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Series GSE20189 Query DataSets for GSE20189
Status Public on Sep 23, 2011
Title A gene expression signature from peripheral whole blood for stage I lung adenocarcinoma
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Affordable early screening in subjects with high risk of lung cancer has great potential to improve survival from this deadly disease. We measured gene expression from lung tissue and peripheral whole blood (PWB) from adenocarcinoma cases and controls to identify dysregulated lung cancer genes that could be tested in blood to improve identification of at-risk patients in the future. Genome-wide mRNA expression analysis was conducted in 153 subjects (73 adenocarcinoma cases, 80 controls) from the Environment And Genetics in Lung cancer Etiology (EAGLE) study using PWB and paired snap-frozen tumor and non-involved lung tissue samples. Analyses were conducted using unpaired t-tests, linear mixed effects and ANOVA models. The area under the receiver operating characteristic curve (AUC) was computed to assess the predictive accuracy of the identified biomarkers. We identified 50 dysregulated genes in stage I adenocarcinoma versus control PWB samples (False Discovery Rate ≤0.1, fold change ≥1.5 or ≤0.66). Among them, eight (TGFBR3, RUNX3, TRGC2, TRGV9, TARP, ACP1, VCAN, and TSTA3) differentiated paired tumor versus non-involved lung tissue samples in stage I cases, suggesting a similar pattern of lung cancer-related changes in PWB and lung tissue. These results were confirmed in two independent gene expression analyses in a blood-based case-control study (n=212) and a tumor-non tumor paired tissue study (n=54). The eight genes discriminated patients with lung cancer from healthy controls with high accuracy (AUC=0.81, 95% CI=0.74-0.87). Our finding suggests the use of gene expression from PWB for the identification of early detection markers of lung cancer in the future.
 
Overall design Samples from 164 subjects were initially included in the study. Two samples with poor quality profile based on quality assessment (described in Supplemental Material 2) were excluded before normalization. The remaining 162 samples were processed and normalized with the Robust Multichip Average (RMA) method. Nine additional subjects were excluded after data normalization because of reclassification to non-adenocarcinoma morphology during histologic review. The final analyses were based on 73 adenocarcinoma cases and 80 controls. All 22,277 probe sets based on RMA summary measures were used in the analyses.
 
Contributor(s) Rotunno M, Hu N, Su H, Wang C, Goldstein AM, Bergen AW, Consonni D, Pesatori AC, Bertazzi P, Wacholder S, Shih J, Caporaso NE, Taylor PR, Landi M
Citation(s) 21742797
Submission date Feb 04, 2010
Last update date Dec 06, 2018
Contact name Melissa Rotunno
E-mail(s) rotunnom@mail.nih.gov
Phone 301-402-1622
Fax 301-402-4489
Organization name NIH/NCI
Department DCEG
Lab GEB
Street address 6120 Executive Blvd
City Rockville
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
Samples (162)
GSM506423 S0001
GSM506424 S0002
GSM506425 S0003
Relations
BioProject PRJNA125685

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
GSE20189_RAW.tar 299.0 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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