ddPCR™ Copy Number Determination Assays: QX200™, QX600™, and QX700™

Bio-Rad’s ddPCR Copy Number Determination Assays

Bio-Rad’s ddPCR Copy Number Determination Assays deliver the precision and resolution needed to discriminate small changes in copy number. Digital PCR can detect subtle fold changes, such as a 1.2-fold difference between five and six copies, addressing a key technical challenge in CNV analysis: statistically distinguishing between consecutive copy number states. By partitioning each ddPCR reaction, the technology provides the resolution required to reliably resolve these small differences. Optimized for the QX200^**, QX600^*, and QX700^* ddPCR systems, these assays support flexible multiplexing with an expanded fluorophore menu, enabling confident target discrimination even in complex samples.

Browse list of wet-lab validated Copy Number Determination Assays and Centromeric CNV Assays.

Features and benefits

• Wet-lab validated assays available for more than 700 targets
• Centromeric reference assays available for more than 60 targets
• Absolute copy number accuracy through direct quantification of target copy number using Poisson statistics. No calibration curves or reference standards required.
• High tolerance to PCR efficiency differences and inhibitors
• Expanded multiplexing flexibility with 7-channel fluorophore support on QX700 systems (FAM, HEX, ATTO 550, ROX, ATTO 590, Cy5, Cy5.5), which enables higher-order multiplex CNV designs in a single reaction
• Improved cluster resolution with ATTO 550, which expands spacing between HEX and ROX for cleaner cluster separation
• Consistent performance across systems and dye combinations, with ATTO 550 demonstrating equivalent performance compared to HEX-labeled assays of identical sequence
• Reproducible copy number calling across instruments and dye combinations, supported by clear droplet separation for confident 1D and 2D analysis

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Assay Availability & Formats

• Species: human, mouse, rat
• Chemistry: probe-based ddPCR assays available in the portal
• Pack sizes: 200, 1,000, or 2,500 × 20 μL reactions

QX700 Assay Highlights

• ATTO 550–labeled GEX assays expand the dye menu for multiplex balancing
• naica™ Multiplex ddPCR Mix (5x or 10x) is the recommended master mix for probe-based assays on QX700 Systems

Platforms

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QX200 System^**

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QX600 System^*

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QX700 System^*

*For Research Use Only. Not for use in diagnostic procedures.

**For Research Use Only. In vitro diagnostic (IVD) option is available.

The copy number per microliter is reproducibly measured across the QX platforms. (QX700 assays were performed using naica Multiplex ddPCR Mix. Expected copy number: 1000 copies/µL) 

Copy Number Determination Panel demonstrates consistent performance across QX Systems, allowing you to select the system that best suits your needs. ddPCR CNV Assays are run on the QX200, QX600, and QX700 ddPCR Systems using Bio-Rad supermixes for consistent separation between positive and negative droplets.  

Related Products

• Digital Assays Portal—Copy Number Variation
• QX700 E Droplet Digital PCR System
• QX600 Droplet Digital PCR System
• naicaTM 5x Multiplex ddPCR Mix

Packaging Options

ddPCR Copy Number Determination Assays are available in multiple probe fluorophores. The ddPCR CNV Assays are provided in a 20X, ready-to-use primer-probe mix optimized for use with ddPCR Supermix for Probes (No dUTP). Each tube contains 18uM primers and 5uM probe