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| 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
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| 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.
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| 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.
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| 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 |
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| Submission date |
May 11, 2015 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Chu Chen |
| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
PHS
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| Street address |
1100 Fairview Ave. N, PO Box 19024, M/S M5-C800
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| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platforms (1) |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (150)
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| Relations |
| BioProject |
PRJNA283500 |
| 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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