Determination of PCR Efficiency  (main)
Determination of PCR Efficiency  (1)
Determination of PCR Efficiency  (2)
Determination of PCR Efficiency  (3)
Determination of PCR Efficiency  (4)
Determination of PCR Efficiency  (5)

• Real-Time PCR:  A Review of Approaches to Data Analysis (Rebrikov & Trofimov 2006)

• Estimation via classical  "calibration dilution curve and slope calculation"
• real-time PCR Standard Curve Slope to Efficiency Calculator (by Stratagene)
• on each individual cDNA (Rasmussen 2001)
• on each individual cDNA (Stahlberg et al. 2003)
• on a mixture of multiple cDNA (cDNA pool, Pfaffl 2001)
• Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis (Peirson, 2003)
• Mathematics of quantitative kinetic PCR and the application of standard curves (Rutledge & Cote 2003)
• Qiagen Manual: High PCR efficiency enable more accurate quantification in real-time PCR (QNews 2, 2004, page 49)
• Accurate and statistically verified quantification of relative mRNA abundances using SYBR Green I and real-time RT-PCR (Marino et al. 2003)
• Impact of DNA polymerases and their buffer systems on quantitative real-time PCR. (Wolffs et al. 2004)
• Addressing fluorogenic real-time qPCR inhibition using the novel custom Excel file system 'FocusField2- 6Gallup qPCR Set-upTool-001' to attain consistently high fidelity qPCR reactions. (Gallup & Ackermann, 2006)
• Effect of DNA damage on PCR amplification efficiency with the relative threshold cycle method (Sikorsky et al., 2004)

• Estimation via increase in  "absolute fluorescence"
  
• Estimation via increase in "absolute fluorescence" method 1 (linear regression, Pfaffl 2001)
• Estimation via increase in "absolute fluorescence" method 2 (Liu & Saint 2002)
• Estimation via increase in "absolute fluorescence" method 3  (3 data points, Peccoud & Jacob 1998)
• Estimation via increase in "absolute fluorescence" method 4  (window-of-linearity, Ramakers et al. 2003)
• Estimation via increase in "absolute fluorescence" method 5  (Shiao et al. 2003)

• Potential influence of the first PCR cycles in real-time comparative gene quantifications (Nogva & Rudi, 2004)

• A kinetic model of quantitative real-time polymerase chain reaction (Mehra S, Hu WS., 2005)

• Q-Gene: processing quantitative real-time RT–PCR data  (Perikles Simon, 2003)
  

• Kinetic Outlier Detection
• KOD (Kinetic Outlier Detection) in real-time PCR  (Tzachi Bar et al., 2003)
• Kinetics quality assessment for relative quantification by real-time PCR. (Bar T, Muszta A., 2005)
  

• Estimation via "sigmoidal" or "logistic"  curve fitting models
  
• Estimation via "theoretical sigmoidal fit"  (all fluorescence data points, Liu & Saint 2002)
• Estimation via "experimental four parametric sigmoidal model fit"  (all data points, Tichopad et al. 2002)
• Estimation via "experimental four parametric logistic model fit"  (all fluorescence data points, Tichopad et al. 2003)
• ERRATUM:  correction of Figure 2 Tichopad et al. 2003
• PCR Efficiency estimation via "experimental four parametric sigmoidal model fit"  (all data points, Tichopad et al. MCP 2004 - Inhibition of real-time RT–PCR quantification due to tissue-specific contaminants) 
• Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR using a SDM method (Johnson et al. 2004) 
• Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications. (Rutledge 2004)
• Improved real-time RT-PCR method for high-throughput measurements using second derivative calculation and double correction. (Luu The et al. 2005)
• Gene expression of HIF-1 α and XRCC4 measured in human samples by real-time RT-PCR using the sigmoidal curve-fitting method  (Hao-Qiu et al., 2007)
  
• Model based analysis of real-time PCR data from DNA binding dye protocols  (Alvarez et al., 2007)
• A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR (Rutledge & Stewart, 2008)
• A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition (Guescini et al., 2008)
• Highly accurate sigmoidal fitting of real-time PCR data by introducing a parameter for asymmetry. (Spiess et al., 2008)
• qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis (Ritz & Spiess, 2008)

• CAmpER - Real-time PCR analysis software
  
  CAmpER - Calculation of Amplification Efficiencies for RT-PCR experiments is a tool for the automatic analysis of real time PCR experiments. Automatic analysis, annotation and storage of  real-time PCR experiments performed with different qPCR systems, currently the LightCycler® and the Opticon®.

• New Roche E-method
• The E-Method: a highly accurate technique for gene-expression analysis

Determination of PCR efficiencies in competitive RT-PCR

• Estimation via classical regression method:    Quantification of Insulin-like Growth Factor-1  (IGF-1) mRNA: Development & validation of an internally standardised competitive RT-PCR (Pfaffl et al. 1998)
• Estimation via classical regression method:    Quantification of androgen receptor mRNA in tissues by competitive co-amplification of a template in reverse transcription-polymerase chain reaction (Malucelli et al. 1996)

Various external effects on PCR amplification effiency

• Effect of DNA damage on PCR amplification efficiency with the relative threshold cycle method (Sikorsky et al. 2004)
• Amplification effiency of thermostable DNA polymerases (Arezi et al. 2003)
• Evaluation of Real-Time PCR Amplification Efficiencies to Detect PCR Inhibitors (Elias J. Kontanis and Floyd A. Reed, 2006)
• Influence of segmenting fluids on efficiency, crossing point and fluorescence level in real time quantitative PCR (Walsh et al. 2006)
• Quantitative real-time polymerase chain reaction: methodical analysis and mathematical model (Wilkening S, Bader A., 2004)
  

• Comparing Algorithms for Calculating Amplification Efficiencies of Real-Time PCR.
  Emi Arikawa and Jingping Yang. SuperArray Bioscience Corporation, Frederick, MD   download PDF   Presented at the 1st US qPCR Symposium 2007
  

• Absolute and relative real-time PCR in the quantification of tst gene expression among methicillin-resistant Staphylococcus aureus: evaluation by two mathematical models.
  Chini V, Foka A, Dimitracopoulos G, Spiliopoulou I. 2007   download PDF
  

• Enhancing the efficiency of a PCR using gold nanoparticles.
  Li M, Lin YC, Wu CC, Liu HS.  2006    download PDF

• PCR inhibition by reverse transcriptase leads to an overestimation of amplification efficiency.
  Suslov O, Steindler DA.    download PDF

• Relative quantification of mRNA: comparison of methods currently used for real-time PCR data analysis.
  Cikos S, Bukovská A, Koppel J., 2007      download PDF
  

• Determination of real-time PCR efficiency  - An overview.
  Talk on the 1st qPCR Symposium 2004  by M.W. Pfaffl     download PDF

• Overview article - Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction
Sheng Zhao and Russell D. Fernald, 2005    download PDF

• Technical Note - Evaluation of Real-Time PCR Amplification Efficiencies to Detect PCR Inhibitors
  Elias J. Kontanis and Floyd A. Reed, 2006    download PDF

• Estimation of the reaction efficiency in polymerase chain reaction
  Nadia Lalam, 2006     download PDF  

• Molelling the PCR amplification process by a size-dependent branching process and estimation of the efficiency
  Lalam et al., 2004   download PDF

• Statistical Inference for Quantitative Polymerase Chain Reaction Using a Hidden Markov Model: A Bayesian Approach       Lalam, 2007    download PDF

• Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR
  Goll et al., 2006   download PDF
  

• Mathematical Model of Real-Time PCR Kinetics
Gevertz et al., 2005    download PDF

• Quantitative real-time RT-PCR based transcriptomics: Improvement of evaluation methods.
  PhD. Thesis - Ales Tichopad, 2004
  Lehrstuhl für Physiologie, Fakultät Wissenschaftszentrum Weihenstephan, Technische Universität München, Germany.