Development of FISH Molecular Diagnostics to support Clinical Trials at NCI

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The Chromosome Pathology Unit (CPU)was set up in 2010 to fulfill the need in the "in house" laboratory FISH tests required to support clinical trials at NCI. The official CAP accreditation and CLIA certification has been accomplished by the CPU team in November 22, 2010. From January 2011 the Lab started receiving clinical cases for FISH testing. The CPU performed more than 750 tests since its opening. This includes FISH assay for probe validation (335 tests), collaboration with LP and other NIH researchers (165 tests), and over 240 clinical tests that has been performed since opening clinical service in November 2010. FISH diagnostics are an integral part of the Pathology molecular diagnostics currently offered by the Lab of Pathology. The sensitivity and specificity of FISH diagnostics was found to be near 100% in recent reports of CAP that puts them in front line among other available tests based on PCR and immunohistochemistry that have a long-known specificity problem. The Chromosome Pathology Unit (CPU) in the Laboratory of Pathology performs Fluorescence In Situ Hybridization (FISH) assays on formalin-fixed paraffin-embedded (FFPE) tissues to support active clinical trials at the NCI and NIH. The demand for this testing is high; the CPU receives orders for FISH tests on clinical tumor samples daily, and currently supports 17 clinical trials at the NCI. That includes requests from the entire community of CCR investigators: Molecular Oncology Branch, Surgery Branch, Office of the Director, Pediatric Oncology Branch, Neuro-Oncology Branch, Urologic Oncology Branch. The active test menu includes FISH assays for clinically significant chromosomal translocations and amplification events in solid tumors and hematologic malignancies. The developed/ validated tests include Her-2 amplification in Breast, Lung, and GI tract cancer, cmyc translocation in Burkitt and Diffuse Large B Cell Lymphoma, BCL2 translocation in Follicular Lymphoma, 1p/19q deletion tests for brain tumors, ALK translocation in lung cancer and inflammatory myofibroblastic tumors, PDGFR and PIK3A amplification in lung cancer, NTRK1 amplification in thymic tumors, TFE-3 translocation in renal tumors, alveolar soft part sarcoma, EWSR1/FLI1 and FKHR translocations in pediatric tumors (Ewing's sarcoma and Rabdomyosarcoma), etc. In addition, the CPU is currently developing and validating ten new FISH tests for additional frequent chromosomal abnormalities in cancers that have been requested by NCI investigators. Among the tests in the pipeline are FGFR1, cMET amplification in lung cancer, ERG translocation in prostate cancer, Urovision (Abbott) for the detection of altered cells in bladder cancer, The Unit has been equipped as state-of-the art laboratory that includes a new Zeiss epifluorescence microscope with the ApoTome feature that allows FISH analysis and imaging of thick tissue sections, SKY-cube for spectral karyotyping - a modern tool for the detection of chromosomal translocations in cancer cells and various hereditary syndromes. All small equipment to measure the DNA quantity, run PCR to validate the FISH data, the CO2 incubator to grow cells were purchased as well.