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Series GSE29598 Query DataSets for GSE29598
Status Public on Jun 24, 2011
Title A Methodology for Utilization of Predictive Genomic Signatures in FFPE Samples
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Purpose: Gene expression signatures developed to measure the activity of oncogenic signaling pathways have been used to dissect the heterogeneity of tumor samples and to predict sensitivity to various cancer drugs that target components of the relevant pathways, thus potentially identifying therapeutic options for subgroups of patients. To facilitate broad use, including in a clinical setting, the ability to generate data from formalin-fixed, paraffin-embedded (FFPE) tissues is essential. Experimental Design: Patterns of pathway activity in matched fresh-frozen and FFPE xenograft tumor samples were generated using the MessageAmp Premier methodology in combination with assays using Affymetrix arrays. Results generated were compared with those obtained from fresh-frozen samples using a standard Affymetrix assay. In addition, gene expression data from patient matched fresh-frozen and FFPE melanomas were also utilized to evaluate the consistency of predictions of oncogenic signaling pathway status. Results: Significant correlation of pathway activity predictions was observed between paired fresh-frozen and FFPE xenograft tumor samples. In addition, significant concordance of pathway activity predictions was also observed between patient matched fresh-frozen and FFPE melanomas. Conclusion: Reliable and consistent predictions of oncogenic pathway activities can be obtained from FFPE tumor tissue samples. The ability to reliably utilize FFPE patient tumor tissue samples for genomic analyses will lead to a better understanding of the biology of disease progression and, in the clinical setting, will provide tools to guide the choice of therapeutics to those most likely to be effective in treating a patient’s disease.
Overall design 8 replicates of HMECs infected with adenovirus expressing GFP, 8 replicates of HMECs infected with adenovirus expressing RAS, 6 replicates of HMECs infected with adenovirus expressing MYC, 25 fresh-frozen melanoma xenografts, 25 FFPE melanoma xenografts, 6 FFPE human melanoma
Contributor(s) Freedman JA, Augustine CK, Dressman HK, Tyler DS, Nevins JR
Citation(s) 21745407
Submission date May 27, 2011
Last update date Dec 06, 2018
Contact name Holly Kloos Dressman
Organization name Duke University Medical Center
Department Institute for Genome Sciences and Policy
Street address 101 Science Drive
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
Platforms (1)
GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
Samples (125)
GSM732749 g2 One-Cycle
GSM732750 g3 One-Cycle
GSM732751 g4 One-Cycle
BioProject PRJNA141283

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
GSE29598_RAW.tar 230.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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