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

ntification of mutations in a patient's tumor genome. Different research groups use different algorithms for this, and CGHub scientists found that these algorithms give inconsistent answers.

"That was a big shocker to me when the TCGA and International Cancer Genome consortiums started comparing the algorithms used by different institutions," Stuart said. "You'd think we'd know which one to install, but there are more than a dozen of them and they all came up with different answers. Only in the last year have we sorted that out, and David Haussler has created a unified effort to identify mutations for TCGA."

The mutation data, together with information on gene locations, then feeds into higher-level analyses. Stuart's lab, for example, uses this information to identify the genetic pathways affected by a patient's mutations. Using knowledge about how genes work in groups by signaling and regulating each other, he is able to find connections between different mutations that affect the same pathways. In previous work on TCGA data, results from Stuart's pathway analysis proved to be better predictors of overall survival in glioblastoma patients than a lower level of genomic analysis, and pathway signatures also revealed novel connections between mutations and drug response in breast cancers.

As with the mutation-finding algorithms, higher-level analyses are likely to differ among research groups. To find out who has the best algorithm for any particular type of analysis, they have to be compared side by side in blinded competitions. For the BMEG project, Stuart has teamed up with Adam Margolin of Sage Bionetworks, a nonprofit bioinformatics company, to run a series of such competitions.

"We've done this before, and it will be fun. We'll run competitions and then hold a conference at the end to go over the results," Stuart said. "To participate, people will give us their code and we'll run it on a test dataset. That's how we'll bui
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Contact: Tim Stephens
stephens@ucsc.edu
831-459-2495
University of California - Santa Cruz
Source:Eurekalert

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