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Computer algorithms help find cancer connections
Date:5/1/2013

of exclusivity and predicts that groups of genes with high exclusivity are probably working together.

"Where we see those patterns of exclusivity," Raphael said, "it suggests a possible pathway." The group has tested Dendrix on cancers in which the pathways were already known, just to see if the program would find them. Indeed, the pathways "just fall right out of the data," Raphael said.

For the AML paper, Raphael's group developed an improved algorithm Dendrix++ which better handles extremely rare mutations. Dendrix++ picked out three potential new pathways in AML for doctors to investigate.

Raphael and Vandin, along with computational biology graduate students Max Leiserson and Hsin-Ta Wu, are continuing to improve their algorithms and to apply them to new datasets. The group recently started putting the algorithms to work on what's called the Pan-Cancer project, which looks for commonalities in mutations across cancer types.

"For us as computational people, it's fun to push these algorithms and apply them to new datasets," Raphael said. "At the same time, in analyzing cancer data we hope that the algorithms produce actionable information that is clinically important."


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Contact: Kevin Stacey
kevin_stacey@brown.edu
401-863-3766
Brown University
Source:Eurekalert

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