Gene Set: LIN_MELANOMA_COPY_NUMBER_UP

Standard name LIN_MELANOMA_COPY_NUMBER_UP
Systematic name M346
Brief description Candidate genes in significant regions of chromosomal copy number gains in a panel of melanoma samples.
Full description or abstract The classification of human tumors based on molecular criteria offers tremendous clinical potential; however, discerning critical and druggable effectors on a large scale will also require robust experimental models reflective of tumor genomic diversity. Here, we describe a comprehensive genomic analysis of 101 melanoma short-term cultures and cell lines. Using an analytic approach designed to enrich for putative driver events, we show that cultured melanoma cells encompass the spectrum of significant genomic alterations present in primary tumors. When annotated according to these lesions, melanomas cluster into subgroups suggestive of distinct oncogenic mechanisms. Integrating gene expression data suggests novel candidate effector genes linked to recurrent copy gains and losses, including both phosphatase and tensin homologue (PTEN)-dependent and PTEN-independent tumor suppressor mechanisms associated with chromosome 10 deletions. Finally, sample-matched pharmacologic data show that FGFR1 mutations and extracellular signal-regulated kinase (ERK) activation may modulate sensitivity to mitogen-activated protein kinase/ERK kinase inhibitors. Genetically defined cell culture collections therefore offer a rich framework for systematic functional studies in melanoma and other tumors.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 18245465   Authors: Lin WM,Baker AC,Beroukhim R,Winckler W,Feng W,Marmion JM,Laine E,Greulich H,Tseng H,Gates C,Hodi FS,Dranoff G,Sellers WR,Thomas RK,Meyerson M,Golub TR,Dummer R,Herlyn M,Getz G,Garraway LA
Exact source Table 1
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(show 344 gene sets from the same authors)
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Organism Homo sapiens
Contributed by Jessica Robertson (Broad Institute)
Source platform HUMAN_GENE_SYMBOL
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Compendia expression profiles Human tissue compendium (Novartis)
NCI-60 cell lines (National Cancer Institute)
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Version history 3.0: First introduced

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