E-GEOD-2280 - Transcription profiling of oral cavity samples from human squamous cell carcinoma patients

Status
Submitted on 16 February 2005, released on 25 August 2007, last updated on 27 March 2012
Organism
Homo sapiens
Samples (27)
Array (1)
Protocols (2)
Description
Metastasis via the lymphatics is a major risk factor in squamous cell carcinoma of the oral cavity (OSCC). We sought to determine whether the presence of metastasis in the regional lymph node could be predicted by a gene expression signature of the primary tumor. A total of 18 OSCCs were characterized for gene expression by hybridizing RNA to Affymetrix U133A gene chips. Genes with differential expression were identified using a permutation technique and verified by quantitative RT-PCR and immunohistochemistry. A predictive rule was built using a support vector machine, and the accuracy of the rule was evaluated using crossvalidation on the original data set and prediction of an independent set of four patients. Metastatic primary tumors could be differentiated from nonmetastatic primary tumors by a signature gene set of 116 genes. This signature gene set correctly predicted the four independent patients as well as associating five lymph node metastases from the original patient set with the metastatic primary tumor group. We concluded that lymph node metastasis could be predicted by gene expression profiles of primary oral cavity squamous cell carcinomas. The presence of a gene expression signature for lymph node metastasis indicates that clinical testing to assess risk for lymph node metastasis should be possible.
Experiment types
transcription profiling by array, co-expression, disease state, organism part comparison
Contact
Citation
Gene expression signature predicts lymphatic metastasis in squamous cell carcinoma of the oral cavity. Rebekah K O'Donnell, Michael Kupferman, S Jack Wei, Sunil Singhal, Randal Weber, Bert O'Malley, Yi Cheng, Mary Putt, Michael Feldman, Barry Ziober, Ruth J Muschel. Oncogene 24(7):1244-51 (2005)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-2280.idf.txt
Sample and data relationshipE-GEOD-2280.sdrf.txt
Raw data (1)E-GEOD-2280.raw.1.zip
Processed data (1)E-GEOD-2280.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-2280.eSet.r
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