Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (153K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Bar, T.
Right arrow Articles by Kubista, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bar, T.
Right arrow Articles by Kubista, M.
Related Collections
Right arrow Nucleic acid amplification
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 17 e105
© 2003 Oxford University Press

Kinetic Outlier Detection (KOD) in real-time PCR

Tzachi Bar*,1, Anders Ståhlberg1, Anders Muszta2 and Mikael Kubista1,3

1 Department of Chemistry and Bioscience, Chalmers University of Technology, Medicinargatan 7B, 405 30 Gothenburg, Sweden, 2 Department of Mathematical Statistics, Eklandagatan 86, 412 96, Gothenburg, Sweden and 3 TATAA Biocenter, Medicinargatan 7B, 405 30 Gothenburg, Sweden

*To whom correspondence should be addressed. Tel: +46 31 7733916; Fax: +46 31 7733910; Email: tzachi.bar{at}molbiotech.chalmers.se

Real-time PCR is becoming the method of choice for precise quantification of minute amounts of nucleic acids. For proper comparison of samples, almost all quantification methods assume similar PCR efficiencies in the exponential phase of the reaction. However, inhibition of PCR is common when working with biological samples and may invalidate the assumed similarity of PCR efficiencies. Here we present a statistical method, Kinetic Outlier Detection (KOD), to detect samples with dissimilar efficiencies. KOD is based on a comparison of PCR efficiency, estimated from the amplification curve of a test sample, with the mean PCR efficiency of samples in a training set. KOD is demonstrated and validated on samples with the same initial number of template molecules, where PCR is inhibited to various degrees by elevated concentrations of dNTP; and in detection of cDNA samples with an aberrant ratio of two genes. Translating the dissimilarity in efficiency to quantity, KOD identifies outliers that differ by 1.3–1.9-fold in their quantity from normal samples with a P-value of 0.05. This precision is higher than the minimal 2-fold difference in number of DNA molecules that real-time PCR usually aims to detect. Thus, KOD may be a useful tool for outlier detection in real-time PCR.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
J. M. Ruijter, C. Ramakers, W. M. H. Hoogaars, Y. Karlen, O. Bakker, M. J. B. van den Hoff, and A. F. M. Moorman
Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data
Nucleic Acids Res., April 1, 2009; 37(6): e45 - e45.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. B. Shain and J. M. Clemens
A new method for robust quantitative and qualitative analysis of real-time PCR
Nucleic Acids Res., August 1, 2008; 36(14): e91 - e91.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Physiol. Endocrinol. Metab.Home page
M. Granado, A. I. Martin, M. Lopez-Menduina, A. Lopez-Calderon, and M. A. Villanua
GH-releasing peptide-2 administration prevents liver inflammatory response in endotoxemia
Am J Physiol Endocrinol Metab, January 1, 2008; 294(1): E131 - E141.
[Abstract] [Full Text] [PDF]

Home page
 J EndocrinolHome page
M Granado, A I Martin, T Priego, A Lopez-Calderon, and M A Villanua
Tumour necrosis factor blockade did not prevent the increase of muscular muscle RING finger-1 and muscle atrophy F-box in arthritic rats.
J. Endocrinol., October 1, 2006; 191(1): 319 - 326.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. Suslov and D. A. Steindler
PCR inhibition by reverse transcriptase leads to an overestimation of amplification efficiency
Nucleic Acids Res., November 27, 2005; 33(20): e181 - e181.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.