This is a preview of subscription content, log in via an institution to check access.
References
Bastien P, Procop GW, Reischl U (2008) Quantitative real-time PCR is not more sensitive than “conventional” PCR. J Clin Microbiol 46:1897–1900. doi:10.1128/JCM.02258-07
Behets J, Declerck P, Delaedt Y, Creemers B, Olleviera F (2007) Development and evaluation of a TaqMan duplex real-time PCR quantification method for reliable enumeration of Legionella pneumophila in water samples. J Microbiol Methods 68:137–144. doi:10.1016/j.mimet.2006.07.002
Brankatschk R, Bodenhausen N, Zeyer J, Bürgmann H (2012) Simple absolute quantification method correcting for quantitative PCR efficiency variations for microbial community samples. Appl Environ Microbiol 78(12):4481–4489. doi:10.1128/AEM.07878-11
Freeman WM, Walker SJ, Vrana KE (1999) Quantitative RT-PCR: pitfalls and potential. Biotechniques 26:112–125
Haramoto E, Katayama H, Oguma K, Ohgaki S (2005) Application of cation-coated filter method to detection of noroviruses, enteroviruses, adenoviruses, and torque teno viruses in the Tamagawa River in Japan. Appl Environ Microbiol 71:2403–2411. doi:10.1128/AEM.71.5.2403-2411.2005
Higuchi R, Fokler C, Dollinger G, Watson R (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology 11:1026–1030. doi:10.1038/nbt0993-1026
Jothikumar N, Cromeans TL, Hill VR, Lu X, Sobsey MD, Erdman DD (2005) Quantitative real-time PCR assays for detection of human adenoviruses and identification of serotypes 40 and 41. Appl Environ Microbiol 71:3131–3136. doi:10.1128/AEM.71.6.3131-3136.2005
Kitchen RR, Kubista M, Tichopad A (2010) Statistical aspects of quantitative real-time PCR experiment design. Methods 50(4):231–236. doi:10.1016/j.ymeth.2010.01.025
Layton A, Mckay L, Williams D, Garrett VR, Sayler G (2006) Development of Bacteroides 16S rRNA gene Taqman-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Appl Environ Microbiol 72:4214–4224. doi:10.1128/AEM.01036-05
Love JL, Scholes P, Gilpin B, Savill M, Lin S, Samuel L (2006) Evaluation of uncertainty in quantitative real-time PCR. J Microbiol Methods 67:349–356. doi:10.1016/j.mimet.2006.04.005
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. doi:10.1016/S0304-3940(02)01423-4
Rasmussen R (2001) Quantification on the LightCycler. In: Meuer S, Wittwer C, Nakagawara K (eds) Rapid cycle real-time PCR—methods and applications. Springer Press, Heidelberg, pp 21–34
Rebrikov DV, Trofimov DY (2006) Real-time PCR: a review of approaches to data analysis. Appl Biochem Microbiol 42(5):455–463. doi:10.1134/S0003683806050024
Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB, Moorman AFM (2009) Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucl Acids 37:e45. doi:10.1093/nar/gkp045
Rutledge RG, Côté C (2003) Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Res 31(16):e93. doi:10.1093/nar/gng093
Töwe S, Kleindeindam K, Schloter M (2010) Differences in amplification efficiency of standard curves in quantitative real-time PCR assays and consequences for gene quantification in environmental samples. J Microbiol Methods 82:338–341. doi:10.1016/j.mimet.2010.07.005
Tuomi JM, Voorbraak F, Jones DL, Ruijter JM (2010) Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value. Methods 50(4):313–322. doi:10.1016/j.ymeth.2010.02.003
Acknowledgments
We thank the Ministry of Education and Science of Spain and the Comissionat per a Universitats i Recerca del Departament d’Innovacio´ and Universitats i Empresa de la Generalitat de Catalunya i del Fons Social Europeu, for supporting this study. Financial support was provided by Alfa Network TECSPAR (RED ALFA II-0543- FI-FAFCD; Sustainable technologies for potabilization and wastewater treatment), and by grant CTM2008-06676-C05-02/TECNO from the Ministry of Science and Innovation of Spain to Jordi Morató. The authors also want to thank to the peer review process of Folia Microbiologica for improving the quality of the present work.
Author information
Authors and Affiliations
Corresponding author
Example 1
Example 1
Using Eq 4 for the same reaction at the same Cq (i.e. 25)
Rights and permissions
About this article
Cite this article
Pérez, L.M., Fittipaldi, M., Adrados, B. et al. Error estimation in environmental DNA targets quantification due to PCR efficiencies differences between real samples and standards. Folia Microbiol 58, 657–662 (2013). https://doi.org/10.1007/s12223-013-0255-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12223-013-0255-5