Assessing the performance capabilities of LRE-based assays for absolute quantitative real-time PCR

PLoS ONE

Volumn 5, Issue 3, 2010, Pages

  Rutledge, Robert G ^a   Stewart, Don ^a  

^a LAURENTIAN FORESTRY CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ORGANIC COMPOUND; PRIMER DNA; SYBR GREEN I;

ARTICLE; AUTOMATED PATTERN RECOGNITION; CALIBRATION; GENE EXPRESSION PROFILING; GENETIC PROCEDURES; GENETICS; METABOLISM; METHODOLOGY; POISSON DISTRIBUTION; POLYMERASE CHAIN REACTION; REGRESSION ANALYSIS; STANDARD; STATISTICAL ANALYSIS; STATISTICAL MODEL; THEORETICAL MODEL;

CALIBRATION; DATA INTERPRETATION, STATISTICAL; DNA PRIMERS; GENE EXPRESSION PROFILING; GENETIC TECHNIQUES; MODELS, STATISTICAL; MODELS, THEORETICAL; ORGANIC CHEMICALS; PATTERN RECOGNITION, AUTOMATED; POISSON DISTRIBUTION; POLYMERASE CHAIN REACTION; REGRESSION ANALYSIS;

EID: 77953872597     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009731     Document Type: Article

References (32)

1. Rutledge RG, Côté C (2003) Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Res 31: e93.
2. Rutledge RG, 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.
3. Wiesner RJ, Ruegg JC, Morano I (1992) Counting target molecules by exponential polymerase chain reaction: copy number of mitochondrial DNA in rat tissues. Biochem Biophys Res Commun 183: 553-559.
4. Gentle A, Anastasopoulos F, McBrien NA (2001) High-resolution semiquantitative real-time PCR without the use of a standard curve. BioTechniques 31: 502, 504-506, 508.
5. Ramakers C, Ruijter JM, Deprez RH, Moorman AF (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339: 62-66.
6. Zhao S, Fernald RD (2005) Comprehensive algorithm for quantitative real-time polymerase chain reaction. J Comput Biol 12: 1047-1064.
7. Rutledge RG, Stewart D (2008) Critical evaluation of methods used to determine amplification efficiency refutes the exponential character of real-time PCR. BMC Mol Biol 9: 96.
8. Rutledge RG (2004) Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications. Nucleic Acids Res 32: e178.
9. Nolan T, Hands RE, Bustin SA (2006) Quantification of mRNA using real-time RT-PCR. Nat Protoc 1: 1559-1582.
10. Wang Z, Spadoro J (1998) Determination of target copy number of quantitative standards used in PCR-based diagnostic assays. In: Ferr F, ed. Gene Quantification. Boston: Birkhäuser. pp 31-43.
11. Meijerink J, Mandigers C, van de Locht L, Tonnissen E, Goodsaid F, et al. (2001) A novel method to compensate for different amplification efficiencies between patient DNA samples in quantitative real-time PCR. J Mol Diagn 3: 55-61.
12. Stahlberg A, Aman P, Ridell B, Mostad P, Kubista M (2003) Quantitative realtime PCR method for detection of B-lymphocyte monoclonality by comparison of kappa and lambda immunoglobulin light chain expression. Clin Chem 49: 51-59.
13. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: RESEARCH0034.
14. Bustin SA, Nolan T (2004) Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech 15: 155-166.
15. Skern R, Frost P, Nilsen F (2005) Relative transcript quantification by quantitative PCR: roughly right or precisely wrong? BMC Mol Biol 6: 10.
16. Yun JJ, Heisler LE, Hwang II, Wilkins O, Lau SK, et al. (2006) Genomic DNA functions as a universal external standard in quantitative real-time PCR. Nucleic Acids Res 34: e85.
17. Karlen Y, McNair A, Perseguers S, Mazza C, Mermod N (2007) Statistical significance of quantitative PCR. BMC Bioinformatics 8: 131.
18. Gutierrez L, Mauriat M, Pelloux J, Bellini C, Van Wuytswinkel O (2008) Towards a systematic validation of references in real-time rt-PCR. Plant Cell 20: 1734-1735.
19. Gutierrez L, Mauriat M, Guenin S, Pelloux J, Lefebvre JF, et al. (2008) The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol J 6: 609-618.
20. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55: 611-622.
21. Garson JA, Huggett JF, Bustin SA, Pfaffl MW, Benes V, et al. (2009) Unreliable real-time PCR analysis of human endogenous retrovirus-W (HERV-W) RNA expression and DNA copy number in multiple sclerosis. AIDS Res Hum Retroviruses 25: 377-378; author reply 379-381.
22. Murphy J, Bustin SA (2009) Reliability of real-time reverse-transcription PCR in clinical diagnostics: gold standard or substandard? Expert Rev Mol Diagn 9: 187-197.
23. Guenin S, Mauriat M, Pelloux J, Van Wuytswinkel O, Bellini C, et al. (2009) Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot 60: 487-493.
24. Rasoolizadeh A, Beliveau C, Stewart D, Cloutier C, Cusson M (2009) Tranosema rostrale ichnovirus repeat element genes display distinct transcriptional patterns in caterpillar and wasp hosts. J Gen Virol 90: 1505-1514.
25. Boyle B, Dallaire N, MacKay J (2009) Evaluation of the impact of single nucleotide polymorphisms and primer mismatches on quantitative PCR. BMC Biotechnol 9: 75.
26. Liu W, Saint DA (2002) Validation of a quantitative method for real time PCR kinetics. Biochem Biophys Res Commun 294: 347-353.
27. Spandidos A, Wang X, Wang H, Dragnev S, Thurber T, et al. (2008) A comprehensive collection of experimentally validated primers for Polymerase Chain Reaction quantitation of murine transcript abundance. BMC Genomics 9: 633.
28. Kang JJ, Watson RM, Fisher ME, Higuchi R, Gelfand DH, et al. (2000) Transcript quantitation in total yeast cellular RNA using kinetic PCR. Nucleic Acids Res 28: e2.
29. Holland MJ (2002) Transcript abundance in yeast varies over six orders of magnitude. J Biol Chem 277: 14363-14366.
30. Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root-and shoot-specific genes. Plant J 38: 366-379.
31. Draghici S, Khatri P, Eklund AC, Szallasi Z (2006) Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 22: 101-109.
32. Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, et al. (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 10: 347.