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Series GSE9845 Query DataSets for GSE9845
Status Public on Jun 22, 2008
Title Copy number alterations of 103 hepatocellular carcinomas with hepatitis C virus etiology
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary To characterize the genetic alterations that instigate hepatitis C virus-induced hepatocellular carcinoma (HCC), we conducted an integrative genomic analysis of 103 HCCs. Most tumors harbored 1q gain, 8q gain or 8p loss, with occasional alterations in 13 additional chromosome arms. In addition to amplifications at 11q13 in 6 tumors, 4 tumors harbored focal gains at 6p21 incorporating VEGFA, which were confirmed in 4 of 113 HCC in an independent validation set. Strikingly, this locus overlapped with copy gains in 4 of 371 lung adenocarcinomas. Overexpression of VEGFA via 6p21 gain suggested a cell-nonautonomous mechanism of oncogene activation. Hierarchical clustering of gene expression among 91 tumors identified 5 classes, including ‘Wnt-CTNNB1’, ‘proliferation’ and ‘interferon-related’ gene classes. We also discovered a novel class defined by polysomy of chromosome 7, gains of which were associated with early tumor recurrence after resection. These findings reveal key alterations in HCC pathogenesis and implicate potential therapeutic targets.
Keywords: disease state analysis
Overall design 103 hepatocellular carcinomas and 95 adjacent cirrhotic, non-tumoral liver tissue were obtained at the time of surgical resection of orthotopic transplantation.
Contributor(s) Chiang DY, Villanueva A, Hoshida Y, Peix J, Newell P, Minguez B, Cozza A, Donovan DJ, Thung SN, Sole M, Tovar V, Alsinet C, Ramos A, Barretina J, Roayaie S, Schwartz M, Najfeld V, Bruix J, Mazzaferro V, Ligon AH, Waxman S, Friedman S, Sellers WR, Meyerson M, Llovet JM
Citation(s) 18701503
Submission date Dec 11, 2007
Last update date Aug 21, 2013
Contact name Derek Chiang
Organization name University of North Carolina
Department Department of Genetics
Street address UNC Lineberger Cancer Center, 450 West Drive, CB #7295
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7295
Country USA
Platforms (1)
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (197)
GSM248782 B13
GSM248783 B15
GSM248784 B17
This SubSeries is part of SuperSeries:
GSE9829 Focal gains of VEGFA and molecular classification of hepatocellular carcinoma
BioProject PRJNA105127

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
GSE9845_RAW.tar 5.1 Gb (http)(custom) TAR (of CEL)
GSE9845_clinical_info.txt 5.6 Kb (ftp)(http) TXT
Processed data included within Sample table

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