The Molecular Diagnostics Section is currently the only CLIA and College of American Pathology approved clinical laboratory within the NCI certified for performing molecular oncology testing on pathology materials from NIH patients. In 2016 the molecular diagnostics laboratory processed 1726 unique clinical samples from NCI/NIH patients, and performed 6075 tests. The laboratory utilizes a variety of technologies to perform these assays including conventional DNA PCR, RT-PCR, qPCR, allele suppression PCR, capillary electrophoresis, pyrosequencing, bisulfite pyrosequencing, and small panel next generation sequencing (NGS). The assays we perform include tests to identify B and T-cell clonality, lymphoma specific translocations (e.g., BCL-1/IG, BCL-2/IG), translocations associated with pediatric sarcomas (e.g., EWS-FLI-1, EWS-ERG, EWS-WT-1, PAX-7/FKHD, PAX-3/FKHD, SYT-SSX-1, and SYT-SSX-2), cancer associated viruses (e.g., EBV, HTLV, HHV-8), and mutations associated with a variety of cancers (e.g., EGFR, KRAS, NRAS, BRAF, PIK3CA, IDH1/2, AKT, MYD88, ERBB2, STAT3, and STAT5b). Quantitative PCR is performed for HTLV 1/2 to follow viral load in ATL clinical trials, and for the EGFRvIII to assess expression of this cancer-specific transcript for clinical trial eligibility. MGMT methylation analysis is performed using bisulfite pyrosequencing to provide predictive information regarding response to temozolomide in the glioblastoma setting. IDH1/2 is performed to assist in glioma diagnosis and as a prognostic marker. The laboratory also offers a 50 gene NGS panel for clinical use, interrogating some of the more commonly involved genes in cancer. This panel is currently our standard CLIA level mutation panel when it is necessary to assess mutations in more than one gene as is the case in lung cancer. The laboratory's developmental research effort has been focused on the application of next generation sequencing (NGS) technologies to assist in cancer genotyping and diagnostics. In addition to the 50 gene panel currently in clinical use, the laboratory has developed more focused tumor specific panels that will better assess the mutational spectra of specific tumor types. The laboratory has developed a primary brain tumor panel to assist with diagnosis and classification of central nervous system cancers as part of a major collaboration with the Neuro-Oncology Branch of CCR. This panel has already been shown to have clinical utility. Fourteen of the first 150 cases studied have had diagnoses changed as a result of the information provided by the new panel. The laboratory has also initiated a program in the use of circulating tumor DNA (ctDNA) as a biomarker for disease response and early detection. These two efforts (NGS and ctDNA) are linked as the genotyping is not only used to identify potential therapeutic targets, but it is also used to identify targets for the circulating DNA (ctDNA) studies. Early studies targeting BRAF V600E ctDNA in melanoma patients (collaboration with Dr. S. Rosenberg) indicated the potential use of this technology in predicting responses to cellular immunotherapy, and recurrence. We have expanded our initial studies with Dr. Rosenberg in melanoma to a wide range of other TIL treated tumors (breast, ovary, colon) targeting patient specific exome and transcriptome sequence identified targets, with similar results. We have initiated new studies with other investigators in diverse cancer subtypes cancer types including uveal melanoma, lung and pancreatic cancer. We have continued to study rare hematopoietic cancers in collaboration with Dr. Elaine Jaffe and are currently investigating the molecular biology of Histiocytic Sarcoma taking advantage of the samples collected and archived by Dr. Jaffe in her consult practice. The molecular diagnostics laboratory also supports translational research of NCI and NIH researchers. Among the NCI and NIH investigators and clinicians that have utilized the laboratory's resources in 2016-17 are: Dr. A. Apolo (NCI), Dr. Fred Barr (NCI), Dr. Austin Barrett (NHLBI), Dr. Jeffrey Cohen (NIAID), Dr. William Gahl (NHGRI), Dr. Mark Gilbert (NCI), Dr. Raffit Hassan (NCI), Dr. Steven Holland (NIAID), Dr. Elaine Jaffe (NCI), Dr. Udai Kammula (NCI), Dr. Amy Klion (NHLBI) Dr. Robert Kreitman (NCI) Dr. Markku Mietinnen (NCI), Dr. Stefania Pittaluga (NCI), Dr. Martha Quezado (NCI), Dr. Arun Rajan (NCI)Dr. Koneti Rao (NIAID), Dr. Steven Rosenberg (NCI), Dr. Udo Rudoff (NCI), Dr. Helen Su (NHLBI), Dr. Anish Thomas, Dr. Thomas Uldrick (NCI), Dr. Gulbu Uzel (NIAID), Dr. Katherine Warren (NCI), Dr. Wyndham Wilson (NCI), Dr. James Yang (NCI), Dr. Neil Young (NHLBI).
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