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E-GEOD-34573 - A Global View of the Oncogenic Landscape in Nasopharyngeal Carcinoma:An Integrated Analysis at the Genetic and Expression Levels

Status
Released on 10 December 2012, last updated on 13 May 2014
Organism
Homo sapiens
Samples (64)
Arrays (3)
Protocols (20)
Description
Previous studies have reported that the tumour cells of nasopharyngeal carcinoma (NPC) exhibit both recurrent chromosome abnormalities and changes in the expression of numerous genes. However, it is not known to what extent changes in the copy number of individual genes are associated with the observed expression changes. To address this, a genome wide analysis of chromosome copy number and gene expression was performed in tumour cells micro-dissected from the same NPC biopsies. Significant gene expression changes were identified in tumour suppressor genes (TSGs) and in tumour-promoting genes (TPGs) but almost 60% of these can be either upregulated or downregulated in different types of cancer. This suggests that the simplistic classification of genes as TSGs or TPGs may not be entirely appropriate and that the concept of onco-suppressors may be more extensive than previously recognised. Several genomic regions showing frequent copy number gain or loss were identified. Whereas TSGs were significantly enriched within regions of frequent loss, no significant enrichment of TPGs was observed in regions of frequent gain. However, on a gene by gene basis little correlation was found between DNA copy number and alterations in gene expression except for loss of expression from homozygous deletions and a single highly amplified segment which showed enhanced gene expression. Gene expression and DNA copy number of nasopharyngeal carcinoma was compared with those of normal controls.
Experiment types
transcription profiling by array, genotyping by array, comparative genomic hybridization by array 
Contacts
Aicha Amari, Andrew I Bell, Christopher W Dawson, Chunfang Hu, Ciaran B Woodman, Dalia Derkaoui, Irène Joab, Jian-Yong Shao, John Nicholls, John R Arrand, Lawrence S Young, Paul G Murray, Sim K Sihota, Stephanie L Maloney, Wenbin Wei, Xiaoyi Chen, Yunhong Yao
Citation
A global view of the oncogenic landscape in nasopharyngeal carcinoma: an integrated analysis at the genetic and expression levels. Hu C, Wei W, Chen X, Woodman CB, Yao Y, Nicholls JM, Joab I, Sihota SK, Shao JY, Derkaoui KD, Amari A, Maloney SL, Bell AI, Murray PG, Dawson CW, Young LS, Arrand JR. , PMID:22815911
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