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Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay
BACKGROUND: The real-time quantitative polymerase chain reaction (qPCR) is routinely used for quantification of nucleic acids and is considered the gold standard in the field of relative nucleic acid measurements. The efficiency of the qPCR reaction is one of the most important parameters in data an...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6543629/ https://www.ncbi.nlm.nih.gov/pubmed/31146686 http://dx.doi.org/10.1186/s12859-019-2911-5 |
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author | Panina, Yulia Germond, Arno David, Brit G. Watanabe, Tomonobu M. |
author_facet | Panina, Yulia Germond, Arno David, Brit G. Watanabe, Tomonobu M. |
author_sort | Panina, Yulia |
collection | PubMed |
description | BACKGROUND: The real-time quantitative polymerase chain reaction (qPCR) is routinely used for quantification of nucleic acids and is considered the gold standard in the field of relative nucleic acid measurements. The efficiency of the qPCR reaction is one of the most important parameters in data analysis in qPCR experiments. The Minimum Information for publication of Quantitative real-time PCR Experiments (MIQE) guidelines recommends the calibration curve as the method of choice for estimation of qPCR efficiency. The precision of this method has been reported to be between SD = 0.007 (three replicates) and SD = 0.022 (no replicates). RESULTS: In this article, we present a novel approach to the analysis of qPCR data which has been obtained by running a dilution series. Unlike previously developed methods, our method, Pairwise Efficiency, involves a new formula that describes pairwise relationships between data points on separate amplification curves and thus enables extensive statistics. The comparison of Pairwise Efficiency with the calibration curve by Monte Carlo simulation shows the two-folds improvement in the precision of estimations of efficiency and gene expression ratios on the same dataset. CONCLUSIONS: The Pairwise Efficiency nearly doubles the precision in qPCR efficiency determinations compared to standard calibration curve method. This paper demonstrates that applications of combinatorial treatment of data provide the improvement of the determination. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2911-5) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6543629 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65436292019-06-04 Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay Panina, Yulia Germond, Arno David, Brit G. Watanabe, Tomonobu M. BMC Bioinformatics Methodology Article BACKGROUND: The real-time quantitative polymerase chain reaction (qPCR) is routinely used for quantification of nucleic acids and is considered the gold standard in the field of relative nucleic acid measurements. The efficiency of the qPCR reaction is one of the most important parameters in data analysis in qPCR experiments. The Minimum Information for publication of Quantitative real-time PCR Experiments (MIQE) guidelines recommends the calibration curve as the method of choice for estimation of qPCR efficiency. The precision of this method has been reported to be between SD = 0.007 (three replicates) and SD = 0.022 (no replicates). RESULTS: In this article, we present a novel approach to the analysis of qPCR data which has been obtained by running a dilution series. Unlike previously developed methods, our method, Pairwise Efficiency, involves a new formula that describes pairwise relationships between data points on separate amplification curves and thus enables extensive statistics. The comparison of Pairwise Efficiency with the calibration curve by Monte Carlo simulation shows the two-folds improvement in the precision of estimations of efficiency and gene expression ratios on the same dataset. CONCLUSIONS: The Pairwise Efficiency nearly doubles the precision in qPCR efficiency determinations compared to standard calibration curve method. This paper demonstrates that applications of combinatorial treatment of data provide the improvement of the determination. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2911-5) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-30 /pmc/articles/PMC6543629/ /pubmed/31146686 http://dx.doi.org/10.1186/s12859-019-2911-5 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Methodology Article Panina, Yulia Germond, Arno David, Brit G. Watanabe, Tomonobu M. Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay |
title | Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay |
title_full | Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay |
title_fullStr | Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay |
title_full_unstemmed | Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay |
title_short | Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay |
title_sort | pairwise efficiency: a new mathematical approach to qpcr data analysis increases the precision of the calibration curve assay |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6543629/ https://www.ncbi.nlm.nih.gov/pubmed/31146686 http://dx.doi.org/10.1186/s12859-019-2911-5 |
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