A methodology for utilization of predictive genomic signatures in FFPE samples

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.Significant correlation was observed between pathway activity predictions from 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.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.Gene expression profiling continues to contribute to advances in clinical oncology, providing a basis for understanding the complex biology of tumors, improving the accuracy of disease diagnosis as well as disease prognosis, and providing tools to determine which targeted therapeutic agents are likely to be effective in the treatment of particular tumors. While the majority of studies have made use of fresh tissue samples so as to optimize the measurement of gene expression, an ability to generate reliable and consistent data from formalin-fixed, paraffin-embedded (FFPE) tissue samples has several advantages. First, FFPE tissue samples are readily available in large numbers across multiple stages of disease and thus the capability to utilize FFPE tissue samples broadens the scope of poten