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

PROVIDENCE, R.I. [Brown University] Powerful data-sifting algorithms developed by computer scientists at Brown University are helping to untangle the profoundly complex genetics of cancer.

In a study reported today in the New England Journal of Medicine, researchers from Washington University in St. Louis used two algorithms developed at Brown to assemble the most complete genetic profile yet of acute myeloid leukemia (AML), an aggressive form of blood cancer. The researchers hope the work will lead to new AML treatments based on the genetics of each patient's disease.

The algorithms, developed by Ben Raphael, Eli Upfal, and Fabio Vandin from the Department of Computer Science and the Center for Computational Molecular Biology (CCMB), played a key role in making sense of the giant datasets required for the study. The work was part of The Cancer Genome Atlas project, which aims to catalog the genetic mutations that cause cells to become cancerous. Doing that requires sequencing the entire genome of cancer cells and comparing it to the genome of healthy cells. Without computational tools like the ones the Brown team has developed, analyzing those data would be impossible.

The AML study used two algorithms developed by the Brown team: HotNet and Dendrix. Both aim to find networks of genes that are important in creating cancerous cells. To understand how they work and why they are important, it helps to know a little about the genetics of cancer.

"Genes don't usually act or their own, but instead act together in pathways or networks," said Raphael, associate professor computer science. "Cancer-causing mutations often target these networks and pathways." This presents a problem for researchers trying to find important mutations, because these mutations are often spread across the network and hidden in the genetic data.

Imagine a cellular pathway containing five genes. If any one of those genes acquires a mutation,
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Contact: Kevin Stacey
kevin_stacey@brown.edu
401-863-3766
Brown University
Source:Eurekalert

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