A well-designed and optimized ddPCR reaction yields highly reproducible and robust results. Before running a ddPCR experiment, it is important to understand the goal or expected outcome of the experiment, as different types of experiments require different sample preparation methods, different amounts of input target DNA, and different types of data analysis. Here, we discuss the fundamental experimental parameters to consider in designing a ddPCR assay. Many factors, such as amplicon selection and primer and probe design, will be familiar to researchers experienced in designing qPCR assays, while others are unique to the ddPCR system. This section explores ddPCR assay design, selecting target sequences, designing primers and probes, and sample preparation for a ddPCR assay.

Related Topics: Droplet Digital™ PCR (ddPCR™) Technology, Absolute Quantification of PCR Targets with the Droplet Digital PCR System.