Mermel, Craig H.Schumacher, Steven E.Hill, BarbaraMeyerson, Matthew L.Beroukhim, RameenGetz, Gad2019-10-052011Mermel, Craig H, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, and Gad Getz. 2011. “GISTIC2.0 Facilitates Sensitive and Confident Localization of the Targets of Focal Somatic Copy-Number Alteration in Human Cancers.” Genome Biology 12 (4). https://doi.org/10.1186/gb-2011-12-4-r41.1474-75961474-760Xhttp://nrs.harvard.edu/urn-3:HUL.InstRepos:41482911We describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, we improve the estimation of background rates for each category. We additionally describe a probabilistic method for defining the boundaries of selected-for SCNA regions with user-defined confidence. Here we detail this revised computational approach, GISTIC2.0, and validate its performance in real and simulated datasets.en-USJournal Article2019-10-0510.1186/gb-2011-12-4-r41