Copy number variation analysis

Copy number variation (CNV) analysis determines the number of copies of a particular gene in an individual's genome. It is known that genes occur in two copies per genome; however, these genes can occur more often in some cases. Gene amplification (which activates oncogenes) and deletion (which inactivates tumor suppressor genes) are important copy number alterations (CNAs) that affect cancer-related genes, in addition to the genomic changes such as point mutations, translocations and inversions. Most cancer-related genes affected by CNAs have been defined as critical genes in cancer-signaling pathways involved in carcinogenesis and cancer progression. CNVs are an essential source of genetic diversity (deletion or duplication of a locus) and allow studying genes associated with common neurological and autoimmune diseases, genetic conditions and adverse drug responses.

Benefits of using nanoplate dPCR for CNV analysis

  • Detection of less than 1.2-fold change in CNVs, with results in about 2 hours
  • Improved economic and throughput level of dPCR CNV analysis with the 8.5K Nanoplate or multiplexing capabilities or finer discrimination of consecutive copy number states with the 26K Nanoplate
  • Automatic calculation of CNVs with the QIAcuity Software Suite and possibility to design custom assays

Multiplex digital PCR for mitochondrial and genomic target copy number analysis

Explore a workflow for high-throughput analyses of target copy numbers in cultured cells. The process combines fast and accurate cell sorting from CellenONE to ensure an exact number of cells are used in downstream reactions. The samples are subjected to probe-based detection on the QIAcuity Digital PCR System with multiplexing of up to 12 targets in a single dPCR reaction with minimal optimization. The workflow achieves accurate absolute DNA quantification by dPCR for analysis of low abundance targets as well as multi-copy targets at single-cell level.

Download now
Copy variation

Related publications

Bacman SR et al. mitoTALEN reduces the mutant mtDNA load in neurons. Mol Ther Nucleic Acids. 2024;35(1):102132.

Toffoli M et al. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene. Communications Biology. 2022;5:670.

Tergemina E et al. A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment. Science Advances. 2022;8(20).

Shoop WK et al. Precise and simultaneous quantification of mitochondrial DNA heteroplasmy and copy number by digital PCR. Journal of Biological Chemistry. 2022;298(11):102574.

Further resources

Karalay O et al. Detection of rare events using the QIAcuity® Digital PCR System. QIAGEN, 2023.

Customize your dPCR CNV assay
Looking for a very specific target? Design your own dPCR CNV assay in just a few minutes with our custom design tool.
Start now