Evaluation of a Gene Expression Microarray Assay To Determine Tissue of Origin in Body Fluid Specimens
GA Stancel, D Mody, K Alvarez, T Fairley, FA Monzon. The Methodist Hospital and The Methodist Hospital Research Institute, Houston, TX; Weil-Cornell Medical College, New York, NY
Background: Identification of the tissue of origin is a common challenge for cytology specimens since tumors with uncertain origin represent 5-10% of all new cancer cases. Cytologic body fluids are routinely obtained in the diagnostic workup of these cases. The Pathwork Tissue of Origin test was cleared by the FDA as an in vitro diagnostic device for frozen tissue, and a version of the test has been developed that works with formalin-fixed paraffin embedded (FFPE) tissue, but is not cleared by FDA. Here, we present initial results for the evaluation of this assay in body fluid specimens using both the thrombin and CellientTM cell block methodologies.
Design: We retrieved 8 tumor-positive and 7 negative body FFPE fluid specimens processed with both thrombin and Cellient™(Hologic, Bedford, MA) cell block methods (30 total samples). Two negative body fluids and two non-cytology tumor samples were used as controls. RNA was extracted from the FFPE samples and assays were performed according to a standardized amplification protocol and hybridized to PathchipTM microarrays (Pathwork Diagnostics, Redwood City, CA). A Tissue of Origin report was generated for each sample, and compared with that of the primary tumor site. In addition, results between the thrombin and Cellient cell block methods are compared.
Results: All 30 samples provided sufficient RNA of adequate quantity and quality for the Tissue of Origin assay. To test the FFPE Tissue of Origin assay in our laboratory, we analyzed RNA from 2 primary tumors (one frozen, one FFPE), which correlated with the gene expression pattern of the original primary tumor (kidney and lymphoma). Complete data on 2 samples (1 thrombin, 1 Cellient) negative for tumor showed good performance with the Pathchip array, passing all quality thresholds and producing reliable gene expression profiles consistent with inflammatory and mesothelial cells.
Conclusions: Our preliminary results show that it is possible to obtain gene expression profiles from FFPE body fluid cytology specimens using the FFPE version of the Pathwork Tissue of Origin test. The remainder of our samples will be analyzed to determine the ability to detect tissue of origin and the results from the thrombin and Cellient methods will be compared. These preliminary results suggest that gene expression profiling could be a useful approach for body fluid cytology specimens.
Wednesday, March 24, 2010 1:00 PM
Poster Session VI # 58, Wednesday Afternoon