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ddpcRquant: threshold determination for single channel droplet digital PCR experiments

Wim Trypsteen (UGent) , Matthijs Vynck (UGent) , Jan De Neve (UGent) , Pawel Bonczkowski (UGent) , Maja Kiselinova, Eva Malatinková (UGent) , KAREN VERVISCH (UGent) , Olivier Thas (UGent) , Linos Vandekerckhove (UGent) and Ward De Spiegelaere (UGent)
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Abstract
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.
Keywords
Data analysis, Droplet digital PCR, R software, Rain, Automation, Extreme value distribution, Threshold determination, POLYMERASE-CHAIN-REACTION, DNA COPY NUMBER, QUANTIFICATION, QUANTITATION, ASSAY, MODE, RNA

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Chicago
Trypsteen, Wim, Matthijs Vynck, Jan De Neve, Pawel Bonczkowski, Maja Kiselinova, Eva Malatinková, KAREN VERVISCH, Olivier Thas, Linos Vandekerckhove, and Ward De Spiegelaere. 2015. “ddpcRquant: Threshold Determination for Single Channel Droplet Digital PCR Experiments.” Analytical and Bioanalytical Chemistry 407 (19): 5827–5834.
APA
Trypsteen, W., Vynck, M., De Neve, J., Bonczkowski, P., Kiselinova, M., Malatinková, E., VERVISCH, K., et al. (2015). ddpcRquant: threshold determination for single channel droplet digital PCR experiments. ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 407(19), 5827–5834.
Vancouver
1.
Trypsteen W, Vynck M, De Neve J, Bonczkowski P, Kiselinova M, Malatinková E, et al. ddpcRquant: threshold determination for single channel droplet digital PCR experiments. ANALYTICAL AND BIOANALYTICAL CHEMISTRY. 2015;407(19):5827–34.
MLA
Trypsteen, Wim et al. “ddpcRquant: Threshold Determination for Single Channel Droplet Digital PCR Experiments.” ANALYTICAL AND BIOANALYTICAL CHEMISTRY 407.19 (2015): 5827–5834. Print.
@article{5954399,
  abstract     = {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.},
  author       = {Trypsteen, Wim and Vynck, Matthijs and De Neve, Jan and Bonczkowski, Pawel and Kiselinova, Maja and Malatinková, Eva and VERVISCH, KAREN and Thas, Olivier and Vandekerckhove, Linos and De Spiegelaere, Ward},
  issn         = {1618-2642},
  journal      = {ANALYTICAL AND BIOANALYTICAL CHEMISTRY},
  keywords     = {Data analysis,Droplet digital PCR,R software,Rain,Automation,Extreme value distribution,Threshold determination,POLYMERASE-CHAIN-REACTION,DNA COPY NUMBER,QUANTIFICATION,QUANTITATION,ASSAY,MODE,RNA},
  language     = {eng},
  number       = {19},
  pages        = {5827--5834},
  title        = {ddpcRquant: threshold determination for single channel droplet digital PCR experiments},
  url          = {http://dx.doi.org/10.1007/s00216-015-8773-4},
  volume       = {407},
  year         = {2015},
}

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