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Major grant funds UCSC researchers using big data to predict cancer outcomes
Date:6/17/2013

her NIH cancer genomics research programs. Because CGHub holds genome sequences from thousands of individual patients, access is strictly controlled and limited to researchers approved by NIH. But the BMEG will hold higher-level data derived from analyses of the raw genome sequences and will not require the same level of security restrictions.

"The idea is to build a shared knowledge base and create a playground where lots of researchers can interact, test their algorithms, and compare results," Stuart said. "TCGA researchers have built a lot of great tools for data analysis, and we need to get those installed in the BMEG so the rest of the world can engage in that higher level analysis. We want to establish the tools and data analysis pipelines that will be useful for current and future collections of data."

The BMEG complements a parallel project, called Medbook, which will link together patients, biopsy samples, doctors, and researchers into a social network framework. Stuart and recent Ph.D. graduate Ted Goldstein created Medbook for their work on a prostate cancer project funded by Stand Up To Cancer (SU2C). "The BMEG will provide patient-level genome information to Medbook, creating a powerful partnership between the two efforts," Stuart said.

The BMEG will enable outside researchers to securely analyze CGHub-related data without needing to transmit vast amounts of data over the internet. Currently, TCGA data analysis centers download huge files of raw data from CGHub for analysis on their own computers. BMEG will be co-located with the CGHub servers at the San Diego Supercomputer Center, and researchers will be able to run their analyses as apps on the BMEG platform.

Cancer genomics researchers involved in TCGA and related projects are still working to develop and refine the analytical tools needed to extract predictive evidence from their rapidly growing databases. This includes the very first layer of analysis, the ide
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Contact: Tim Stephens
stephens@ucsc.edu
831-459-2495
University of California - Santa Cruz
Source:Eurekalert

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