title: Simultaneous estimation of detection sensitivity and absolute copy number from digital PCR serial dilution.
abstract: Digital polymerase chain reaction (dPCR) is a refinement of the conventional PCR approach to nucleic acid detection and absolute quantification. Digital PCR works by partitioning a sample of DNA or cDNA into many individual, parallel PCR reactions. Current quantification methods rely on the assumption that the PCR reactions are always able to detect single target molecules. When the assumption does not hold, the copy numbers will be severely underestimated. We developed a novel dPCR quantification method which determines whether the single copy assumption is violated or not by simultaneously estimating the assay sensitivity and the copy numbers using serial dilution data sets. The implemented method is available as an R package "digitalPCR".
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA. Electronic address: xdeng@bloodsystems.org.
authors.forename: Xutao
authors.initials: X
authors.lastname: Deng
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA. Electronic address: bcuster@bloodsystems.org.
authors.forename: Brian S
authors.initials: BS
authors.lastname: Custer
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA. Electronic address: mbusch@bloodsystems.org.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Busch
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA. Electronic address: sbakkour@bloodsystems.org.
authors.forename: Sonia
authors.initials: S
authors.lastname: Bakkour
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA. Electronic address: tlee@bloodsystems.org.
authors.forename: Tzong-Hae
authors.initials: TH
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D004247:DNA / Q000235:genetics*; D016133:Polymerase Chain Reaction
chemical_list: D004247:DNA
keywords: Copy number estimation; Digital PCR; Maximum likelihood; Poisson distribution; Serial dilution; Virus