Droplet Digital PCR (ddPCR™)

Bio-Rad QX200 and QX600 Droplet Digital PCR (ddPCR) Systems

Digital PCR (dPCR) is a breakthrough technology that provides ultrasensitive, absolute nucleic acid quantification. This technique is particularly useful for detecting low-abundance targets, analyzing targets in complex backgrounds, identifying allelic variants (SNPs), measuring copy number variation, and monitoring subtle changes in target levels. In the Bio-Rad Droplet Digital PCR (ddPCR™) workflow, each PCR sample is partitioned into approximately 20,000 microscopic droplets prior to amplification. Each droplet functions as an individual PCR reaction. Following end-point PCR, fluorescence is measured in each droplet. Droplets containing amplified target sequence are scored as positive, while droplets without target amplification are scored as negative. Using Poisson statistics, the fraction of positive droplets is converted to the absolute number of target molecules in the starting sample without the need for standard curves.

In the Droplet Digital™ PCR (ddPCR™) System, each PCR sample is partitioned into a large number of microscopic droplets prior to amplification. Each droplet is an individual PCR reaction. After end-point amplification, fluorescence is detected in the droplets in which target sequence was amplified and scored as positive. Droplets without the target sequence show little or no fluorescence and are scored as negative. Using the Poisson distribution law, the fraction of positive droplets is converted to the number of molecules in the starting sample, without the need for standard curves (absolute quantification).

The CCR Genomics Core maintains both the Bio-Rad QX200 ddPCR System and the Bio-Rad QX600 ddPCR System to support a wide range of digital PCR applications. The QX200 system includes a droplet generator, a C1000 Touch™ Thermal Cycler, and a droplet reader, providing robust two-color digital PCR using FAM and HEX (or VIC) detection chemistries.

The QX600 ddPCR System expands these capabilities with six-color multiplex detection, enabling simultaneous analysis of up to six targets in a single reaction while maintaining the precision and sensitivity of droplet digital PCR. This enhanced multiplexing capability is ideal for complex applications such as rare variant detection, copy number analysis, gene expression profiling, pathogen detection, biomarker studies, and cell and gene therapy research.

The QX Manager Software for data analysis is available at the Core and is free to download. The systems support EvaGreen® chemistry as well as hydrolysis probe (TaqMan®) assays. The QX200 system supports two-color multiplexing (FAM and HEX/VIC), while the QX600 system supports advanced six-color multiplex assays, providing greater flexibility for high-content digital PCR experiments.

To get started with ddPCR, explore the Core resources below or contact the CCR Genomics Core to schedule a project consultation, training, or instrument access.