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Series GSE68717 Query DataSets for GSE68717
Status Public on Mar 23, 2016
Title Genome-wide LOH and DNA copy number alteration in HPV-neg OSCC and their associations with disease-specific survival
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Oral squamous cell carcinoma (OSCC) is associated with high case-fatality. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we examined paired DNA from peripheral blood and tumor cells to assess genome-wide LOH and DNA copy number alteration (CNA) and their associations with risk factors, tumor characteristics, and disease-specific mortality among 75 patients with HPV-negative OSCC.
We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p, and 11q that seem to play an important role in oral cancer biology and survival from this disease.
Overall design We used Affymetrix 6.0 SNP arrays to test paired DNA from peripheral blood and tumor cells isolated by laser capture microdissection from 75 patients with HPV-negative OSCC. Peripheral blood DNA is used as reference for CNA to LOH.
Contributor(s) Chen C, Zhang Y, Loomis MM, Upton MP, Lohavanichbutr P, Houck JR, Doody DR, Mendez E, Futran N, Schwartz SM, Wang P
Citation(s) 26247464
Submission date May 11, 2015
Last update date Nov 27, 2018
Contact name Chu Chen
Organization name Fred Hutchinson Cancer Research Center
Department PHS
Street address 1100 Fairview Ave. N, PO Box 19024, M/S M5-C800
City Seattle
State/province Washington
ZIP/Postal code 98109
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (150)
GSM1679474 1_tumor
GSM1679475 1_blood
GSM1679476 2_tumor
BioProject PRJNA283500

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
GSE68717_RAW.tar 4.5 Gb (http)(custom) TAR (of CEL)
GSE68717_processed_CNV_probe_level.txt.gz 7.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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