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Series GSE72660 Query DataSets for GSE72660
Status Public on Nov 01, 2016
Title Integrated Analysis of Genome-Wide DNA Copy Number and Gene Expression with Patient Outcomes in Esophageal Adenocarcinoma [Copy Number]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by SNP array
Summary Esophageal adenocarcinoma (EAC) is now the most common esophageal malignancy in the United States with >15,000 new cases per year. Prognosis for patients with EAC is poor due to both late diagnosis and early metastasis to lymph nodes. The goal of this study was to perform an integrated analysis of genome-wide DNA copy number changes, gene expression and patient clinical data in order to identify events and genes associated with clinical endpoints or that may play a key role in EAC development and therefore provide potential therapeutic targets. Specifically, we report on a series of 116 EAC specimens studied using Affymetrix SNP 6.0 and U133 Plus 2 GeneChip arrays plus additional cohorts of 73 and 114 EAC patients whose tumors were analyzed using Affymetrix StyI 250K arrays and fluorescence in-situ hybridization (FISH) respectively. Integration of this genomic data with clinical information and outcomes enabled identification of copy number changes and coordinate gene expression events that are associated with patient prognosis, that validate known or suspected oncogenes and tumor suppressor genes and that also facilitate identification of novel, putative driver genes in large regions of copy number gain and loss. These findings add to our understanding of the basic biology of EAC and provide a guide for development of novel prognostic tools and therapies.
Overall design Copy number analysis of Affymetrix 250K Sty (n=73) and SNP6.0 arrays (n=116) was performed for 189 esophageal adenocarcinoma samples. There are also 72 samples from normal squamous esophageal epithelium, which were used as references for copy number inference for the 250K Sty array data and 15 samples from white blood cells used as references for copy number inference for the SNP6.0 array data.
Contributor(s) Godfrey T, Bandla S
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Submission date Sep 02, 2015
Last update date Nov 27, 2018
Contact name Tony Edward Godfrey
Phone 6174148013
Organization name Boston University
Department Surgery
Lab Godfrey
Street address 700 Albany Street
City Boston
State/province Massachusetts
ZIP/Postal code 02118
Country USA
Platforms (2)
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (276)
GSM1867449 UPittTumor1_copy_number
GSM1867450 UPittTumor2_copy_number
GSM1867451 UPittTumor3_copy_number
BioProject PRJNA294613

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
GSE72660_RAW.tar 17.1 Gb (http)(custom) TAR (of CEL, CHP, CNCHP, TXT)
Processed data provided as supplementary file

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