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Series GSE10143 Query DataSets for GSE10143
Status Public on Oct 15, 2008
Title Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Background: It is a challenge to identify those patients who, after undergoing potentially curative treatments for hepatocellular carcinoma, are at greatest risk of recurrence. Such high-risk patients could receive novel interventional measures. An obstacle to the development of genome-based predictors of outcome in patients with hepatocellular carcinoma has been the lack of a means to carry out genomewide expression profiling of fixed, as opposed to frozen, tissues.
Methods: We aimed to demonstrate the feasibility of gene-expression profiling of more than 6000 human genes in formalin-fixed paraffin-embedded tissues. We applied the method to tissues from 307 patients with hepatocellular carcinoma, from four series of patients, to discover and validate a gene-expression signature associated with survival.
Results: The expression-profiling method for formalin-fixed, paraffin-embedded tissue was highly effective: samples from 90% of the patients yielded data of high quality, including samples that had been archived for more than 24 years. Gene-expression profiles of tumor tissue failed to yield a significant association with survival. In contrast, profiles of the surrounding nontumoral liver tissue were highly correlated with survival in a training set of 82 Japanese patients, and the signature was validated in tissues from an independent group of 225 patients from the United States and Europe (p = 0.04).
Conclusions: We have demonstrated the feasibility of genomewide expression profiling of formalin-fixed, paraffin-embedded tissues and have shown that a reproducible gene-expression signature correlating with survival is present in liver tissue adjacent to the tumor in patients with hepatocellular carcinoma.

This SuperSeries is composed of the SubSeries listed below.
 
Overall design Training cohort: 80 tumor and 82 non-tumor liver tissues surgically resected from patients with hepatocellular carcinoma (HCC); Validation cohort: 225 non-tumor liver tissues surgically resected from patients with HCC.

Clinical data has been withheld from GEO due to privacy concerns.
 
Contributor(s) Hoshida Y, Villanueva A, Kobayashi M, Peix J, Chiang D, Camargo A, Gupta S, Moore J, Wrobel MJ, Lerner J, Reich M, Chan JA, Ikeda K, Hashimoto M, Watanabe G, Roayaie S, Schwartz M, Thung S, Gabriel S, Mazzaferro V, Bruix J, Friedman S, Kumada H, Llovet JM, Golub TR
Citation(s) 18923165, 31344396
Submission date Jan 10, 2008
Last update date Apr 14, 2020
Contact name Yujin Hoshida
E-mail(s) Yujin.Hoshida@UTSouthwestern.edu
Organization name University of Texas Southwestern Medical Center
Street address 5323 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platforms (1)
GPL5474 Human 6k Transcriptionally Informative Gene Panel for DASL
Samples (387)
GSM256342 Hepatitis/cirrhotic liver (bkg_002)
GSM256343 Hepatitis/cirrhotic liver (bkg_003)
GSM256344 Hepatitis/cirrhotic liver (bkg_005)
This SuperSeries is composed of the following SubSeries:
GSE10140 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma (Training Set, Liver)
GSE10141 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma (Training Set, HCC)
GSE10142 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma (Validation Set)
Relations
BioProject PRJNA108689

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
GSE10143_GSE10140_DAP_file_list.txt 8.6 Kb (ftp)(http) TXT
GSE10143_GSE10141_DAP_file_list.txt 8.5 Kb (ftp)(http) TXT
GSE10143_GSE10142_DAP_file_list.txt 25.5 Kb (ftp)(http) TXT
GSE10143_RAW.tar 1.1 Gb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table
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