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Series GSE20939 Query DataSets for GSE20939
Status Public on Mar 18, 2010
Title Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted (Affymetrix Copy Number)
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
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 references were hybrizided to Affymetrix Human Mapping 500k arrays and copy number was determined via HMM with Copy Number Analysis Tool v4.0.1.
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 copy number portion only. Each patient tumor has been de-identified and assigned a number (1-19) and the blood samples with the same number correspond to the respectively-numbered tumor.

The supplementary file 'GSE20939_tumor_copy_number.txt' contains the (blood normalized) copy number calls for each tumor sample.
Contributor(s) Poage GM, Kelsey KT, Houseman EA
Citation(s) 20300172
Submission date Mar 17, 2010
Last update date May 17, 2017
Contact name Graham M Poage
Organization name Brown University
Street address 70 Ship St
City Providence
State/province RI
ZIP/Postal code 02903
Country USA
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (76)
GSM523618 Tumor_1nsp
GSM523619 Tumor_1sty
GSM523620 Tumor_2nsp
BioProject PRJNA124387

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
GSE20939_RAW.tar 2.0 Gb (http)(custom) TAR (of CEL, CHP)
GSE20939_tumor_copy_number.txt.gz 2.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record
Processed data provided as supplementary file

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