Copy Number Variation (CNV)

Copy Number Variation (CNV) is common throughout the human genome and can significantly impact human health. One area of research where CNV is of particular importance is pharmacogenomics, as this testing can provide information on drug metabolism. While several methods and instruments are on the market for this purpose, there remains an unmet need for a fully-automated method of CNV analysis.

The IntelliQube® qPCR system is designed to address this need by producing accurate and reliable results with walk-away automation that substantially reduces reagent expenditures and labor requirements.


In a recent CNV study, CYP2D6 copy number was determined for 51 genomic DNA samples using three TaqMan® CNV assays in miniaturized (1.6 µL) reactions on the IntelliQube as compared with the ViiA™ 7 Real-Time qPCR System. The calculated Cq values from both instruments were analyzed in CopyCaller® Software (Thermo Fisher Scientific Inc) using the sample with the median Cq value as the two copy calibrator (Figure 1).

CNV Determination

Figure 1: Copy Number Determination: Bar graphs indicating the copy number predicted by CopyCaller for assays Intron2 (A), Intron6 (B), and Exon9 (C) of CYP2D6 are shown for both the IntelliQube (Blue) and the ViiA 7 (Orange). Error bars indicate the range for the calculated copy number of the four replicates for each sample.

The copy number results for all samples were 100% concordant between the IntelliQube and ViiA 7, and matched previously published data. This study shows that CNV assays can be successfully miniaturized in Array Tape® and offer a 68% reduction in cost per data point (Table 1). Therefore, the IntelliQube provides laboratories a compelling new high throughput alternative to traditional PCR-based CNV techniques.

PerfeCta® qPCR ToughMix®, UNG, ROX™
CYP2D6 Copy Number Assay
RNaseP Reference Assay

Table 1: Reagent cost comparison between 1.6 µL reactions in Array Tape and 5 µL reactions in 384-well PCR plates. Reagent pricing may vary based on order size.

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