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Series GSE2280 Query DataSets for GSE2280
Status Public on Feb 19, 2005
Title Prediction of lymphatic metastasis from primary squamous cell carcinoma of the oral cavity
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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.
Keywords = oral carcinoma lymphatic metastasis predict
Keywords: repeat sample
 
 
Contributor(s) O'Donnell RK, Kupferman M, Wei S, Singhal S, Weber R, O'Malley B Jr, Cheng Y, Putt M, Feldman M, Ziober B, Muschel RJ
Citation(s) 15558013
Submission date Feb 16, 2005
Last update date Aug 10, 2018
Contact name Rebekah K O'Donnell
E-mail(s) rodonnel@mail.med.upenn.edu
Phone 267-426-5488
Organization name Children's Hospital of Philadelphia
Department Pathology
Lab Muschel
Street address
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
Samples (27)
GSM42246 1N
GSM42247 1T
GSM42248 2N
Relations
BioProject PRJNA91453

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
GSE2280_RAW.tar 90.4 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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