Detecting copy number variations
Copy number variation (CNV) analysis determines the number of copies of a specific gene in an individual's genome. While most genes occur in two copies, CNVs help drive genetic diversity or arise in neurological and autoimmune diseases and adverse drug responses. Copy number alterations (CNAs) are a subset of CNVs that are typically cancer-related. CNAs mostly affect oncogenes and tumor suppressor genes either through amplification or deletions of DNA segments. These gains or losses disturb gene function, contributing to cancer initiation and progression.
Why use nanoplate dPCR for CNV analysis
- Detection of less than 1.2-fold change in CNV mutations with results in about 2 hours
- Improved economic and throughput level of dPCR CNV analysis with the 8.5K Nanoplate or multiplexing capabilities and finer discrimination of consecutive copy number states with the 26K Nanoplate
- Automatic calculation of copy number variations with the QIAcuity Software Suite and possibility to design custom assays
Common methods for CNV analysis
CNV analysis with nanoplate dPCR
Customer experience: QIAcuity for CNV analysis
Related products
Scientific publications with dPCR for CNV analysis
Tanaka J, et al. Highly multiplexed digital PCR assay for simultaneous quantification of variant allele frequencies and copy number alterations of KRAS and GNAS in pancreatic cancer precursors. Mol Oncol. 2025. doi:10.1002/1878-0261.70011.
Herdt LR, et al. NSCLC digital PCR panel returns low-input sample results where sequencing fails. Diagnostics. 2024;14(3):243.
Andric F et al. Immune Microenvironment in Sporadic Early-Onset Versus Average-Onset Colorectal Cancer. Cancers. 2023;15(5):1457.
Hélias-Rodzewicz Z et al. Molecular and clinicopathologic characterization of pediatric histiocytosis. American Journal of Hematology. 2023;DOI:10.1002/ajh.26938.
Crucitta S et al. Comparison of digital PCR systems for the analysis of liquid biopsy samples of patients affected by lung and colorectal cancer. Clinica Chimica Acta. 2023;541:117239.
Further resources on detecting copy number variations with dPCR
Detection of rare events using the QIAcuity Digital PCR System
FAQs on dPCR for copy number variation analysis
Q1: How does digital PCR detect copy number variations?A1: Digital PCR measures copy number by partitioning the reagents for two fluorescence assays (one for the CNV of interest, such as HER2 and one for a control reference locus of known copy number, such as GAPDH) into thousands of partitions. A fluorescence signal indicates the presence of a DNA molecule, whereas no fluorescence signal indicates the absence of a DNA molecule. Copy number is calculated by comparing the number of molecules arising from the CNV segment of interest (calculated from the number of positive partitions) to the number of molecules arising from the reference genomic locus. Unlike qPCR, which only estimates the copy numbers that are present in each genome, dPCR can measure the precise, integer level in an individual’s genome.
Q2: What are common applications of CNV analysis with dPCR?
A2: Digital PCR can be used to identify copy number variations in disease, drug response, cancer development, genetic diversity, cell and gene therapy and more. On GeneGlobe, you can find dPCR assays for more than 90,000 targets of interest or even design your own. Digital PCR is also readily applicable to rare CNVs, such as HTT (Huntington’s Disease), 22q11.2 deletion/duplication (DiGeorge syndrome, etc.), CYP2D6 (for drug therapy guidance), amongst others.
Q3: How does digital PCR compare to NGS for CNV analysis?
A3: Digital PCR offers a low limit of detection with high sensitivity and absolute quantification of even rare CNV mutations. NGS requires no prior knowledge of sequence information and can be used to study multiple CNVs in parallel. Because of their differences, dPCR and NGS could be considered as complementary methods instead. For example, NGS can provide comprehensive CNV profiling and serve as a tool for CNV discovery. Once the CNVs of interest have been identified by NGS, dPCR can validate the data and be used for routine analysis, such as tracking resistance levels to therapies over time.