PathScan: a tool for discerning mutational significance in groups of putative cancer genes.

ABSTRACT:

Motivation

The expansion of cancer genome sequencing continues to stimulate development of analytical tools for inferring relationships between somatic changes and tumor development. Pathway associations are especially consequential, but existing algorithms are demonstrably inadequate.

Methods

Here, we propose the PathScan significance test for the scenario where pathway mutations collectively contribute to tumor development. Its design addresses two aspects that established methods neglect. First, we account for variations in gene length and the consequent differences in their mutation probabilities under the standard null hypothesis of random mutation. The associated spike in computational effort is mitigated by accurate convolution-based approximation. Second, we combine

SUBMITTER: Wendl MC 

PROVIDER: S-EPMC3106187 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature