The main goal of this work is to locate and evaluate molecular targets for brain cancers, starting with glioblastoma. This project serves as a pilot for larger cancer re-sequencing projects. We have teamed with the Venter Institute and its associated Joint Technology Center to perform state-of-the-art and low cost sequencing using their SNP detection pipeline. For our first specific aim, we will re-sequence all known kinase domains in the cancer genomes of 30 glioblastomas. Once a kinase domain mutation is detected we expand our analysis to the entire gene in 50 additional glioblastomas and a panel of other brain cancers, including pediatric glioblastomas and medulloblastomas. In our preliminary analysis of the first 40 kinase genes, novel tyrosine receptor kinase mutations were found in FGFR1 and PDGFRA. We have also found additional mutations in PIK3CA in adult and pediatric glioblastoma.
In specific aim 2, we propose to create a high-resolution copy number map of our 30 glioblastomas using Digital Karyotyping, so we can evaluate in the same samples point mutations, amplifications and deletions. We have completed Digital Karyotyping in 8 glioblastomas, and previously published on using this powerful technique to find a developmental gene genomic amplification in medulloblastoma.
In specific aim 3 we will functionally evaluate the mutations we find with frequency greater than 10%, starting with two kinase mutations we have already found in glioblastoma. We will create a model system of the mutation in cell lines and determine the target of altered phosphorylation and if the cell-cycle, apoptosis and/or invasion are altered. To ensure rapid reporting and integration of our work into larger efforts we propose an online database and reporting for our fourth and final specific aim. Glioblastomas have poor survival and new treatments are needed. Our long-term goal is to choose the best molecular targets from this systematic analysis and determine if inhibition of these new mutations will be a successful therapeutic strategy.
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