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Genome Research publishes special issue: Cancer Genomics
Date:2/1/2012

1/gr.118919.110

4. Cutting-edge methods to detect the genes and networks that drive cancer

The special Cancer Genomics issue of Genome Research also features cutting-edge methodological advances, including three reports that address the problem of identifying the genes, networks, and pathways that drive cancer.

A significant challenge to the identification of genetic alterations that lead to cancer is the experimental determination of which mutations are driving cancer and which mutations are random "passengers." Further complicating discovery of drivers is that driver mutations can target multiple cellular pathways and processes, and each cancer can present different mutations that are sufficient to disrupt critical pathways.

Two reports in this issue present new computational strategies to finding biological pathways that are commonly disrupted by diverse genomic alterations. Vandin and colleagues developed a pair of computational strategies collectively called Dendrix to spot groups of genes that constitute "driver pathways." Applying Dendrix to three cancer studies, Vandin et al. successfully identify sets of genes that are mutated in large numbers of patients, including well-known cancer-related pathways such as Rb, p53, mTOR, and MAPK.

Ciriello and colleagues have developed the Mutual Exclusivity Modules in Cancer (MEMo) method to identify previously unrecognized oncogenic pathways. Applying MEMo to datasets of genomic alterations in glioblastoma and ovarian cancer, MEMo successfully identified known oncogenic pathways and presented evidence for a new hypothesis for the striking genomic instability of ovarian tumors. Dendrix and MEMo will be particularly useful for the interpretation of very large cancer genome sequencing studies, many currently underway.

Also in this issue, Xiong et al. present Gene Set Association Analysis (GSAA), a statistical framework that integrates and simul
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Contact: Peggy Calicchia
calicchi@cshl.edu
516-422-4012
Cold Spring Harbor Laboratory
Source:Eurekalert

Page: 1 2 3 4 5 6 7

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