A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR

BMC Biotechnology

Volumn 8, Issue , 2008, Pages

  Rutledge, Robert G ^a   Stewart, Don ^a  

^a LAURENTIAN FORESTRY CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DATA PROCESSING; DATA REDUCTION; DNA; LINEAR REGRESSION;

PLATEAU DISTORTIONS; POLYMERASE CHAIN REACTION; SIGMOIDAL MODELING;

BIOTECHNOLOGY;

DNA; RNA; TAQ POLYMERASE; VIRUS DNA;

ACCURACY; AMPLICON; ANALYTICAL ERROR; ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS SOFTWARE; DILUTION; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; INFORMATION PROCESSING; INTERMETHOD COMPARISON; LINEAR REGRESSION ANALYSIS; MOLECULAR WEIGHT; NONHUMAN; POLYMERASE CHAIN REACTION; QUALITY CONTROL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STATISTICAL MODEL; ALGORITHM; ARTIFACT; AUTOMATED PATTERN RECOGNITION; BACTERIOPHAGE LAMBDA; CALIBRATION; CHEMICAL MODEL; COMPUTER PROGRAM; DNA SEQUENCE; FLUORESCENCE; GENETICS; KINETICS; METABOLISM; METHODOLOGY; REFERENCE VALUE; REGRESSION ANALYSIS; REPRODUCIBILITY; STANDARD;

ALGORITHMS; ARTIFACTS; BACTERIOPHAGE LAMBDA; CALIBRATION; DNA, VIRAL; FLUORESCENCE; GENE EXPRESSION PROFILING; KINETICS; MODELS, CHEMICAL; PATTERN RECOGNITION, AUTOMATED; POLYMERASE CHAIN REACTION; QUALITY CONTROL; REFERENCE STANDARDS; REFERENCE VALUES; REGRESSION ANALYSIS; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; SEQUENCE ANALYSIS, DNA; SOFTWARE; TAQ POLYMERASE; WEIGHTS AND MEASURES;

EID: 44449099134     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-8-47     Document Type: Article

References (40)

1. Canales RD Luo Y Willey JC Austermiller B Barbacioru CC Boysen C Hunkapiller K Jensen RV Knight CR Lee KY Ma Y Maqsodi B Papallo A Peters EH Poulter K Ruppel PL Samaha RR Shi L Yang W Zhang L Goodsaid FM Evaluation of DNA microarray results with quantitative gene expression platforms Nat Biotechnol 2006, 24(9):1115-1122. 10.1038/nbt1236 16964225
2. Wang Y Barbacioru C Hyland F Xiao W Hunkapiller KL Blake J Chan F Gonzalez C Zhang L Samaha RR Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays BMC Genomics 2006, 7:59. 1435885 16551369 10.1186/ 1471-2164-7-59
3. Qin LX Beyer RP Hudson FN Linford NJ Morris DE Kerr KF Evaluation of methods for oligonucleotide array data via quantitative real-time PCR BMC Bioinformatics 2006, 7:23. 1360686 16417622 10.1186/1471-2105-7-23
4. Draghici S Khatri P Eklund AC Szallasi Z Reliability and reproducibility issues in DNA microarray measurements Trends Genet 2006, 22(2):101-109. 10.1016/j.tig.2005.12.005 16380191
5. Miller LD Liu ET Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine Breast Cancer Res 2007, 9(2):206. 1868923 17397520 10.1186/bcr1662
6. Buyse M Loi S van't Veer L Viale G Delorenzi M Glas AM d'Assignies MS Bergh J Lidereau R Ellis P Harris A Bogaerts J Therasse P Floore A Amakrane M Piette F Rutgers E Sotiriou C Cardoso F Piccart MJ Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer J Natl Cancer Inst 2006, 98(17):1183-1192. 16954471
7. Fan C Oh DS Wessels L Weigelt B Nuyten DA Nobel AB van't Veer LJ Perou CM Concordance among gene-expression-based predictors for breast cancer N Engl J Med 2006, 355(6):560-569. 10.1056/NEJMoa052933 16899776
8. Schramm A Vandesompele J Schulte JH Dreesmann S Kaderali L Brors B Eils R Speleman F Eggert A Translating expression profiling into a clinically feasible test to predict neuroblastoma outcome Clin Cancer Res 2007, 13(5):1459-1465. 10.1158/1078-0432.CCR-06-2032 17332289
9. Rutledge RG Côté C Mathematics of quantitative kinetic PCR and the application of standard curves Nucleic Acids Res 2003, 31(16):e93. 169985 12907745 10.1093/nar/gng093
10. Gentle A Anastasopoulos F McBrien NA High-resolution semi-quantitative real-time PCR without the use of a standard curve Biotechniques 2001, 31(3):502, 504-6, 508. 11570493
11. Liu W Saint DA A new quantitative method of real time reverse transcription polymerase chain reaction assay based on simulation of polymerase chain reaction kinetics Anal Biochem 2002, 302:52-59. 10.1006/ abio.2001.5530 11846375
12. Ramakers C Ruijter JM Deprez RH Moorman AF Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data Neurosci Lett 2003, 339(1):62-66. 10.1016/S0304-3940(02)01423-4 12618301
13. Peirson SN Butler JN Foster RG Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis Nucleic Acids Res 2003, 31(14):e73. 167648 12853650 10.1093/nar/gng073
14. Bar T Stahlberg A Muszta A Kubista M Kinetic Outlier Detection (KOD) in real-time PCR Nucleic Acids Res 2003, 31(17):e105. 212825 12930979 10.1093/nar/gng106
15. Zhao S Fernald RD Comprehensive algorithm for quantitative real-time polymerase chain reaction J Comput Biol 2005, 12(8):1047-1064. 10.1089/ cmb.2005.12.1047 16241897
16. Liu W Saint DA Validation of a quantitative method for real time PCR kinetics Biochem Biophys Res Commun 2002, 294(2):347-353. 10.1016/ S0006-291X(02)00478-3 12051718
17. Tichopad A Dzidic, A., Pfaffl, M.W. Improving quantitative real-time RT-PCR reproducibility by boosting primer-linked amplification efficiency Biotechnol Lett 2002, 24:2053-2056. 10.1023/A:1021319421153
18. Rutledge RG Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications Nucleic Acids Res 2004, 32(22):e178. 545475 15601990 10.1093/nar/gnh177
19. Alvarez MJ Vila-Ortiz GJ Salibe MC Podhajcer OL Pitossi FJ Model based analysis of real-time PCR data from DNA binding dye protocols BMC Bioinformatics 2007, 8:85. 1838433 17349040 10.1186/1471-2105-8-85
20. Chervoneva I Li Y Iglewicz B Waldman S Hyslop T Relative quantification based on logistic models for individual polymerase chain reactions Stat Med 2007, 26(30):5596-5611. 10.1002/sim.3127 17968873
21. Mehra S Hu WS A kinetic model of quantitative real-time polymerase chain reaction Biotechnol Bioeng 2005, 91(7):848-860. 10.1002/bit.20555 15986490
22. Saha N Watson LT Kafadar K Ramakrishnan N Onufriev A Mane S Vasquez-Robinet C Validation and estimation of parameters for a general probabilistic model of the PCR process J Comput Biol 2007, 14(1):97-112. 10.1089/cmb.2006.0123 17381349
23. Smith MV Miller CR Kohn M Walker NJ Portier CJ Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process BMC Bioinformatics 2007, 8:409. 2194744 17956631 10.1186/1471-2105-8-409
24. Gevertz JL Dunn SM Roth CM Mathematical model of real-time PCR kinetics Biotechnol Bioeng 2005, 92(3):346-355. 10.1002/bit.20617 16170827
25. Lalam N Estimation of the reaction efficiency in polymerase chain reaction J Theor Biol 2006, 242(4):947-953. 10.1016/j.jtbi.2006.06.001 16843498
26. Lalam N Statistical inference for quantitative polymerase chain reaction using a hidden markov model: A Bayesian approach Stat Appl Genet Mol Biol 2007, 6:ARticle10. 17402916
27. Goll R Olsen T Cui G Florholmen J Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR BMC Bioinformatics 2006, 7:107. 1450306 16515700 10.1186/1471-2105-7-107
28. Karlen Y McNair A Perseguers S Mazza C Mermod N Statistical significance of quantitative PCR BMC Bioinformatics 2007, 8:131. 1868764 17445280 10.1186/1471-2105-8-131
29. Roussel Y Harris A Lee MH Wilks M Novel methods of quantitative real-time PCR data analysis in a murine Helicobacter pylori vaccine model Vaccine 2007, 25(15):2919-2929. 10.1016/j.vaccine.2006.07.013 16905224
30. Qiu H Durand K Rabinovitch-Chable H Rigaud M Gazaille V Clavere P Sturtz FG Gene expression of HIF-1alpha and XRCC4 measured in human samples by real-time RT-PCR using the sigmoidal curve-fitting method Biotechniques 2007, 42(3):355-362. 17390542
31. Cikos S Bukovska A Koppel J Relative quantification of mRNA: Comparison of methods currently used for real-time PCR data analysis BMC Mol Biol 2007, 8:113. 2235892 18093344 10.1186/1471-2199-8-113
32. Durtschi JD Stevenson J Hymas W Voelkerding KV Evaluation of quantification methods for real-time PCR minor groove binding hybridization probe assays Anal Biochem 2007, 361(1):55-64. 10.1016/ j.ab.2006.11.023 17188229
33. Swillens S Dessars B Housni HE Revisiting the sigmoidal curve fitting applied to quantitative real-time PCR data Anal Biochem 2008, 373(2):370-376. 10.1016/j.ab.2007.10.019 17996715
34. Swillens S Goffard JC Marechal Y de Kerchove d'Exaerde A El Housni H Instant evaluation of the absolute initial number of cDNA copies from a single real-time PCR curve Nucleic Acids Res 2004, 32(6):e53. 390351 15037663 10.1093/nar/gnh053
35. Higuchi R Fockler C Dollinger G Watson R Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions Biotechnology 1993, 11:1026-1030. 10.1038/nbt0993-1026 7764001
36. Wang Z Spadoro J Determination of target copy number of quantitative standards used in PCR-based diagnostic assays Gene Quantification Boston, Birkhäuser Ferré F 1998:31-43.
37. Bustin SA Nolan T Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction J Biomol Tech 2004, 15(3):155-166. 15331581
38. Nolan T Hands RE Bustin SA Quantification of mRNA using real-time RT-PCR Nat Protoc 2006, 1(3):1559-1582. 10.1038/nprot.2006.236 17406449
39. Skern R Frost P Nilsen F Relative transcript quantification by quantitative PCR: Roughly right or precisely wrong? BMC Mol Biol 2005, 6(1):10. 1090581 15854230 10.1186/1471-2199-6-10
40. Livak KJ Schmittgen TD Analysis of relative gene expression data using real-time quantitative PCR and the 2-DDCt method Methods 2001, 25:402-408. 10.1006/meth.2001.1262 11846609