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).
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
Gabriele Zoppoli, MD, PhD, Internal Medicine and Clinical Oncology Division, Department of Internal Medicine, University of Genova, Genova, Italy
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
Application Note: Copy number variation analysis using the QuantStudio 3D Digital PCR System
Product Bulletin: QuantStudio 3D Digital PCR System
User Guide: QuantStudio 3D Digital PCR System
Digital PCR Experiment Design Guide
For Research Use Only. Not for use in diagnostic procedures.