Evaluation of a New Accurate, Automated and Cost-effective Approach for the Analysis of Pharmacologically Important Copy Number Variation

Copy number variation (CNV) of the cytochrome P450 2D6 (CYP2D6) gene, including deletions and gene  multiplications, can result in reduced or increased metabolism of many clinically relevant drugs. Recent advances within personalized medicine have led medical practitioners to increasingly rely on CYP2D6 CNV status, along with routine SNP genotype data, to guide drug dosage decisions for their patients. 

Research within this field continues to evolve and quantitative PCR (qPCR) has become a common method for assessing CNV status, with various probe-based assays widely available for analysis of genomic DNA. Moreover, while there are  several PCR instruments on the market upon which these assays could be performed, there remains an unmet need for a fully-automated solution that provides  laboratories the flexibility and scalability necessary to economically expand the access to the valuable genetic information provided by PCR analysis. 

The IntelliQube® from Douglas Scientific® is designed to address this need by producing accurate and reliable results for studies such as CNV determination, with walk-away automation that substantially reduces reagent expenditures and  labor needs. In this study we assessed the performance of the IntelliQube by analyzing human genomic DNA with commercially available CYP2D6 CNV assays to  determine CNV status. Using highly characterized  reference samples from Coriell Institute for Medical  Research, we compared copy number results from the  IntelliQube to those previously published in the  literature. An additional comparative data set was produced with the same samples and assays in a 5 μL reaction format using a ViiA™ 7 Real-Time PCR instrument (Thermo Fisher Scientific Inc.). In the study, we found that the IntelliQube demonstrates accurate and reproducible CYP2D6 CNV results consistent with those generated using standard plate-based methods and instruments. Combined with the automated workflow and economic benefits of Array Tape®, the IntelliQube proves to be a useful and powerful platform for high throughput CNV testing.