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Series GSE57100 Query DataSets for GSE57100
Status Public on May 01, 2014
Title Affymetrix SNP array data for nasopharyngeal carcinoma samples
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Nasopharyngeal carcinoma (NPC) has extremely skewed ethnic and geographic distributions, is poorly understood at the genetic level and is in need of effective therapeutic approaches. We determined the genomic landscape of 52 NPC cases with SNP-array analysis. This approach identified multiple recurrent SCNVs, with the most frequent deletion peak spanning the CDKN2A gene on 9p21. Additional SCNVs involving established cancer genes including CCND1, AKT2, MYC and TP53 were observed. Notably, we identified that one component of the SWI/SNF complex, ARID1A, was frequently deleted in NPC.
 
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen nasopharyngeal carcinoma biopsy tissues
Copy number analysis of Affymetrix 250K SNP arrays was performed for 52 nasopharyngeal carcinoma samples.

Please note that the sample characteristics 'primary tumor size, metastasis, and regional lymph node' represents T, M and N in WHO TNM staging of nasopharyngeal cancer (according to American Joint Committee on Cancer (AJCC)), respectively.
 
Contributor(s) Lin D, Koeffler HP
Citation(s) 24952746
Submission date Apr 25, 2014
Last update date May 17, 2017
Contact name Lizhen Liu
E-mail csiliul@nus.edu.sg
Organization name Cancer Science Institute
Street address 14 Medical Drive
City Singapore
ZIP/Postal code 117599
Country Singapore
 
Platforms (1)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
Samples (52)
GSM1375265 Nasopharyngeal carcinoma NPC15F
GSM1375266 Nasopharyngeal carcinoma NPC29F
GSM1375267 Nasopharyngeal carcinoma NPC10F
Relations
BioProject PRJNA245424

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE57100_RAW.tar 1.4 Gb (http)(custom) TAR (of CEL, CHP)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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