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GISTIC is a tool to identify genes targeted by somatic copy number variation (CNV). The GISTIC algorithm defines CNV boundaries by a user-defined confidence level.
Alternative name: GISTIC2.


Genetics; Oncology; Genetic variation


  • Operation: Variant detection; Copy number estimation
  • Software interface: Command-line user interface
  • Language: Matlab
  • Operating system: Linux
  • License: Other
  • Cost: Free
  • Version name: 2.0.23
  • Maturity: Stable
  • Credit: Genome Characterization Center Grant (U24CA143867) awarded as part of the NCI/NHGRI funded Cancer Genome Atlas (TCGA) project, the National Institute of General Medical Sciences, V Foundation Scholarship, and the Doris Duke Charitable Foundation
  • Contact: Craig H Mermel cmermel _at_ | Steven E Schumacher steven_schumacher _at_ | Barbara Hill bhill _at_ | Matthew L Meyerson Matthew_Meyerson _at_ | Rameen Beroukhim Rameen_Beroukhim _at_ | Gad Getz gadgetz _at_
  • Collection: -


Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G "GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers." Genome Biol. 2011;12(4):R41.
PMID: 21527027
PMCID: PMC3218867

Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, Demichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M. "The landscape of somatic copy-number alteration across human cancers" Nature
PMID: 20164920
PMCID: PMC2826709

Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S, Du J, Kau T, Thomas RK, Shah K, Soto H, Perner S, Prensner J, Debiasi RM, Demichelis F, Hatton C, Rubin MA, Garraway LA, Nelson SF, Liau L, Mischel PS, Cloughesy TF, Meyerson M, Golub TA, Lander ES, Mellinghoff IK, Sellers WR "Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma." Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):20007-12. Epub 2007 Dec 6.
PMID: 18077431
PMCID: PMC2148413

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