GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

Mermel, C. H., Schumacher, S. E., Hill, B., Meyerson, M. L., Beroukhim, R., and Getz, G. (2011). GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol, 12(4), R41. doi: 10.1186/gb-2011-12-4-r41. Published: 2011.03.28

Craig Mermel, Steven Schumacher, Barbara Hill, Matthew Meyerson, Rameen Beroukhim, and Gad Getz

Read Manuscript

Abstract

We 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.

Keywords: GISTIC, SNP Array

Supplemental Data

Description	Link/Filename
Installation Instructions	ftp://ftp.broadinstitute.org/pub/GISTIC2.0/INSTALL.txt
GISTIC 2.0.22 Source (.tar.gz)	ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTIC_2_0_22.tar.gz
GISTIC 2.0 Documentation	ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm
Human Reference Genome (build 19)	ftp://ftp.broadinstitute.org/pub/GISTIC2.0/hg19.mat
Source Archives	ftp://ftp.broadinstitute.org/pub/GISTIC2.0/all_versions