Abstract Enumeration and characterization of circulating tumor cells (CTCs) by the CellSearch™ instrument platform, which uses antibody capture of fixed cells from blood, provides prognostic information and assists in monitoring therapy for patients with certain epithelial cancers. Our laboratory is clinically evaluating an antibody-independent CTC enrichment technology, ApoStream™, which was co-developed by NCI and SAIC-F with ApoCell Inc. The ApoStream isolates living CTCs from a wide variety of malignancies including sarcomas and lymphomas as well as epithelial cancers, enabled by critical differences in morphology and dielectric properties rather than surface marker expression. In contrast to the CellSearch™ platform, CTCs isolated with the ApoStream™ instrument are amenable to tests that unambiguously identify isolated cells as malignant cells. To validate the performance of the ApoStream™ device for clinical specimens, we focused on isolation of CTCs from patients with advanced alveolar soft part sarcoma (ASPS). Patient samples from an ongoing clinical study at the NCI provided the opportunity to demonstrate the utility of ApoStream™ technology for the isolation of CTCs from patients with this rare non-epithelial malignancy. ASPS is characterized by a specific, unbalanced genetic translocation of der(17)t(X;17)(p11;q25) involving the ASPL and TFE3 genes. The detection of the fusion product has been reported in primary tumors and peripheral blood based on RT-PCR but not in CTCs. Here we show that the ASPL-TFE3 gene translocation can be unambiguously confirmed in CTCs by break-apart fluorescent in situ hybridization (FISH), and the presence of the fusion protein in CTCs was confirmed with specific monoclonal antibodies. Efficient recovery was demonstrated using specified numbers of cancer cells spiked into buffer and normal donor control PBMCs; clinical utility was demonstrated with blood samples from ASPS patients. This study provides not only initial results demonstrating isolation of CTCs from metastatic ASPS patients using the ApoStream™ technology without the need for antibody capture but also a rationale for exploring ApoStream™ technology in additional tumor histologies that cannot be evaluated with the CellSearch™ platform. Our current efforts are focused on evaluating the utility of ApoStream™-isolated CTCs for assessing pharmacodynamic effects of new targeted agents during early stage clinical trials. Funded by NCI Contract No. HHSN261200800001E. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C197. Citation Format: Priya Balasubramanian, Lihua Wang, Shivaani Kummar, Melinda Hollingshead, Francis Owusu, Ralph E. Parchment, Joseph E. Tomaszewski, James H. Doroshow, Robert J. Kinders. Fluorescent in situ hybridization confirmation of circulating alveolar soft part sarcoma cells (CTCs) isolated from peripheral blood specimens using ApoStream™ instrumentation. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C197.