# Copy number alteration (CNA)

Source: https://onco.cc/terms/copy-number-variation-term/  
OnCo record `copy-number-variation-term` (Term). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

A copy number alteration is a stretch of DNA that a tumour has gained extra copies of or lost, from a single gene to a whole chromosome arm.

## Summary

Copy number variation is a form of structural variation in which sections of the genome are duplicated or deleted (Wikipedia); in tumours the acquired form is called a somatic copy number alteration. Arm-level and focal events are called from arrays or sequencing, and GISTIC2.0 is the standard method for finding regions amplified or deleted more often than chance across a cohort. CNA is one of TCGA's core data types and a modality in most multi-omic models.

## Fields

- Kind: Term
- Last checked: 2026-09-24
- Also known as: copy number alteration; copy-number alteration; copy number alterations; somatic copy number alteration; SCNA; CNA; copy number variation; copy-number variation; CNV
- Tags: cansim-terms

## Notes

- Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/copy-number-alteration.

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Copy_number_variation
- Mermel et al., GISTIC2.0 (Genome Biology 2011): https://doi.org/10.1186/gb-2011-12-4-r41
- Wikipedia: https://en.wikipedia.org/wiki/Copy_number_variation

## Connected records

- terms: [Cancer AI vocabulary (CanSim terms map)](https://onco.cc/terms/cancer-ai-vocabulary/), [Co-amplification and the 17q12 HER2 amplicon](https://onco.cc/terms/co-amplification/), [GISTIC (copy number driver detection)](https://onco.cc/terms/gistic/)
- technologies: [Whole-exome & whole-genome sequencing](https://onco.cc/technologies/wes-wgs/)

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