E-GEOD-8398 - Comparative genomic hybridization proling of human Ewing Sarcoma tumour samples (26)

Status
Submitted on 6 July 2007, released on 16 June 2008, last updated on 2 May 2014
Organism
Homo sapiens
Samples (50)
Array (1)
Protocols (5)
Description
Ewing’s Sarcoma (ES) is characterized by specific chromosomal translocations, the most common being t(11;22)(q24;q12). Additionally, other types of genetic abnormalities may occur and be relevant to explain the variable tumoural biology and clinical outcome. We have carried out a high-resolution array CGH and expression profiling on 25 ES tumour samples to characterize the DNA copy number aberrations (CNA) occurring in these tumours and to determine their association with gene expression profiles (GEO Series accession number: GSE8303) and their clinical outcome. CNA were observed in 84% of the cases. We observed a median number of 3 aberrations per case. Besides numerical chromosomal changes, smaller aberrations were found and defined at chromosomes 5p, 7q and 9p. All CNA were compiled to define the smallest overlapping regions of imbalance (SORI). Thirty five SORI were delimited. Bioinformatic analyses were conducted to identify subgroups according to the pattern of genomic instability obtained. Unsupervised and supervised clustering analyses (using SORI as variables) segregated the tumours into two distinct groups: one genomically stable (≤ 3 CNA) and another genomically unstable one (> 3 CNA). The genomic unstable group showed a statistically significant shorter overall survival and was more refractory to chemotherapy. This report elucidates data about genomic instability in ES, based on CNA and expression profiling for the first time, and shows that a genomically unstable group of Ewing tumours is correlated with a significant poor prognosis. Experiment Overall Design: Comparative experiment: pheripheral blood pool of ten healthy female donors: CONTROL vs. 26 Ewing Sarcoma Tumour Samples. Experiment Overall Design: Note that although 26 samples were profiled, only 25 were analysed (sample #11 did not pass quality control).
Experiment types
comparative genomic hybridization by array, unknown experiment type
Contact
Citation
Array CGH and gene-expression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing's sarcoma. B I Ferreira, J Alonso, J Carrillo, F Acquadro, C Largo, J Suela, M R Teixeira, N Cerveira, A Molares, G Goméz-López, A Pestaña, A Sastre, P Garcia-Miguel, J C Cigudosa. Oncogene 27(14):2084-90 (2008)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-8398.idf.txt
Sample and data relationshipE-GEOD-8398.sdrf.txt
Processed data (1)E-GEOD-8398.processed.1.zip
Array designA-AGIL-20.adf.txt
Links