Copy Number Variation (CNV) Using Digital PCR

Precise genomic copy number variation analysis

Copy number variation (CNV) is defined as a modification in the genome where the number of copies of a genomic DNA sequence differs from a reference or standard. Genomic alterations such as insertions, deletions, inversions, or translocation can lead to biallelic or multiallelic CNVs. CNVs are linked to susceptibility or resistance to disease, and thus are an important area for detailed study. Many methods of CNV detection exist today, including fluorescent in situ hybridization (FISH), comparative genomic hybridization (CGH), array comparative genomic hybridization (aCGH), real-time PCR (qPCR), and next-generation sequencing (NGS).   

Despite advances in some of these technologies, in many cases, measurements are not sufficiently precise for determining copy number differences where the ratios between the target and reference are very small. Digital PCR, a technology capable of highly precise measurements, enables the detection of low percent copy number differences to be detected and accurately quantified.

A representative panel of 9 genomic DNA samples, procured from the Coriell repository, was analyzed using the QuantStudio™ 3D system and a standard TaqMan® Copy Number Assay specific to the CCL3L1 genetic locus found on the long arm of chromosome 17, 6, or 8. Replicate measurements indicated that the samples represent copy number variations from 0 to 8 copies per genome (Figure 1A). A statistically significant difference between samples containing 7 and 8 copies was clearly discernable as a result of the high degree of precision achieved, confirming that digital PCR can differentiate less than a 1.2-fold difference (Figure 1B).

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Figure 1. Precision demonstrated for copy number analysis of the CCL3L1 genetic locus on chromosome 17. (A) Copy number was measured across 9 DNA samples. The CV (column 6) was below 2.5% for each set of replicates, demonstrating a high degree of measurement reproducibility within each replicate group. (B) As demonstrated by non-overlapping error bars, the achieved measurement precision enables statistical discernment of the CCL3L1 copy number in samples containing 7 and 8 copies.

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Gabriele Zoppoli, MD, PhD, Internal Medicine and Clinical Oncology Division, Department of Internal Medicine, University of Genova, Genova, Italy

Gabriele Zoppoli, MD, PhD, Internal Medicine and Clinical Oncology Division, Department of Internal Medicine, University of Genova, Genova, Italy

When performing CNV with digital PCR, you're performing an absolute quantitation of the actual locus of interest. To convert absolute quantities to a copy number, compare a target to a reference locus that has not been amplified or changed in any way.

 

Bruno Ping, Lab Manager, Royal Surrey County Hospital, Guildford, United Kingdom

Bruno Ping, Lab Manager, Royal Surrey County Hospital, Guildford, United Kingdom

Literature
Bruno Ping

Your Innovative Research: "Copy number variation in breast cancer translational research; QuantStudio™ 3D Digital PCR System as a cost-effective and sensitive alternative for HER2 gene amplification assessment" by Bruno Ping, Lab Manager, Royal Surrey County Hospital, Guildford, United Kingdom

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QuantStudio™ 3D Digital PCR System

QuantStudio™ 3D Digital PCR System

Absolute quantification, using sealed-chip technology, for a reliable method and precise, sensitive data.

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Sku Name Size Price Qty
4428234 GeneAmp® PCR System 9700, Dual Flat Block 1 instrument Contact Us  
4485513 QuantStudio™ 3D Digital PCR Chip Adapter Kit for Flat Block Thermal Cycler 1 kit USD 46.35
4485507 QuantStudio™ 3D Digital PCR Chips 12 chips USD 102.00
4482710 QuantStudio™ 3D Digital PCR Master Mix 1.5 mL USD 140.00
4485718 QuantStudio™ 3D Digital PCR Master Mix 5 mL USD 410.00
4489084 QuantStudio™ 3D Digital PCR Instrument with Power Cord 1 instrument USD 30,900.00