Simple binary segmentation frameworks for identifying variation in DNA copy number.

ABSTRACT:

Background

Variation in DNA copy number, due to gains and losses of chromosome segments, is common. A first step for analyzing DNA copy number data is to identify amplified or deleted regions in individuals. To locate such regions, we propose a circular binary segmentation procedure, which is based on a sequence of nested hypothesis tests, each using the Bayesian information criterion.

Results

Our procedure is convenient for analyzing DNA copy number in two general situations: (1) when using data from multiple sources and (2) when using cohort analysis of multiple patients suffering from the same type of cancer. In the first case, data from multiple sources such as different platforms, labs, or preprocessing methods are used to study variation in copy number in the same indi

SUBMITTER: Yang TY 

PROVIDER: S-EPMC3571941 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature