The molecular diagnostics laboratory processed 2228 unique clinical samples in 2012 from NCI/NIH patients, and performed over 9300 tests. Another 1000+ tests were performed to support a variety of collaborative translational research projects. The majority of the laboratory's tests are conventional PCR assays, including both DNA and RT-PCR assays, however mutation-based testing is rapidly increasing in volume. The assays performed by the molecular diagnostics laboratory include assays for B and T-cell clonality, for lymphoma related translocations, for cancer associated viruses (EBV, HTLV, HHV-8), and RT-PCR assays for translocations associated with pediatric sarcomas. Quantitative PCR is performed for HTLV 1/2 to follow viral load for the Metabolism Branch's ATL clinical trials, and for EGFRvIII to assess expression of this cancer-specific target transcript. KRAS, BRAF, and EGFR mutation analyses are performed to assess eligibility and response to EGFR-targeted therapies for several Medicine Branch clinical trials. BRAF mutation analysis is provided for eligibility for novel RAF inhibitors, and to a novel Surgery Branch trial combining targeted immunotherapy with the BRAF inhibitor vemurafinib. We continued to offer a multiplexed assay panel (TOP) for the Thoracic Oncology Groups Molecular profiling Protocol, which stratified patients to one of 6 treatment arms based on the mutational composition of the patient's tumor. This panel includes the above mentioned mutations plus NRAS, AKT1, PIK3CA and ERBB2. MGMT methylation analysis is performed to determine eligibility for Neuro-Oncology branch protocols and predict response to temozolomide, and IDH1/2 is performed to assist in glioma diagnosis and as a prognostic marker. The laboratory also has developed a qRT-PCR assay to assess the presence of the tumor specific variant EGFRvIII, which is required for eligibility to a novel immunotherapy protocol targeting this EGFR variant. Assays are performed on materials derived from a variety of sources.Paraffin fixed tissue specimens account for about 50% of the samples, blood bone marrow, 45%. The remaining 5% of samples are derived from fresh or frozen tissue, cerebrospinal fluid, and other body fluids. The laboratory's developmental research effort is focused on the application of multiplexing technologies for clinical purposes, especially next generation sequencing technologies, and on developing clinical assays for circulating tumor DNA. The laboratory is completing validation of a flexible 50 gene Next Generation Sequencing (NGS) based targeted mutation panel that will be available in 2013 for use in multiple clinical oncology protocols, and has initiated a program with Surgery branch to follow patient responses to immunotherapy, by measuring changes in circulating DNA targets. A high percentage of the paraffin section studies are complex and labor intensive, requiring macro or microdissection of specific components of lesional tissues, and are performed under the guidance of a fellow or staff pathologist. The molecular laboratory is particularly expert in extracting nucleic acids from small fragments of archival paraffin-embedded tissues, and our expertise in this area has been widely sought out in a number of laboratories within and outside of NIH. The laboratory is actively involved in identifying and developing methodologies to improve mutation detection and other types of biomarkers in small biopsy samples, including cytology samples. This includes incorporation of a variety of laser capture microdissection technologies. The laboratory maintains 4 Perkin-Elmer 9700 PCR platforms, one ABI 7900HT real-time PCR machine, one ABI 3130xl capillary electrophoresis unit, one Pyromark 24 pyrosequencing instrument. one Fluidigm Biomark System, 1 Roche 454 Junior, and 1 Ion Torrent personal Genome Analyzer. The molecular diagnostics laboratory supports translational research of both NCI and NIH researchers. Among the NCI and NIH tenured investigators and clinicians that have utilized the laboratory's resources in 2012 are: Dr. Austin Barrett (NHLBI) Dr. Susan Bates (NCI) Dr. John Bennett (NIAID) Dr. Michael Bishop (NCI) Dr. Howard Fine (NCI) Dr. Daniel Fowler (NCI) Dr. William Gahl (NHGRI) Dr. Giuseppe Giaccone (NCI) Dr. Steven Holland (NIAID) Dr. Elaine Jaffe (NCI) Dr. Su Young Kim (NCI) Dr. Daniel Kastner (NHGRI) Dr. Amy Klion (NHLBI) Dr. Robert Kreitman (NCI) Dr. Shivaani Kummar (NCI) Dr. Gerald Marti (FDA) Dr. Dean Metcalfe (NIAID) Dr. Kenneth Olivier (NIAID) Dr. Stefania Pittaluga (NCI) Dr. Martha Quezado (NCI) Dr. Koneti Rao (NIAID) Dr. Steven Rosenberg (NCI) Dr. Claude Sportes (NCI) Dr. Helen Su (NHLBI) Dr. Maria Turner (NCI) Dr. Thomas Uldrick (NCI) Dr. Gulbu Uzel (NIAID) Dr. Katherine Warren (NCI) Dr. Samuel Wells (NCI) Dr. Wyndham Wilson (NCI) Dr. James Yang (NCI) Dr. Neil Young (NHLBI)

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Scientific Cores Intramural Research (ZIC)
Project #
1ZICBC011079-06
Application #
8763759
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
6
Fiscal Year
2013
Total Cost
$444,657
Indirect Cost
Name
National Cancer Institute Division of Basic Sciences
Department
Type
DUNS #
City
State
Country
Zip Code
Jee, Youn Hee; Sadowski, Samira M; Celi, Francesco S et al. (2016) Increased Pleiotrophin Concentrations in Papillary Thyroid Cancer. PLoS One 11:e0149383
Edison, Natalia; Belhanes-Peled, Hila; Eitan, Yuval et al. (2016) Indolent T-cell lymphoproliferative disease of the gastro-intestinal tract following treatment with Adalimumab in resistant Crohn's colitis. Hum Pathol :
Alberobello, Anna Teresa; Wang, Yisong; Beerkens, Frans Joseph et al. (2016) PI3K as a Potential Therapeutic Target in Thymic Epithelial Tumors. J Thorac Oncol 11:1345-56
Nicolae, A; Xi, L; Pham, T H et al. (2016) Mutations in the JAK/STAT and RAS signaling pathways are common in intestinal T-cell lymphomas. Leukemia 30:2245-2247
Dumitriu, Bogdan; Ito, Sawa; Feng, Xingmin et al. (2016) Alemtuzumab in T-cell large granular lymphocytic leukaemia: interim results from a single-arm, open-label, phase 2 study. Lancet Haematol 3:e22-9
Xi, Liqiang; Pham, Trinh; Payabyab, Eden C et al. (2016) Circulating Tumor DNA as an Early Indicator of Response to T-Cell Transfer Immunotherapy in Metastatic Melanoma. Clin Cancer Res :
Carter, C A; Rajan, A; Keen, C et al. (2016) Selumetinib with and without erlotinib in KRAS mutant and KRAS wild-type advanced nonsmall-cell lung cancer. Ann Oncol 27:693-9
Xiao, Wenbin; Chen, Wayne W; Sorbara, Lynn et al. (2016) Hodgkin lymphoma variant of Richter transformation: morphology, Epstein-Barr virus status, clonality, and survival analysis-with comparison to Hodgkin-like lesion. Hum Pathol 55:108-16
Rosenberg, Avi Z; Armani, Michael D; Fetsch, Patricia A et al. (2016) High-Throughput Microdissection for Next-Generation Sequencing. PLoS One 11:e0151775
Acquavella, Nicolas; Clever, David; Yu, Zhiya et al. (2015) Type I cytokines synergize with oncogene inhibition to induce tumor growth arrest. Cancer Immunol Res 3:37-47

Showing the most recent 10 out of 73 publications