Copy Number Calculators

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Copy number refers to the number of copies of a particular DNA segment — such as a gene, exon, or genomic region — present in a cell's genome. While most diploid human cells carry two copies of every autosomal gene, copy number variation (CNV) is surprisingly common — insertions, deletions, and duplications mean that many individuals carry more or fewer than two copies of specific genomic regions. CNVs can affect gene expression dosage, drive cancer evolution, and contribute to susceptibility to numerous diseases. Measuring gene copy number with qPCR is also a routine task in gene therapy, GMO detection, and viral genomics.

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What Is Copy Number?

In genetics, copy number is the number of times a particular DNA sequence appears in a cell's genome. In a normal diploid cell, autosomal genes are present in two copies (one from each parental chromosome). Copy number variation (CNV) refers to genomic regions where copy number differs between individuals — some people may have 0, 1, 3, 4, or more copies of a particular gene or segment.

Types of Copy Number Variation

  • Deletion: One or more copies of a genomic segment are missing — reducing gene dosage. May be heterozygous (1 copy instead of 2) or homozygous (0 copies).
  • Duplication: Extra copies of a segment — increasing gene dosage. May involve tandem repeats or insertions elsewhere in the genome.
  • Amplification: Many extra copies, especially of oncogenes in cancer (e.g., HER2 amplification in breast cancer — typically 20+ copies).

Clinical Significance of CNVs

  • Cancer: Amplification of oncogenes (MYCN, HER2, EGFR) and deletion of tumor suppressors (TP53, BRCA1) are hallmarks of cancer genomes. CNV profiling is standard in cancer genomics.
  • Neurodevelopmental disorders: CNVs at specific loci cause conditions such as DiGeorge syndrome (22q11 deletion), Williams syndrome (7q11 deletion), and Prader-Willi syndrome.
  • Drug metabolism: CYP2D6 copy number varies widely — individuals with CNV > 2 copies are ultra-rapid metabolizers; those with 0 copies are poor metabolizers of many drugs.

Measuring Copy Number with qPCR

Relative copy number by qPCR uses the 2^−ΔΔCt method, comparing a target locus to a single-copy reference gene in a DNA sample. If ΔCt (target − reference) differs by ~1 cycle compared to a diploid standard, this represents a single copy change:

Relative copy number = 2 × 2^(−ΔΔCt)

The factor 2 accounts for the diploid reference. Values of ~1 = 1 copy (deletion); ~2 = normal diploid; ~3+ = gain.

Array CGH and SNP Arrays

Array comparative genomic hybridization (aCGH) and SNP arrays detect CNVs genome-wide by comparing the hybridization intensity of test vs. reference DNA across thousands of probes. NGS-based CNV calling (from WGS or targeted panels) is increasingly used for high-resolution, quantitative CNV detection.

Glossary

Copy Number Variation (CNV)
Differences in the number of copies of a genomic DNA segment between individuals. Normal diploid = 2 copies. CNVs include deletions (fewer copies) and duplications/amplifications (more copies). Affect gene dosage and contribute to disease.
Gene Amplification
An extreme copy number increase, producing many copies of a genomic region — especially of oncogenes in cancer. HER2, MYCN, and EGFR amplification drive specific cancer subtypes and are targets for therapy.
Array CGH (Comparative Genomic Hybridization)
A microarray-based method for genome-wide CNV detection. Test and reference DNA are differentially labeled and co-hybridized to probes; intensity ratios indicate copy number gains or losses at each probe location.

Frequently Asked Questions

Copy number variation is the presence of more or fewer than the expected two copies of a genomic DNA segment in an individual. CNVs range from a few hundred base pairs to megabases in size and affect ~12% of the human genome. They can delete genes (reducing expression), duplicate them (increasing expression), or amplify oncogenes in cancer. CNVs are a major source of genetic variation between individuals alongside SNPs.

Use 2^−ΔΔCt with DNA (not RNA). Compare the Ct of the target gene to a known diploid single-copy reference gene in your sample, then to a calibrator sample with known copy number (typically 2). Relative copy number = 2 × 2^(−ΔΔCt). A relative copy number of ~1 indicates one copy (deletion); ~2 is normal diploid; ~3 indicates a single-copy gain. Accuracy requires high PCR efficiency and technical replicates.

HER2 (ERBB2) is a gene encoding a receptor tyrosine kinase on chromosome 17q12. In ~15–20% of breast cancers, this region is amplified — cells may contain 20+ copies of HER2. Amplification leads to overexpression of the HER2 protein, driving tumor cell proliferation. HER2-positive tumors are targeted by trastuzumab (Herceptin), pertuzumab, and T-DM1. HER2 status is routinely tested by FISH, CISH, or IHC on tumor biopsies.

A SNP (single nucleotide polymorphism) is a single base-pair change in the DNA sequence — the sequence is present in both chromosomes but the nucleotide differs. A CNV is a difference in the number of copies of a DNA segment — entire gene(s) may be present in 0, 1, 3, or more copies instead of the normal 2. SNPs are the most common type of genetic variation; CNVs affect larger segments and typically have larger effects on gene expression per variant.