GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
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 add...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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BioMed Central Ltd.
2011
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| Online Access: | http://hdl.handle.net/1721.1/66962 |
| _version_ | 1826215095362912256 |
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| author | Mermel, Craig H. Schumacher, Steven E. Hill, Barbara Meyerson, Matthew L. Beroukhim, Rameen Getz, Gad |
| author2 | Whitaker College of Health Sciences and Technology |
| author_facet | Whitaker College of Health Sciences and Technology Mermel, Craig H. Schumacher, Steven E. Hill, Barbara Meyerson, Matthew L. Beroukhim, Rameen Getz, Gad |
| author_sort | Mermel, Craig H. |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T16:16:28Z |
| format | Article |
| id | mit-1721.1/66962 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:16:28Z |
| publishDate | 2011 |
| publisher | BioMed Central Ltd. |
| record_format | dspace |
| spelling | mit-1721.1/669622022-10-02T07:28:10Z GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers Mermel, Craig H. Schumacher, Steven E. Hill, Barbara Meyerson, Matthew L. Beroukhim, Rameen Getz, Gad Whitaker College of Health Sciences and Technology Broad Institute of MIT and Harvard Harvard University--MIT Division of Health Sciences and Technology Meyerson, Matthew L. Mermel, Craig H. Schumacher, Steven E. Hill, Barbara Meyerson, Matthew L. Beroukhim, Rameen Getz, Gad 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. 2011-11-07T21:27:08Z 2011-11-07T21:27:08Z 2011-04 2011-02 Article http://purl.org/eprint/type/JournalArticle 1474-760X 1474-7596 http://hdl.handle.net/1721.1/66962 Mermel, Craig H et al. “GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.” Genome Biology 12 (2011): R41. en_US http://dx.doi.org/10.1186/gb-2011-12-4-r41 Genome Biology Creative Commons Attribution http://creativecommons.org/licenses/by/2.0/ application/pdf BioMed Central Ltd. BMC |
| spellingShingle | Mermel, Craig H. Schumacher, Steven E. Hill, Barbara Meyerson, Matthew L. Beroukhim, Rameen Getz, Gad GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers |
| title | GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers |
| title_full | GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers |
| title_fullStr | GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers |
| title_full_unstemmed | GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers |
| title_short | GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers |
| title_sort | gistic2 0 facilitates sensitive and confident localization of the targets of focal somatic copy number alteration in human cancers |
| url | http://hdl.handle.net/1721.1/66962 |
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