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| 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
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| 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.
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| 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
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| 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 |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke University Medical Center
|
| Department |
Institute for Genome Sciences and Policy
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| Street address |
101 Science Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platforms (1) |
| GPL571 |
[HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array |
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| Samples (125)
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| Relations |
| BioProject |
PRJNA141283 |
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