Statistical algorithm for assuring similar efficiency in standards and samples for absolute quantification by real-time reverse transcription polymerase chain reaction

Analytical Biochemistry

Volumn 348, Issue 2, 2006, Pages 198-208

  Chervoneva, Inna ^a,b   Hyslop, Terry ^a,b   Iglewicz, Boris ^c   Johns, Laura ^d   Wolfe, Henry R ^d,e   Schulz, Stephanie ^b   Leong, Elinor ^d   Waldman, Scott ^b  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

^c TEMPLE UNIVERSITY   (United States)

^d Targeted Diagnostics and Therapeutics Inc   (United States)

^e Genaera Corporation   (United States)

Author keywords

Accuracy of absolute quantification; Amplification rate; Kinetic outliers; RT PCR efficiency

Indexed keywords

CALIBRATION; DISEASES; EFFICIENCY; KINETICS; STATISTICS;

ABSOLUTE QUANTIFICATION; AMPLIFICATION EFFICIENCIES; AMPLIFICATION RATE; CALIBRATION STANDARD; PCR EFFICIENCY; REVERSE TRANSCRIPTION; REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION; STATISTICAL ALGORITHM;

POLYMERASE CHAIN REACTION;

MESSENGER RNA;

ACCURACY; ALGORITHM; ARTICLE; CALIBRATION; FLUORESCENCE; GENE AMPLIFICATION; GENE EXPRESSION; GENETIC TRANSCRIPTION; KINETICS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STATISTICAL ANALYSIS;

EID: 29244463844     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2005.10.042     Document Type: Article

References (34)

1. S.A. Bustin Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays J. Mol. Endocrinol. 25 2000 169 193
2. C. Lockey, E. Otto, and Z. Long Real-time fluorescence detection of a single DNA molecule Biotechniques 24 1998 744 746
3. M.W. Pfaffl, G.W. Horgan, and L. Dempfle Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR Nucleic Acids Res. 30 2002 e36
4. N. Steuerwald, J. Cohen, R.J. Herrera, and C.A. Brenner Analysis of gene expression in single oocytes and embryos by real-time rapid cycle fluorescence monitored RT-PCR Mol. Hum. Reprod. 5 1999 1034 1039
5. C.T. Wittwer, K.M. Ririe, R.V. Andrew, D.A. David, R.A. Gundry, and U.J. Balis The LightCycler: a microvolume multisample fluorimeter with rapid temperature control Biotechniques 22 1997 176 181
6. C. Aberham, C. Pendl, P. Gross, G. Zerlauth, and M. Gessner A quantitative, internally controlled real-time PCR assay for the detection of parvovirus B19DNA J. Virol. Methods 92 2001 183 191
7. M.L. Collins, C. Zayati, J.J. Detmer, B. Daly, J.A. Kolberg, T.A. Cha, B.D. Irvine, J. Tucker, and M.S. Urdea Preparation and characterization of RNA standards for use in quantitative branched DNA hybridization assays Anal. Biochem. 226 1995 120 129
8. M.W. Pfaffl A new mathematical model for relative quantification in real-time RT-PCR Nucleic Acids Res. 29 2001 e45
9. M.S. Rajeevan, S.D. Vernon, N. Taysavang, and E.R. Unger Validation of array-based gene expression profiles by real-time kinetic RT-PCR J. Mol. Diagn. 3 2001 26 31
10. T.D. Schmittgen, B.A. Zakrajsek, A.G. Mills, V. Gorn, M.J. Singer, and M.W. Reed Quantitative reverse transcription-polymerase chain reaction to study mRNA decay: comparison of endpoint and real-time methods Anal. Biochem. 285 2000 194 204
11. D.A. Simpson, S. Feeney, C. Boyle, and A.W. Stitt Retinal VEGF mRNA measured by SYBR green I fluorescence: a versatile approach to quantitative PCR Mol. Vis. 6 2000 178 183
12. W. Liu, and D.A. Saint Validation of a quantitative method for real time PCR kinetics Biochem. Biophys. Res. Commun. 294 2002 347 353
13. T. Bar, A. Stahlberg, A. Muszta, and M. Kubista Kinetic Outlier Detection (KOD) in real-time PCR Nucleic Acids Res. 31 2003 e105
14. A. Tichopad, M. Dilger, G. Schwarz, and M.W. Pfaffl Standardized determination of real-time PCR efficiency from a single reaction set-up Nucleic Acids Res. 31 2003 e122
15. C. Ramakers, J.M. Ruijter, R.H. Deprez, and A.F. Moorman Assumption-free analysis of quantitative real-time polymerase chain reaction PCR data Neurosci. Lett. 339 2003 62 66
16. J. Peccoud, and C. Jacob Theoretical uncertainty of measurements using quantitative polymerase chain reaction Biophys. J. 71 1996 101 108
17. I.G. Wilson Inhibition and facilitation of nucleic acid amplification Appl. Environ. Microbiol. 63 1997 3741 3751
18. D.L. Wiedbrauk, J.C. Werner, and A.M. Drevon Inhibition of PCR by aqueous and vitreous fluids J. Clin. Microbiol. 33 1995 2643 2646
19. L. Rossen, P. Norskov, K. Holmstrom, and O.F. Rasmussen Inhibition of PCR by components of food samples, microbial diagnostic assays and DNA-extraction solutions Int. J. Food Microbiol. 17 1992 37 45
20. D.P. Chandler, C.A. Wagnon, and H. Bolton Jr. Reverse transcriptase (RT) inhibition of PCR at low concentrations of template and its implications for quantitative RT-PCR Appl. Environ. Microbiol. 64 1998 669 677
21. G.J. Hahn, and W.Q. Meeker Statistical Intervals. A Guide for Practitioners 1991 Wiley-Interscience Somerset, NJ
22. J. Wilhelm, A. Pingoud, and M. Hahn SoFAR: software for fully automatic evaluation of real-time PCR data Biotechniques 34 2003 324 332
23. D. Hoaglin, B. Iglewicz, and J. Tukey Performance of some resistance rules for outlier labeling J. Am. Stat. Assoc. 81 1986 991 999
24. R. Odeh Tables of two-sided tolerance factors for a normal distribution Commun. Stat. B-Simulat. Computat. 72 1978 183 201
25. T.A. Fava, R. Desnoyers, S. Schulz, J. Park, D. Weinberg, E. Mitchell, and S.A. Waldman Ectopic expression of guanylyl cyclase C in CD34+ progenitor cells in peripheral blood J. Clin. Oncol. 19 2001 3951 3959
26. B. Cagir, A. Gelmann, J. Park, T. Fava, A. Tankelevitch, E.W. Bittner, E.J. Weaver, J.P. Palazzo, D. Weinberg, R.D. Fry, and S.A. Waldman Guanylyl cyclase C messenger RNA is a biomarker for recurrent stage II colorectal cancer Ann. Intern. Med. 131 1999 805 812
27. C.H. Sim, F.F. Gan, and T.C. Chang Outlier labeling with boxplot procedures J. Am. Stat. Assoc. 100 2005 642 652
28. F.R. Hampel, E.M. Ronchetti, P.J. Rousseeuw, and W.A. Stahel Robust Statistics 1986 John Wiley & Sons New York
29. K. Livak, ABI Prism 7700 Sequence Detection System. User bulletin 2. PE Applied Biosystems, 2001.
30. E.F. Vonesh, and V.M. Chinchilli Linear and Nonlinear Models for the Analysis of Repeated Measures 1997 Marcel Dekker New York
31. T. Lion, S. Izraeli, T. Henn, A. Gaiger, W. Mor, and H. Gadner Monitoring of residual disease in chronic myelogenous leukemia by quantitative polymerase chain reaction Leukemia 6 1992 495 499
32. J.P. Meijerink, G.J. Goverde, T.F. Smetsers, J.M. Raemaekers, M.J. Bogman, T. de Witte, and E.J. Mensink Quantitation of follicular non-Hodgkin's lymphoma cells carrying t(14;18) in a patient before and after allogeneic bone marrow transplantation Ann. Oncol. 5 Suppl. 1 1994 43 45
33. C.M. Mandigers, J.P. Meijerink, J.M. Raemaekers, A.V. Schattenberg, and E.J. Mensink Graft-versus-lymphoma effect of donor leucocyte infusion shown by real-time quantitative PCR analysis of t(14;18) Lancet 352 1998 1522 1523
34. J. Meijerink, C. Mandigers, L. vandeLocht, E. Tonnissen, F. Goodsaid, and J. Raemaekers A novel method to compensate for different amplification efficiencies between patient DNA samples in quantitative real-time PCR J. Mol. Diagn. 3 2001 55 61