twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis

Chiu, A., Ayub, M., Dive, C., Brady, G., Miller, C. J. and Hancock, J. (2017) twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis. Bioinformatics, 33(17), pp. 2743-2745. (doi: 10.1093/bioinformatics/btx308) (PMID:28475662) (PMCID:PMC5860069)

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Abstract

Summary Droplet Digital PCR (ddPCR) is a sensitive platform used to quantify specific nucleic acid molecules amplified by polymerase chain reactions. Its sensitivity makes it particularly useful for the detection of rare mutant molecules, such as those present in a sample of circulating free tumour DNA obtained from cancer patients. ddPCR works by partitioning a sample into individual droplets for which the majority contain only zero or one target molecule. Each droplet then becomes a reaction chamber for PCR, which through the use of fluorochrome labelled probes allows the target molecules to be detected by measuring the fluorescence intensity of each droplet. The technology supports two channels, allowing, for example, mutant and wild type molecules to be detected simultaneously in the same sample. As yet, no open source software is available for the automatic gating of two channel ddPCR experiments in the case where the droplets can be grouped into four clusters. Here, we present an open source R package ‘twoddpcr’, which uses Poisson statistics to estimate the number of molecules in such two channel ddPCR data. Using the Shiny framework, an accompanying graphical user interface (GUI) is also included for the package, allowing users to adjust parameters and see the results in real-time.

Item Type:Articles
Additional Information:This work was supported by Cancer Research UK via core funding to Cancer Research UK Manchester Institute [C5759/A20971] and funding to Experimental Cancer Medicine Centre [C480/A15578 to C.D.]; and Cancer Research UK Manchester Centre [C147/A18083 to C.D.].
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Miller, Professor Crispin
Authors: Chiu, A., Ayub, M., Dive, C., Brady, G., Miller, C. J., and Hancock, J.
College/School:College of Medical Veterinary and Life Sciences > Institute of Cancer Sciences
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Published Online:05 May 2017
Copyright Holders:Copyright © 2017 The Authors
First Published:First published in Bioinformatics 33(17):2743–2745
Publisher Policy:Reproduced under a Creative Commons Licence

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