovitzky, G.1    Cecchi, G.2
  • 21
    • 3142571337 scopus 로고    scopus 로고
    • Principles of rapid polymerase chain reactions: Mathematical modeling and experimental verification
    • Whitney, S. E., Sudhir, A., Nelson, R. M. and Viljoen, H. J. Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification. Comput. Biol. Chem. 28, 195-209 (2004).
    • (2004) Comput. Biol. Chem. , vol.28 , pp. 195-209
    • Whitney, S.E.1    Sudhir, A.2    Nelson, R.M.3    Viljoen, H.J.4
  • 22
    • 1842477277 scopus 로고    scopus 로고
    • Mathematical models of diffusion-constrained polymerase chain reactions: Basis of high-throughput nucleic acid assays and simple self-organizing systems
    • Aach, J. and Church, G. M. Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems. J. Theor. Biol. 228, 31-46 (2004).
    • (2004) J. Theor. Biol. , vol.228 , pp. 31-46
    • Aach, J.1    Church, G.M.2
  • 23
    • 27744483352 scopus 로고    scopus 로고
    • Mathematical model of real-time PCR kinetics
    • Gevertz, J. L., Dunn, S. M. and Roth, C. M. Mathematical model of real-time PCR kinetics. Biotechnol. Bioeng. 92, 346-355 (2005).
    • (2005) Biotechnol. Bioeng. , vol.92 , pp. 346-355
    • Gevertz, J.L.1    Dunn, S.M.2    Roth, C.M.3
  • 24
    • 84864940083 scopus 로고    scopus 로고
    • Stepwise kinetic equilibrium models of quantitative polymerase chain reaction
    • Cobbs, G. Stepwise kinetic equilibrium models of quantitative polymerase chain reaction. BMC Bioinformatics 13, 203 (2012).
    • (2012) BMC Bioinformatics , vol.13 , pp. 203
    • Cobbs, G.1
  • 25
    • 33645844853 scopus 로고    scopus 로고
    • A quantitative model of error accumulation during PCR amplification
    • Pienaar, E., Theron, M., Nelson, M. and Viljoen, H. A quantitative model of error accumulation during PCR amplification. Comput. Biol. Chem. 30, 102-111 (2006).
    • (2006) Comput. Biol. Chem. , vol.30 , pp. 102-111
    • Pienaar, E.1    Theron, M.2    Nelson, M.3    Viljoen, H.4
  • 26
    • 0029819518 scopus 로고    scopus 로고
    • A mathematical model and a computerized simulation of PCR using complex templates
    • Rubin, E. A mathematical model and a computerized simulation of PCR using complex templates. Nucleic Acids Res. 24, 3538-3545 (1996).
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3538-3545
    • Rubin, E.1
  • 27
    • 0024578237 scopus 로고
    • Delineation of several DR-restricted tetanus toxin T cell epitopes
    • Demotz, S. et al. Delineation of several DR-restricted tetanus toxin T cell epitopes. J. Immunol. 142, 394-402 (1989).
    • (1989) J. Immunol. , vol.142 , pp. 394-402
    • Demotz, S.1
  • 28
    • 84874671063 scopus 로고    scopus 로고
    • Decombinator: A tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine
    • Thomas, N., Heather, J., Ndifon, W., Shawe-Taylor, J. and Chain, B. Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics 29, 542-550 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 542-550
    • Thomas, N.1    Heather, J.2    Ndifon, W.3    Shawe-Taylor, J.4    Chain, B.5
  • 29
    • 80052827649 scopus 로고    scopus 로고
    • Chapter 24, Unit 24.2 (John Wiley and Sons, Inc.)
    • Hall, B. et al. In Curr. Protoc. Mol. Biol. Chapter 24, Unit 24.2 (John Wiley and Sons, Inc., 2009).
    • (2009) Curr. Protoc. Mol. Biol
    • Hall, B.1
  • 30
    • 0029935969 scopus 로고    scopus 로고
    • Theoretical uncertainty of measurements using quantitative polymerase chain reaction
    • Peccoud, J. and Jacob, C. Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys. J. 71, 101-108 (1996).
    • (1996) Biophys. J. , vol.71 , pp. 101-108
    • Peccoud, J.1    Jacob, C.2
  • 31
    • 78650937547 scopus 로고    scopus 로고
    • Paired analysis of TCR? and TCR? Chains at the single-cell level in mice
    • Dash, P. et al. Paired analysis of TCR? and TCR? chains at the single-cell level in mice. J. Clin. Invest. 121, 288-295 (2011).
    • (2011) J. Clin. Invest. , vol.121 , pp. 288-295
    • Dash, P.1
  • 32
    • 84856398949 scopus 로고    scopus 로고
    • Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes
    • Shiroguchi, K., Jia, T. Z., Sims, P. A. and Xie, X. S. Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc. Natl. Acad. Sci. 109, 1347-1352 (2012).
    • (2012) Proc. Natl. Acad. Sci. , vol.109 , pp. 1347-1352
    • Shiroguchi, K.1    Jia, T.Z.2    Sims, P.A.3    Xie, X.S.4
  • 33
    • 84882432416 scopus 로고    scopus 로고
    • Genetic measurement of memory B-cell recall using antibody repertoire sequencing
    • Vollmers, C., Sit, R. V., Weinstein, J. A., Dekker, C. L. and Quake, S. R. Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc. Natl. Acad. Sci. 110, 13463-13468 (2013).
    • (2013) Proc. Natl. Acad. Sci. , vol.110 , pp. 13463-13468
    • Vollmers, C.1    Sit, R.V.2    Weinstein, J.A.3    Dekker, C.L.4    Quake, S.R.5
  • 34
    • 84901857468 scopus 로고    scopus 로고
    • Towards error-free profiling of immune repertoires
    • Shugay, M. et al. Towards error-free profiling of immune repertoires. Nat. Methods 11, 653-655 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 653-655
    • Shugay, M.1


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