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

Genome biology | Oct 20, 2011

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.

Pubmed ID: 21527027 RIS Download

Mesh terms: Algorithms | Computational Biology | Computer Simulation | Gene Dosage | Humans | Models, Theoretical | Neoplasms | Software | Tumor Suppressor Proteins

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GenePattern

A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

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Broad Institute

A biomedical and genomic research center that is independently governed that encompasses three types of organizational units: core member laboratories, programs and platforms which work together and with other collaborators to tackle critical problems in human biology and disease. Data and cutting edge software tools are generated and developed, and these tools analyze those data (increasingly large genome-related datasets) which is shared openly with the scientific community. The Broad faculty includes core members and associate members. All associate members hold primary appointments in a home department at one of the partner institutions, but are deeply involved in the scientific work and culture of the Broad Institute. It is formally affiliated with the Massachusetts Institute of Technology, Harvard University and its affiliated hospitals.

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