# 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/), [KRAS allelic imbalance and mutant KRAS dosage in pancreatic cancer](https://onco.cc/terms/kras-allelic-imbalance/)
- technologies: [Whole-exome & whole-genome sequencing](https://onco.cc/technologies/wes-wgs/)
- cancers: [Colorectal cancer](https://onco.cc/cancers/colorectal/), [Non-small-cell lung cancer](https://onco.cc/cancers/nsclc/), [Pancreatic ductal adenocarcinoma](https://onco.cc/cancers/pancreatic/), [Prostate cancer](https://onco.cc/cancers/prostate/)
- key papers: [Combined tumour suppressor defects characterise clinically defined aggressive variant prostate cancers](https://onco.cc/key-papers/paper-aparicio-aggressive-variant-prostate-tumour-suppressors-ccr-2016/), [Comprehensive genomic characterization of squamous cell lung cancers](https://onco.cc/key-papers/paper-tcga-lung-squamous-nature-2012/), [Comprehensive genomic profiles of small cell lung cancer](https://onco.cc/key-papers/paper-george-sclc-genomic-profiles-nature-2015/), [Differences in prostate cancer genomes by self-reported race](https://onco.cc/key-papers/paper-stopsack-prostate-genomes-by-race-ccr-2022/), [Genetic instability in colorectal cancers](https://onco.cc/key-papers/paper-lengauer-genetic-instability-colorectal-nature-1997/), [Genomic and evolutionary classification of lung cancer in never smokers](https://onco.cc/key-papers/paper-zhang-lung-cancer-never-smokers-nat-genet-2021/), [Genomic hallmarks and structural variation in metastatic prostate cancer](https://onco.cc/key-papers/paper-quigley-structural-variation-mcrpc-cell-2018/), [Genomic landscape of lung adenocarcinoma in East Asians](https://onco.cc/key-papers/paper-chen-east-asian-lung-adenocarcinoma-nat-genet-2020/), [Integrative genomic profiling of human prostate cancer](https://onco.cc/key-papers/paper-taylor-integrative-genomic-profiling-cancer-cell-2010/), [Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution](https://onco.cc/key-papers/paper-chan-seng-yue-pancreatic-transcription-phenotypes-nat-genet-2020/), [Whole-genome and transcriptome sequencing of prostate cancer identifies new genetic alterations driving disease progression](https://onco.cc/key-papers/paper-ren-chinese-prostate-whole-genome-eur-urol-2018/)
- biomarkers: [AR amplification (gene and upstream enhancer)](https://onco.cc/biomarkers/ar-amplification/)

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