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Title: Affymetrix SNP array data for pediatric rhabdomyosarcoma (RMS)      
dateReleased:
08-12-2013
description:
To elucidate the pathogenesis of rhabdomyosarcoma (RMS), particularly for different subgroups, we performed a SNP array-based copy number analysis of 46 RMS specimens from primary cases with ERMS (N = 21), ARMS (N = 14), unclassified RMS (N = 1), and RMS of unknown histology (N = 3) together with 7 RMS-derived cell lines. The ERMS subtype was characterized by hyperploidy and was significantly associated with gains of chromosomes 2, 8, and 12, whereas majority of ARMS cases exhibited near-diploid copy number profiles. Recurrent loss of heterozygosity (LOH) of chromosomes 3 (28.6%) and 15q (35.7%) was detected in ARMS. Uniparental disomy/polysomy of 11p was commonly found in both tumor types. Focal gains/amplifications were associated mostly with PAX3-FOXO1 (5/10) or PAX7-FOXO1 (6/6) fusions, but novel amplified regions were also found, including the IRS2 in 2 ARMS. Gain of 13q was significantly associated with good patient outcome in ERMS. These findings not only illustrate genetic differences between ARMS and ERMS but also provide novel insights into the pathogenesis of RMS. Copy number analysis of Affymetrix 50K/250K SNP arrays was performed for 46 RMS samples.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-41263
refinement:
raw
alternateIdentifiers:
41263
keywords:
functional genomics
dateModified:
08-21-2013
availability:
available
types:
gene expression
name:
Homo sapiens
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-41263/E-GEOD-41263.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-41263/E-GEOD-41263.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41263
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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