Model based analysis of real-time PCR data from DNA binding dye protocols View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2007-12

AUTHORS

Mariano J Alvarez, Guillermo J Vila-Ortiz, Mariano C Salibe, Osvaldo L Podhajcer, Fernando J Pitossi

ABSTRACT

BACKGROUND: Reverse transcription followed by real-time PCR is widely used for quantification of specific mRNA, and with the use of double-stranded DNA binding dyes it is becoming a standard for microarray data validation. Despite the kinetic information generated by real-time PCR, most popular analysis methods assume constant amplification efficiency among samples, introducing strong biases when amplification efficiencies are not the same. RESULTS: We present here a new mathematical model based on the classic exponential description of the PCR, but modeling amplification efficiency as a sigmoidal function of the product yield. The model was validated with experimental results and used for the development of a new method for real-time PCR data analysis. This model based method for real-time PCR data analysis showed the best accuracy and precision compared with previous methods when used for quantification of in-silico generated and experimental real-time PCR results. Moreover, the method is suitable for the analyses of samples with similar or dissimilar amplification efficiency. CONCLUSION: The presented method showed the best accuracy and precision. Moreover, it does not depend on calibration curves, making it ideal for fully automated high-throughput applications. More... »

PAGES

85

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-8-85

DOI

http://dx.doi.org/10.1186/1471-2105-8-85

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1010432928

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17349040


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