Ghent University Academic Bibliography

Advanced

Enhanced analysis of real-time PCR data by using a variable efficiency model: FPK-PCR

Antoon Lievens UGent, Stefan Van Aelst UGent, Marc Van den Bulcke and Els Goetghebeur UGent (2012) NUCLEIC ACIDS RESEARCH. 40(2).
abstract
Current methodology in real-time Polymerase chain reaction (PCR) analysis performs well provided PCR efficiency remains constant over reactions. Yet, small changes in efficiency can lead to large quantification errors. Particularly in biological samples, the possible presence of inhibitors forms a challenge. We present a new approach to single reaction efficiency calculation, called Full Process Kinetics-PCR (FPK-PCR). It combines a kinetically more realistic model with flexible adaptation to the full range of data. By reconstructing the entire chain of cycle efficiencies, rather than restricting the focus on a 'window of application', one extracts additional information and loses a level of arbitrariness. The maximal efficiency estimates returned by the model are comparable in accuracy and precision to both the golden standard of serial dilution and other single reaction efficiency methods. The cycle-to-cycle changes in efficiency, as described by the FPK-PCR procedure, stay considerably closer to the data than those from other S-shaped models. The assessment of individual cycle efficiencies returns more information than other single efficiency methods. It allows in-depth interpretation of real-time PCR data and reconstruction of the fluorescence data, providing quality control. Finally, by implementing a global efficiency model, reproducibility is improved as the selection of a window of application is avoided.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
KINETIC OUTLIER DETECTION, POLYMERASE-CHAIN-REACTION, AMPLIFICATION EFFICIENCIES, THEORETICAL DESCRIPTION, INHIBITION, ALGORITHM, ASSAY, QUANTIFICATION, SAMPLES, GROWTH
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
40
issue
2
article_number
e10
pages
15 pages
Web of Science type
Article
Web of Science id
000299095900001
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
8.278 (2012)
JCR rank
27/288 (2012)
JCR quartile
1 (2012)
ISSN
0305-1048
DOI
10.1093/nar/gkr775
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
2069286
handle
http://hdl.handle.net/1854/LU-2069286
date created
2012-03-19 14:11:34
date last changed
2012-10-02 15:27:45
@article{2069286,
  abstract     = {Current methodology in real-time Polymerase chain reaction (PCR) analysis performs well provided PCR efficiency remains constant over reactions. Yet, small changes in efficiency can lead to large quantification errors. Particularly in biological samples, the possible presence of inhibitors forms a challenge. We present a new approach to single reaction efficiency calculation, called Full Process Kinetics-PCR (FPK-PCR). It combines a kinetically more realistic model with flexible adaptation to the full range of data. By reconstructing the entire chain of cycle efficiencies, rather than restricting the focus on a 'window of application', one extracts additional information and loses a level of arbitrariness. The maximal efficiency estimates returned by the model are comparable in accuracy and precision to both the golden standard of serial dilution and other single reaction efficiency methods. The cycle-to-cycle changes in efficiency, as described by the FPK-PCR procedure, stay considerably closer to the data than those from other S-shaped models. The assessment of individual cycle efficiencies returns more information than other single efficiency methods. It allows in-depth interpretation of real-time PCR data and reconstruction of the fluorescence data, providing quality control. Finally, by implementing a global efficiency model, reproducibility is improved as the selection of a window of application is avoided.},
  articleno    = {e10},
  author       = {Lievens, Antoon and Van Aelst, Stefan and Van den Bulcke, Marc and Goetghebeur, Els},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {KINETIC OUTLIER DETECTION,POLYMERASE-CHAIN-REACTION,AMPLIFICATION EFFICIENCIES,THEORETICAL DESCRIPTION,INHIBITION,ALGORITHM,ASSAY,QUANTIFICATION,SAMPLES,GROWTH},
  language     = {eng},
  number       = {2},
  pages        = {15},
  title        = {Enhanced analysis of real-time PCR data by using a variable efficiency model: FPK-PCR},
  url          = {http://dx.doi.org/10.1093/nar/gkr775},
  volume       = {40},
  year         = {2012},
}

Chicago
Lievens, Antoon, Stefan Van Aelst, Marc Van den Bulcke, and Els Goetghebeur. 2012. “Enhanced Analysis of Real-time PCR Data by Using a Variable Efficiency Model: FPK-PCR.” Nucleic Acids Research 40 (2).
APA
Lievens, A., Van Aelst, S., Van den Bulcke, M., & Goetghebeur, E. (2012). Enhanced analysis of real-time PCR data by using a variable efficiency model: FPK-PCR. NUCLEIC ACIDS RESEARCH, 40(2).
Vancouver
1.
Lievens A, Van Aelst S, Van den Bulcke M, Goetghebeur E. Enhanced analysis of real-time PCR data by using a variable efficiency model: FPK-PCR. NUCLEIC ACIDS RESEARCH. 2012;40(2).
MLA
Lievens, Antoon, Stefan Van Aelst, Marc Van den Bulcke, et al. “Enhanced Analysis of Real-time PCR Data by Using a Variable Efficiency Model: FPK-PCR.” NUCLEIC ACIDS RESEARCH 40.2 (2012): n. pag. Print.