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

the pathway fails and the cell becomes cancerous. That means five patients with the same cancer can have any one of five different mutations. That makes life difficult for researchers trying to find the mutations that cancer cells have in common. The algorithms developed by Raphael and his team are designed to connect those dots and identify the important pathways, rather than looking only at individual genes.

The HotNet algorithm works by plotting mutation data from patients onto a map of known gene interactions and looking for connected networks that are mutated more often than would be expected by chance. The program represents frequently mutated genes as heat sources. By looking at the way heat is distributed and clustered across the map, the program finds the "hot" networks involved in cancer.

HotNet picked out several networks that seem to be active in the AML genome. In a study published in 2011, HotNet identified networks important to ovarian cancer as well.

Dendrix, the newest algorithm developed at Brown, takes the power of HotNet one step further. HotNet works by looking for mutations in networks that are already known to researchers. However, there are countless gene networks that researchers have not yet identified. Dendrix is designed to look for mutations in those previously unknown networks.

To find new networks, Dendrix takes advantage of the fact that cancer-causing mutations are relatively rare. A patient with a mutation in one gene in a network is unlikely to have a concurrent mutation in another gene in that network. Dendrix looks for combinations of mutations that happen frequently across patients but rarely happen together in a single patient. Put another way: Imagine that a substantial number patients with a given cancer have a mutation in gene X. Another large group of patients has a mutation in gene Y. But very few patients have mutations in both X and Y at the same time. Dendrix looks for these patterns
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Contact: Kevin Stacey
kevin_stacey@brown.edu
401-863-3766
Brown University
Source:Eurekalert

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