GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE14994 Query DataSets for GSE14994
Status Public on Jun 02, 2009
Title Patterns of gene expression and copy-number alterations in VHL disease-associated and sporadic ccRCC
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by SNP array
Summary Recent insights into the role of the VHL tumor suppressor gene in hereditary and sporadic clear cell carcinoma of the kidney (ccRCC) have led to new treatments for patients with metastatic ccRCC, although virtually all patients eventually succumb to the disease. We performed an integrated, genome-wide analysis of copy-number changes and gene expression profiles in 90 tumors, including both sporadic and VHL disease-associated tumors, in hopes of identifying new therapeutic targets in ccRCC. We identified 14 regions of nonrandom copy-number change, including 7 regions of amplification (1q, 2q, 5q, 7q, 8q, 12p, and 20q) and 7 regions of deletion (1p, 3p, 4q, 6q, 8p, 9p, and 14q). An analysis aimed at identifying the relevant genes revealed VHL as one of 3 genes in the 3p deletion peak, CDKN2A and CDKN2B as the only genes in the 9p deletion peak, and MYC as the only gene in the 8q amplification peak. An integrated analysis to identify genes in amplification peaks that are consistently overexpressed among amplified samples confirmed MYC as a potential target of 8q amplification and identified candidate oncogenes in the other regions. A comparison of genomic profiles revealed that VHL disease-associated tumors are similar to a subgroup of sporadic tumors, and thus more homogeneous overall. Sporadic tumors without evidence of biallelic VHL inactivation fell into 2 groups: one group with genomic profiles highly dissimilar to the majority of ccRCC, and a second group with genomic profiles that are much more similar to tumors with biallelic inactivation of VHL.

Keywords: comparative genomic hybridization
Overall design 90 clear cell renal cell carcinomas and 21 renal cancer cell lines were subject to 250K SNP analysis.
Contributor(s) Beroukhim R, Signoretti S
Citation(s) 19470766
Submission date Feb 25, 2009
Last update date Jan 17, 2017
Contact name Rameen Beroukhim
Organization name Dana-Farber Cancer Institute
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platforms (2)
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
GPL3921 [HT_HG-U133A] Affymetrix HT Human Genome U133A Array
Samples (229)
GSM374369 RCC 50T (SNP)
GSM374370 RCC 56T (SNP)
GSM374371 RCC 53T (SNP)
BioProject PRJNA111903

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
GSE14994_RAW.tar 4.2 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap