STANDARD_NAME	HEIDENBLAD_AMPLIFIED_IN_SOFT_TISSUE_CANCER
SYSTEMATIC_NAME	M6364
COLLECTION	C2:CGP
MSIGDB_URL	https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HEIDENBLAD_AMPLIFIED_IN_SOFT_TISSUE_CANCER
NAMESPACE	HUMAN_GENE_SYMBOL
DESCRIPTION_BRIEF	Genes from selected recurrently amplified regions in soft tissue tumors with supernumerary  ring chromosomes.
DESCRIPTION_FULL	Ring chromosomes and/or giant marker chromosomes have been observed in a variety of human tumor types, but they are particularly common in a subgroup of mesenchymal tumors of low-grade or borderline malignancy. These rings and markers have been shown to contain amplified material predominantly from 12q13-15, but also sequences from other chromosomes. Such amplified sequences were mapped in detail by genome-wide array comparative genomic hybridization in ring-containing tumor samples from soft tissue (n = 15) and bone (n = 6), using tiling resolution microarrays, encompassing 32 433 bacterial artificial chromosome clones. The DNA copy number profiles revealed multiple amplification targets, in many cases highly discontinuous, leading to delineation of large numbers of very small amplicons. A total number of 356 (median size: 0.64 Mb) amplicons were seen in the soft tissue tumors and 90 (median size: 1.19 Mb) in the bone tumors. Notably, more than 40% of all amplicons in both soft tissue and bone tumors were mapped to chromosome 12, and at least one of the previously reported recurrent amplifications in 12q13.3-14.1 and 12q15.1, including SAS and CDK4, and MDM2, respectively, were present in 85% of the soft tissue tumors and in all of the bone tumors. Although chromosome 12 was the only chromosome displaying recurrent amplification in the bone tumors, the soft tissue tumors frequently showed recurrent amplicons mapping to other chromosomes, that is, 1p32, 1q23-24, 3p11-12, 6q24-25 and 20q11-12. Of particular interest, amplicons containing genes involved in the c-jun NH2-terminal kinase/mitogen-activated protein kinase pathway, that is, JUN in 1p32 and MAP3K7IP2 (TAB2) in 6q24-25, were found to be independently amplified in eight of 11 cases with 12q amplification, providing strong support for the notion that aberrant expression of this pathway is an important step in the dedifferentiation of liposarcomas.
PMID	16732325
GEOID	
AUTHORS	Heidenblad M,Hallor KH,Staaf J,Jönsson G,Borg A,Höglund M,Mertens F,Mandahl N
CONTRIBUTOR	Arthur Liberzon
CONTRIBUTOR_ORG	MSigDB Team
EXACT_SOURCE	Table 2: soft tissue tumors
FILTERED_BY_SIMILARITY	
EXTERNAL_NAMES_FOR_SIMILAR_TERMS	
EXTERNAL_DETAILS_URL	
SOURCE_MEMBERS	APOA2,CDK4,JUN,MAP3K7IP2,MDM2,POU1F1,PTPRT,SAS,SRC,TOP1,USF1,VGL-3,YEATS4
GENE_SYMBOLS	APOA2,CDK4,JUN,TAB2,MDM2,POU1F1,PTPRT,TSPAN31,SRC,TOP1,USF1,VGLL3,YEATS4
FOUNDER_NAMES