ddpcRquant: threshold determination for single channel droplet digital PCR experiments

Digital PCR is rapidly gaining interest in the field of molecular biology for absolute quantification of nucleic acids. However, the first generation of platforms still needs careful validation and requires a specific methodology for data analysis to distinguish negative from positive signals by def...

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Bibliographic Details
Published in:Analytical and bioanalytical chemistry 2015-07, Vol.407 (19), p.5827-5834
Main Authors: Trypsteen, Wim, Vynck, Matthijs, De Neve, Jan, Bonczkowski, Pawel, Kiselinova, Maja, Malatinkova, Eva, Vervisch, Karen, Thas, Olivier, Vandekerckhove, Linos, De Spiegelaere, Ward
Format: Article
Language:English
Subjects:
Analysis
Analytical Chemistry
Automation
Biochemistry
Channels
Characterization and Evaluation of Materials
Chemistry
Chemistry and Materials Science
Data analysis
Data processing
Digital
Droplets
Fluorescence
Food Science
Laboratory Medicine
Mathematical analysis
Methodology
Molecular biology
Monitoring/Environmental Analysis
Nucleic acids
Polymerase chain reaction
Polymerase Chain Reaction - methods
Research Paper
Software
Thresholds
Thyroid
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Summary:Digital PCR is rapidly gaining interest in the field of molecular biology for absolute quantification of nucleic acids. However, the first generation of platforms still needs careful validation and requires a specific methodology for data analysis to distinguish negative from positive signals by defining a threshold value. The currently described methods to assess droplet digital PCR (ddPCR) are based on an underlying assumption that the fluorescent signal of droplets is normally distributed. We show that this normality assumption does not likely hold true for most ddPCR runs, resulting in an erroneous threshold. We suggest a methodology that does not make any assumptions about the distribution of the fluorescence readouts. A threshold is estimated by modelling the extreme values in the negative droplet population using extreme value theory. Furthermore, the method takes shifts in baseline fluorescence between samples into account. An R implementation of our method is available, allowing automated threshold determination for absolute ddPCR quantification using a single fluorescent reporter.
ISSN:1618-2642
1618-2650
DOI:10.1007/s00216-015-8773-4