{"entity":{"id":"copy-number-variation-term","kind":"term","name":"Copy number alteration (CNA)","aka":["copy number alteration","copy-number alteration","copy number alterations","somatic copy number alteration","SCNA","CNA","copy number variation","copy-number variation","CNV"],"tldr":"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.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/Copy_number_variation","links":[{"label":"Mermel et al., GISTIC2.0 (Genome Biology 2011)","url":"https://doi.org/10.1186/gb-2011-12-4-r41"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Copy_number_variation"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":["wes-wgs"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["co-amplification","gistic"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"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."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"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"},"category":"Genomics & genetics"},"route":"/terms/copy-number-variation-term/","neighbours":{"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"co-amplification","kind":"term","name":"Co-amplification and the 17q12 HER2 amplicon","route":"/terms/co-amplification/"},{"id":"gistic","kind":"term","name":"GISTIC (copy number driver detection)","route":"/terms/gistic/"},{"id":"kras-allelic-imbalance","kind":"term","name":"KRAS allelic imbalance and mutant KRAS dosage in pancreatic cancer","route":"/terms/kras-allelic-imbalance/"}],"technology":[{"id":"wes-wgs","kind":"technology","name":"Whole-exome & whole-genome sequencing","route":"/technologies/wes-wgs/"}],"cancer":[{"id":"colorectal","kind":"cancer","name":"Colorectal cancer","route":"/cancers/colorectal/"},{"id":"nsclc","kind":"cancer","name":"Non-small-cell lung cancer","route":"/cancers/nsclc/"},{"id":"pancreatic","kind":"cancer","name":"Pancreatic ductal adenocarcinoma","route":"/cancers/pancreatic/"},{"id":"prostate","kind":"cancer","name":"Prostate cancer","route":"/cancers/prostate/"}],"paper":[{"id":"paper-aparicio-aggressive-variant-prostate-tumour-suppressors-ccr-2016","kind":"paper","name":"Combined tumour suppressor defects characterise clinically defined aggressive variant prostate cancers","route":"/key-papers/paper-aparicio-aggressive-variant-prostate-tumour-suppressors-ccr-2016/"},{"id":"paper-tcga-lung-squamous-nature-2012","kind":"paper","name":"Comprehensive genomic characterization of squamous cell lung cancers","route":"/key-papers/paper-tcga-lung-squamous-nature-2012/"},{"id":"paper-george-sclc-genomic-profiles-nature-2015","kind":"paper","name":"Comprehensive genomic profiles of small cell lung cancer","route":"/key-papers/paper-george-sclc-genomic-profiles-nature-2015/"},{"id":"paper-stopsack-prostate-genomes-by-race-ccr-2022","kind":"paper","name":"Differences in prostate cancer genomes by self-reported race","route":"/key-papers/paper-stopsack-prostate-genomes-by-race-ccr-2022/"},{"id":"paper-lengauer-genetic-instability-colorectal-nature-1997","kind":"paper","name":"Genetic instability in colorectal cancers","route":"/key-papers/paper-lengauer-genetic-instability-colorectal-nature-1997/"},{"id":"paper-zhang-lung-cancer-never-smokers-nat-genet-2021","kind":"paper","name":"Genomic and evolutionary classification of lung cancer in never smokers","route":"/key-papers/paper-zhang-lung-cancer-never-smokers-nat-genet-2021/"},{"id":"paper-quigley-structural-variation-mcrpc-cell-2018","kind":"paper","name":"Genomic hallmarks and structural variation in metastatic prostate cancer","route":"/key-papers/paper-quigley-structural-variation-mcrpc-cell-2018/"},{"id":"paper-chen-east-asian-lung-adenocarcinoma-nat-genet-2020","kind":"paper","name":"Genomic landscape of lung adenocarcinoma in East Asians","route":"/key-papers/paper-chen-east-asian-lung-adenocarcinoma-nat-genet-2020/"},{"id":"paper-taylor-integrative-genomic-profiling-cancer-cell-2010","kind":"paper","name":"Integrative genomic profiling of human prostate cancer","route":"/key-papers/paper-taylor-integrative-genomic-profiling-cancer-cell-2010/"},{"id":"paper-chan-seng-yue-pancreatic-transcription-phenotypes-nat-genet-2020","kind":"paper","name":"Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution","route":"/key-papers/paper-chan-seng-yue-pancreatic-transcription-phenotypes-nat-genet-2020/"},{"id":"paper-ren-chinese-prostate-whole-genome-eur-urol-2018","kind":"paper","name":"Whole-genome and transcriptome sequencing of prostate cancer identifies new genetic alterations driving disease progression","route":"/key-papers/paper-ren-chinese-prostate-whole-genome-eur-urol-2018/"}],"biomarker":[{"id":"ar-amplification","kind":"biomarker","name":"AR amplification (gene and upstream enhancer)","route":"/biomarkers/ar-amplification/"}]}}