STANDARD_NAME	CHIN_BREAST_CANCER_COPY_NUMBER_UP
SYSTEMATIC_NAME	M672
COLLECTION	C2:CGP
MSIGDB_URL	https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/CHIN_BREAST_CANCER_COPY_NUMBER_UP
NAMESPACE	HUMAN_GENE_SYMBOL
DESCRIPTION_BRIEF	Genes from common regions of gains observed in more than 15% of 148 primary breast cancer tumors.
DESCRIPTION_FULL	We analysed 148 primary breast cancers using BAC-arrays containing 287 clones representing cancer-related gene/loci to obtain genomic molecular portraits. Gains were detected in 136 tumors (91.9%) and losses in 123 tumors (83.1%). Eight tumors (5.4%) did not have any genomic aberrations in the 281 clones analysed. Common (more than 15% of the samples) gains were observed at 8q11-qtel, 1q21-qtel, 17q11-q12 and 11q13, whereas common losses were observed at 16q12-qtel, 11ptel-p15.5, 1p36-ptel, 17p11.2-p12 and 8ptel-p22. Patients with tumors registering either less than 5% (median value) or less than 11% (third quartile) total copy number changes had a better overall survival (log-rank test: P=0.0417 and P=0.0375, respectively). Unsupervised hierarchical clustering based on copy number changes identified four clusters. Women with tumors from the cluster with amplification of three regions containing known breast oncogenes (11q13, 17q12 and 20q13) had a worse prognosis. The good prognosis group (Nottingham Prognostic Index (NPI) <or=3.4) tumors had frequent loss of 16q24-qtel. Genes significantly associated with estrogen receptor (ER), Grade and NPI were used to build k-nearest neighbor (KNN) classifiers that predicted ER, Grade and NPI status in the test set with an average misclassification rate of 24.7, 25.7 and 35.7%, respectively. These data raise the prospect of generating a molecular taxonomy of breast cancer based on copy number profiling using tumor DNA, which may be more generally applicable than expression microarray analysis.
PMID	17001317
GEOID	
AUTHORS	Chin SF,Wang Y,Thorne NP,Teschendorff AE,Pinder SE,Vias M,Naderi A,Roberts I,Barbosa-Morais NL,Garcia MJ,Iyer NG,Kranjac T,Robertson JF,Aparicio S,Tavaré S,Ellis I,Brenton JD,Caldas C
CONTRIBUTOR	Arthur Liberzon
CONTRIBUTOR_ORG	MSigDB Team
EXACT_SOURCE	Fig 2b: gains
FILTERED_BY_SIMILARITY	
EXTERNAL_NAMES_FOR_SIMILAR_TERMS	
EXTERNAL_DETAILS_URL	
SOURCE_MEMBERS	1QTEL10,AIB1,CAS,CCND1,COX2,CSE1L,CYP24,DCR3,E2F5,EMS1,ERBB2,EXT1,FGF3,FGF4,GARP,HER2,LAMC2,MOS,MYBL2,MYC,NCOA3,PAK1,PBP,PPARBP,PTGS2,PTK2,PTPN1,SHGC18290,SHGC31110,STK15,STK6,TGFB2,THRA,TNFRSF6B,TOP2A,U11829,WI1341,WI5663,ZABC1,ZNF217
GENE_SYMBOLS	,NCOA3,CSE1L,CCND1,MT-CO2,CSE1L,CYP24A1,TNFRSF6B,E2F5,CTTN,ERBB2,EXT1,FGF3,FGF4,LRRC32,ERBB2,LAMC2,MOS,MYBL2,MYC,NCOA3,PAK1,PEBP1,MED1,PTGS2,PTK2,PTPN1,,,AURKA,AURKA,TGFB2,THRA,TNFRSF6B,TOP2A,,,,ZNF217,ZNF217
FOUNDER_NAMES