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| Status |
Public on Aug 12, 2013 |
| Title |
Affymetrix SNP array data for pediatric rhabdomyosarcoma (RMS) |
| Organism |
Homo sapiens |
| Experiment type |
SNP genotyping by SNP array
Genome binding/occupancy profiling by SNP array
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| Summary |
To elucidate the pathogenesis of rhabdomyosarcoma (RMS), particularly for different subgroups, we performed a SNP array-based copy number analysis of 54 RMS specimens from primary cases with ERMS (N = 30), 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.
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| Overall design |
Copy number analysis of Affymetrix 50K/250K SNP arrays was performed for 54 RMS samples.
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| Contributor(s) |
Nishimrua R, Takita J, Sato-Otsubo A, Kato M, Koh K, Hanada R, Tanaka Y, Sanada M, Hayashi Y, Ogawa S |
| Citation(s) |
23578105 |
| Submission date |
Oct 01, 2012 |
| Last update date |
Nov 24, 2020 |
| Contact name |
Riki Nishimura |
| E-mail(s) |
riki81@hotmail.com
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| Organization name |
University of Tokyo
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| Street address |
7-3-1, Hongo, Bunkyo-ku
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| City |
Tokyo |
| ZIP/Postal code |
1138655 |
| Country |
Japan |
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| Platforms (2) |
| GPL2004 |
[Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array |
| GPL3718 |
[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array |
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| Samples (55)
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| Relations |
| BioProject |
PRJNA176458 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41263_RAW.tar |
1.3 Gb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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