Transcriptomics

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Analysis of genomic instability in esophageal squamous cell carcinoma (ESCC)


ABSTRACT: To characterize genomic instability in esophageal squamous cell carcinoma, we examined loss of heterozygosity, copy number loss, and copy number gain in ESCC patients from a high-risk region of China. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from microdissected esophageal squamous cell carcinoma samples or peripheral blood samples. Tumor DNA samples were normalized individually to the set of 102 peripheral blood samples. Copy number variations and loss of heterozygosity were determined by a paired analysis of tumor and blood DNA from the same individual.

ORGANISM(S): Homo sapiens  

SUBMITTER: Phillip R Taylor   Robert J Clifford  Maxwell P Lee 

PROVIDER: E-GEOD-15526 | ArrayExpress | 2010-04-10

SECONDARY ACCESSION(S): GSE15526PRJNA115701

REPOSITORIES: GEO, ArrayExpress

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Publications

Genomic characterization of esophageal squamous cell carcinoma from a high-risk population in China.

Hu Nan N   Wang Chaoyu C   Ng David D   Clifford Robert R   Yang Howard H HH   Tang Ze-Zhong ZZ   Wang Quan-Hong QH   Han Xiao-You XY   Giffen Carol C   Goldstein Alisa M AM   Taylor Philip R PR   Lee Maxwell P MP  

Cancer research 20090707 14


Genomic instability plays an important role in most human cancers. To characterize genomic instability in esophageal squamous cell carcinoma (ESCC), we examined loss of heterozygosity (LOH), copy number (CN) loss, CN gain, and gene expression using the Affymetrix GeneChip Human Mapping 500K (n = 30 cases) and Human U133A (n = 17 cases) arrays in ESCC cases from a high-risk region of China. We found that genomic instability measures varied widely among cases and separated them into two groups: a  ...[more]

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