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Affymetrix SNP array data for nasopharyngeal carcinoma samples

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57100 | GEO | 2014/05/01

SECONDARY ACCESSION(S): PRJNA245424

REPOSITORIES: GEO

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Affymetrix SNP array data for nasopharyngeal carcinoma samples

Project description: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. 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.

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