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| Status |
Public on Mar 11, 2010 |
| Title |
Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted (GoldenGate methylation) |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
Solid tumors, including head and neck squamous cell carcinomas (HNSCC), arise as a result of genetic and epigenetic alterations in a sustained stress environment. Since it has been hypothesized that epigenetic alterations may act by providing the second carcinogenic hit in gene silencing, we sought to identify genome-wide DNA copy number alterations and CpG dinucleotide methylation events and examine the global/local relationships between these types of alterations in HNSCC. Importantly, we found that the global pattern of copy number alterations in these tumors was significantly associated with tumor methylation profiles. However at the local level, gene promoter regions did not exhibit a correlation between copy number and methylation , and the spectrum of genes affected by each type of alteration was unique. A case-series of 19 tumors and matched blood referents were hybrizided to Affymetrix Human Mapping 500k arrays and copy number was determined via HMM with Copy Number Analysis Tool v4.0.1.
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| Overall design |
This study was designed to investigate the relationship between copy number and DNA methylation alterations in head and neck squamous cell carcinoma. Data in this submission relates to the methylation
portion only. Each patient tumor has been de-identified and assigned a number (1-19). We included 11 normal head and neck samples, procured through the National Research Disease Interchange, that were used for reference when comparing tumor to normal. One ug of tissue DNA extracted using the Qiagen Blood and Tissue Kit was bisulfite-modified using a Zymo Research EZ DNA Methylation Kit. Samples were processed and arrayed on the Illumina GoldenGate Methylation Cancer Panel 1 at the University of California-San Francisco Institute for Genetics, Genomic Core Facility.
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| Contributor(s) |
Poage GM, Kelsey KT, Houseman EA |
| Citation(s) |
20300172 |
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| Submission date |
Mar 10, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Graham M Poage |
| Organization name |
Brown University
|
| Street address |
70 Ship St
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| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02903 |
| Country |
USA |
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| Platforms (1) |
| GPL9183 |
Illumina GoldenGate Methylation Cancer Panel I |
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| Samples (30)
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| Relations |
| BioProject |
PRJNA124985 |
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