The molecular diagnostics laboratory processed 1708 unique clinical samples in 2010 from NCI/NIH patients, and performed over 4997 tests. Another 700+ 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. 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. We recently initiated a new assay panel (TOP) for the Thoracic Oncology Groups Molecular profiling Protocol, which stratifies patients to one of 6 treatment arms based on the mutational composition of the patient's tumor. This panel includes the above mentioned tumors plus NRAS, AKT1, and PIK3CA. MGMT methylation analysis is performed to determine eligibility for Neuro-Oncology branch protocols. Currently we are developing assays to assess p53 mutation and EGFRvIII presence, occurring in a variety of cancers. The laboratory's developmental research effort is focused on the application of multiplexing technologies for clinical purposes, especially next generation sequencing technologies. Assays are performed on materials derived from a variety of sources. Paraffin fixed tissue specimens account for about 60% of the samples and blood, 35%. The remaining 5% of samples are derived from fresh or frozen tissue, cerebrospinal fluid, and other body fluids. 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 maintains 4 Perkin-Elmer 9700 PCR platforms, one ABI 7900 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 utilizing the laboratory's resources 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. 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. S. Rosenberg (NCI) Dr. Phillip Scheinberg (NHLBI) Dr. Helen Su (NHLBI) Dr. Maria Tsokos (NCI) 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)
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