Transcriptomics

Dataset Information

2

Affymetrix SNP array data for pediatric rhabdomyosarcoma (RMS)


ABSTRACT: 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.

ORGANISM(S): Homo sapiens  

SUBMITTER: Katsuyoshi Koh   Junko Takita  Ryoji Hanada  Masashi Sanada  Riki Nishimrua  Yasuhide Hayashi  Aiko Sato-Otsubo  Riki Nishimura  Seishi Ogawa  Motohiro Kato  Yukichi Tanaka 

PROVIDER: E-GEOD-41263 | ArrayExpress | 2013-08-12

SECONDARY ACCESSION(S): GSE41263PRJNA176458

REPOSITORIES: GEO, ArrayExpress

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