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Volumn 20, Issue 9, 2013, Pages 703-711

A new method for quantitative real-time polymerase chain reaction data analysis

Author keywords

background subtraction; initial DNA amount; linear regression; polymerase chain reaction efficiency; quantitative real time polymerase chain reaction

Indexed keywords

DNA;

EID: 84883686482     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0279     Document Type: Article
Times cited : (68)

References (38)
  • 2
    • 39049152539 scopus 로고    scopus 로고
    • Relative quantification of mRNA: Comparison of methods currently used for real-time PCR data analysis
    • Cikos, S., Bukovska, A., and Koppel, J. 2007. Relative quantification of mRNA: comparison of methods currently used for real-time PCR data analysis. BMC Mol. Biol. 8, 113.
    • (2007) BMC Mol. Biol , vol.8 , pp. 113
    • Cikos, S.1    Bukovska, A.2    Koppel, J.3
  • 3
    • 79955535238 scopus 로고    scopus 로고
    • Novel sensitive, specific and rapid pharmacogenomic test for the prediction of abacavir hypersensitivity reaction: HLA-B*57:01 detection by real-time PCR
    • Dello Russo, C., Lisi, L., Lofaro, A., et al. 2010. Novel sensitive, specific and rapid pharmacogenomic test for the prediction of abacavir hypersensitivity reaction: HLA-B*57:01 detection by real-time PCR. Pharmacogenomics 12, 567-576.
    • (2010) Pharmacogenomics , vol.12 , pp. 567-576
    • Dello Russo, C.1    Lisi, L.2    Lofaro, A.3
  • 4
    • 70749085913 scopus 로고    scopus 로고
    • Barcrawl and bartab: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing
    • Frank, D.N. 2009. BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinform. 10, 362.
    • (2009) BMC Bioinform , vol.10 , pp. 362
    • Frank, D.N.1
  • 5
    • 27744483352 scopus 로고    scopus 로고
    • Mathematical model of real-time PCR kinetics
    • Gevertz, J.L., Dunn, S.M., and Roth, C.M. 2005. Mathematical model of real-time PCR kinetics. Biotechnol. Bioeng. 92, 346-355.
    • (2005) Biotechnol. Bioeng , vol.92 , pp. 346-355
    • Gevertz, J.L.1    Dunn, S.M.2    Roth, C.M.3
  • 6
    • 14544302650 scopus 로고    scopus 로고
    • Fifty years of molecular (DNA/RNA) diagnostics
    • Gingeras, T.R., Higuchi, R., Kricka, L.J., et al. 2005. Fifty years of molecular (DNA/RNA) diagnostics. Clin. Chem. 51, 661-671.
    • (2005) Clin. Chem , vol.51 , pp. 661-671
    • Gingeras, T.R.1    Higuchi, R.2    Kricka, L.J.3
  • 7
    • 51349141379 scopus 로고    scopus 로고
    • A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition
    • Guescini, M., Sisti, D., Rocchi, M.B., et al. 2008. A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition. BMC Bioinform. 9, 326.
    • (2008) BMC Bioinform , vol.9 , pp. 326
    • Guescini, M.1    Sisti, D.2    Rocchi, M.B.3
  • 9
    • 15744381713 scopus 로고
    • Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions
    • Higuchi, R., Fockler, C., Dollinger, G., and Watson, R. 1993. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology (N Y) 11, 1026-1030.
    • (1993) Biotechnology (N Y) , vol.11 , pp. 1026-1030
    • Higuchi, R.1    Fockler, C.2    Dollinger, G.3    Watson, R.4
  • 10
    • 0035650542 scopus 로고    scopus 로고
    • Prostanoid receptor gene expression profile in human trabecular meshwork: A quantitative real-time PCR approach
    • Kamphuis, W., Schneemann, A., van Beek, L.M., et al. 2001. Prostanoid receptor gene expression profile in human trabecular meshwork: a quantitative real-time PCR approach. Invest. Ophthalmol. Vis. Sci. 42, 3209-3215.
    • (2001) Invest. Ophthalmol. Vis. Sci , vol.42 , pp. 3209-3215
    • Kamphuis, W.1    Schneemann, A.2    Van Beek, L.M.3
  • 11
    • 33748451624 scopus 로고    scopus 로고
    • Estimation of the reaction efficiency in polymerase chain reaction
    • Lalam, N. 2006. Estimation of the reaction efficiency in polymerase chain reaction. J. Theor. Biol. 242, 947-953.
    • (2006) J. Theor. Biol , vol.242 , pp. 947-953
    • Lalam, N.1
  • 12
    • 25444475785 scopus 로고    scopus 로고
    • A standard curve based method for relative real time PCR data processing
    • Larionov, A., Krause, A., and Miller, W. 2005. A standard curve based method for relative real time PCR data processing. BMC Bioinform. 6, 62.
    • (2005) BMC Bioinform , vol.6 , pp. 62
    • Larionov, A.1    Krause, A.2    Miller, W.3
  • 13
    • 0036499301 scopus 로고    scopus 로고
    • A new quantitative method of real time reverse transcription polymerase chain reaction assay based on simulation of polymerase chain reaction kinetics
    • Liu, W., and Saint, D.A. 2002a. A new quantitative method of real time reverse transcription polymerase chain reaction assay based on simulation of polymerase chain reaction kinetics. Anal. Biochem. 302, 52-59.
    • (2002) Anal. Biochem , vol.302 , pp. 52-59
    • Liu, W.1    Saint, D.A.2
  • 14
    • 0036289137 scopus 로고    scopus 로고
    • Validation of a quantitative method for real time PCR kinetics
    • Liu, W., and Saint, D.A. 2002b. Validation of a quantitative method for real time PCR kinetics. Biochem. Biophys. Res. Commun. 294, 347-353.
    • (2002) Biochem. Biophys. Res. Commun , vol.294 , pp. 347-353
    • Liu, W.1    Saint, D.A.2
  • 15
    • 0035710746 scopus 로고    scopus 로고
    • Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method
    • Livak, K.J., and Schmittgen, T.D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods 25, 402-408.
    • (2001) Methods , vol.25 , pp. 402-408
    • Livak, K.J.1    Schmittgen, T.D.2
  • 16
    • 19044366743 scopus 로고    scopus 로고
    • Determination of PCR efficiency in chelex-100 purified clinical samples and comparison of real-time quantitative PCR and conventional PCR for detection of Chlamydia pneumoniae
    • Mygind, T., Birkelund, S., Birkebaek, N.H., et al. 2002. Determination of PCR efficiency in chelex-100 purified clinical samples and comparison of real-time quantitative PCR and conventional PCR for detection of Chlamydia pneumoniae. BMC Microbiol. 2, 17.
    • (2002) BMC Microbiol , vol.2 , pp. 17
    • Mygind, T.1    Birkelund, S.2    Birkebaek, N.H.3
  • 17
    • 0242317675 scopus 로고    scopus 로고
    • Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis
    • Peirson, S.N., Butler, J.N., and Foster, R.G. 2003. Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Res. 31, e73.
    • (2003) Nucleic Acids Res , vol.31
    • Peirson, S.N.1    Butler, J.N.2    Foster, R.G.3
  • 18
    • 17344392308 scopus 로고    scopus 로고
    • A new mathematical model for relative quantification in real-time RT-PCR
    • Pfaffl, M.W. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45.
    • (2001) Nucleic Acids Res , vol.29
    • Pfaffl, M.W.1
  • 21
    • 47749090868 scopus 로고    scopus 로고
    • Real-time PCR quantification using a variable reaction efficiency model
    • Platts, A.E., Johnson, G.D., Linnemann, A.K., and Krawetz, S.A. 2008. Real-time PCR quantification using a variable reaction efficiency model. Anal. Biochem. 380, 315-322.
    • (2008) Anal. Biochem , vol.380 , pp. 315-322
    • Platts, A.E.1    Johnson, G.D.2    Linnemann, A.K.3    Krawetz, S.A.4
  • 22
    • 0037435395 scopus 로고    scopus 로고
    • Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
    • Ramakers, C., Ruijter, J.M., Deprez, R.H., and Moorman, A.F. 2003. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci. Lett. 339, 62-66.
    • (2003) Neurosci. Lett , vol.339 , pp. 62-66
    • Ramakers, C.1    Ruijter, J.M.2    Deprez, R.H.3    Moorman, A.F.4
  • 23
    • 33750961666 scopus 로고    scopus 로고
    • Real-time PCR: Approaches to data analysis (a review)]
    • Rebrikov, D.V., and Trofimov, D. 2006. [Real-time PCR: approaches to data analysis (a review)]. Prikl. Biokhim. Mikrobiol. 42, 520-528.
    • (2006) Prikl. Biokhim. Mikrobiol , vol.42 , pp. 520-528
    • Rebrikov, D.V.1    Trofimov, D.2
  • 24
    • 64549150047 scopus 로고    scopus 로고
    • Amplification efficiency: Linking baseline and bias in the analysis of quantitative PCR data
    • Ruijter, J.M., Ramakers, C., Hoogaars, W.M., et al. 2009. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 37, e45.
    • (2009) Nucleic Acids Res , vol.37
    • Ruijter, J.M.1    Ramakers, C.2    Hoogaars, W.M.3
  • 25
    • 16544384956 scopus 로고    scopus 로고
    • Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications
    • Rutledge, R.G. 2004. Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications. Nucleic Acids Res. 32, e178.
    • (2004) Nucleic Acids Res , vol.32
    • Rutledge, R.G.1
  • 26
    • 4444337502 scopus 로고    scopus 로고
    • Mathematics of quantitative kinetic PCR and the application of standard curves
    • Rutledge, R.G., and Cote, C. 2003. Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Res. 31, e93.
    • (2003) Nucleic Acids Res , vol.31
    • Rutledge, R.G.1    Cote, C.2
  • 27
    • 44449099134 scopus 로고    scopus 로고
    • A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR
    • Rutledge, R.G., and Stewart, D. 2008. A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR. BMC Biotechnol. 8, 47.
    • (2008) BMC Biotechnol , vol.8 , pp. 47
    • Rutledge, R.G.1    Stewart, D.2
  • 28
    • 33750475626 scopus 로고    scopus 로고
    • Quantitative real-time RT-PCR data analysis: Current concepts and the novel gene expression's CT difference formula
    • Schefe, J.H., Lehmann, K.E., Buschmann, I.R., et al. 2006. Quantitative real-time RT-PCR data analysis: current concepts and the novel "gene expression's CT difference" formula. J. Mol. Med. (Berl.) 84, 901-910.
    • (2006) J. Mol. Med. (Berl.) , vol.84 , pp. 901-910
    • Schefe, J.H.1    Lehmann, K.E.2    Buschmann, I.R.3
  • 29
    • 0031988083 scopus 로고    scopus 로고
    • Use of the recursion formula of the Gompertz function for the quantitation of PCR-amplified templates
    • Schlereth, W., Bassukas, I.D., Deubel, W., et al. 1998. Use of the recursion formula of the Gompertz function for the quantitation of PCR-amplified templates. Int. J. Mol. Med. 1, 463-467.
    • (1998) Int. J. Mol. Med , vol.1 , pp. 463-467
    • Schlereth, W.1    Bassukas, I.D.2    Deubel, W.3
  • 30
    • 44949231424 scopus 로고    scopus 로고
    • Analyzing real-time PCR data by the comparative C(T) method
    • Schmittgen, T.D., and Livak, K.J. 2008. Analyzing real-time PCR data by the comparative C(T) method. Nat. Protoc. 3, 1101-1108.
    • (2008) Nat. Protoc , vol.3 , pp. 1101-1108
    • Schmittgen, T.D.1    Livak, K.J.2
  • 31
    • 49249119064 scopus 로고    scopus 로고
    • A new method for robust quantitative and qualitative analysis of real-time PCR
    • Shain, E.B., and Clemens, J.M. 2008. A new method for robust quantitative and qualitative analysis of real-time PCR. Nucleic Acids Res. 36, e91.
    • (2008) Nucleic Acids Res , vol.36
    • Shain, E.B.1    Clemens, J.M.2
  • 32
    • 0029826566 scopus 로고    scopus 로고
    • Efficiency of DNA replication in the polymerase chain reaction
    • Stolovitzky, G., and Cecchi, G. 1996. Efficiency of DNA replication in the polymerase chain reaction. Proc. Natl. Acad. Sci. U. S. A. 93, 12947-12952.
    • (1996) Proc. Natl. Acad. Sci. U. S. A , vol.93 , pp. 12947-12952
    • Stolovitzky, G.1    Cecchi, G.2
  • 33
    • 1542356381 scopus 로고    scopus 로고
    • Standardized determination of real-time PCR efficiency from a single reaction set-up
    • Tichopad, A., Dilger, M., Schwarz, G., and Pfaffl, M.W. 2003. Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Res. 31, e122.
    • (2003) Nucleic Acids Res , vol.31
    • Tichopad, A.1    Dilger, M.2    Schwarz, G.3    Pfaffl, M.W.4
  • 34
    • 0344012538 scopus 로고    scopus 로고
    • Real-time polymerase chain reaction
    • Wilhelm, J., and Pingoud, A. 2003. Real-time polymerase chain reaction. Chem. Biochem. 4, 1120-1128.
    • (2003) Chem. Biochem , vol.4 , pp. 1120-1128
    • Wilhelm, J.1    Pingoud, A.2
  • 35
    • 0037311918 scopus 로고    scopus 로고
    • SoFAR: Software for fully automatic evaluation of real-time PCR data
    • Wilhelm, J., Pingoud, A., and Hahn, M. 2003a. SoFAR: software for fully automatic evaluation of real-time PCR data. Biotechniques 34, 324-332.
    • (2003) Biotechniques , vol.34 , pp. 324-332
    • Wilhelm, J.1    Pingoud, A.2    Hahn, M.3
  • 36
    • 0037620484 scopus 로고    scopus 로고
    • Validation of an algorithm for automatic quantification of nucleic acid copy numbers by real-time polymerase chain reaction
    • Wilhelm, J., Pingoud, A., and Hahn, M. 2003b. Validation of an algorithm for automatic quantification of nucleic acid copy numbers by real-time polymerase chain reaction. Anal. Biochem. 317, 218-225.
    • (2003) Anal. Biochem , vol.317 , pp. 218-225
    • Wilhelm, J.1    Pingoud, A.2    Hahn, M.3
  • 37
    • 33644844649 scopus 로고    scopus 로고
    • Statistical analysis of real-time PCR data
    • Yuan, J.S., Reed, A., Chen, F., and Stewart, C.N., Jr. 2006. Statistical analysis of real-time PCR data. BMC Bioinform. 7, 85.
    • (2006) BMC Bioinform , vol.7 , pp. 85
    • Yuan, J.S.1    Reed, A.2    Chen, F.3
  • 38
    • 27644482283 scopus 로고    scopus 로고
    • Comprehensive algorithm for quantitative real-time polymerase chain reaction
    • Zhao, S., and Fernald, R.D. 2005. Comprehensive algorithm for quantitative real-time polymerase chain reaction. J. Comput. Biol. 12, 1047-1064.
    • (2005) J. Comput. Biol , vol.12 , pp. 1047-1064
    • Zhao, S.1    Fernald, R.D.2


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