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E-GEOD-29598 - A Methodology for Utilization of Predictive Genomic Signatures in FFPE Samples

Released on 24 June 2011, last updated on 18 August 2015
Homo sapiens
Samples (125)
Array (1)
Protocols (8)
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. 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
Experiment type
transcription profiling by array 
Holly Kloos Dressman <>, Christina K Augustine, Douglas S Tyler, Holly K Dressman, Jennifer A Freedman, Joseph R Nevins
A methodology for utilization of predictive genomic signatures in FFPE samples. Freedman JA, Augustine CK, Selim AM, Holshausen KC, Wei Z, Tsamis KA, Hsu DS, Dressman HK, Barry WT, Tyler DS, Nevins JR.
Investigation descriptionE-GEOD-29598.idf.txt
Sample and data relationshipE-GEOD-29598.sdrf.txt
Raw data (2),
Processed data (1)
Array designA-AFFY-37.adf.txt