Simple binary segmentation frameworks for identifying variation in DNA copy number

BMC Bioinformatics

Tae Young Yang¹ 

[1] Department of Mathematics, Myongji University, Yongin, Kyonggi, 449-728, Korea

关键词: Variation in DNA copy number;    Overall molecular signature;    Consensus molecular signature;    Circular binary segmentation;    Bayesian information criterion;   

Others  :  1088093
DOI  :  10.1186/1471-2105-13-277

 received in 2012-04-30, accepted in 2012-10-22,  发布年份 2012

【 摘 要 】

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 individual. Combining these sources provides a higher resolution, which leads to a more detailed genome-wide survey of the individual. In this case, we provide a simple statistical framework to derive a consensus molecular signature. In the framework, the multiple sequences from various sources are integrated into a single sequence, and then the proposed segmentation procedure is applied to this sequence to detect aberrant regions. In the second case, cohort analysis of multiple patients is carried out to derive overall molecular signatures for the cohort. For this case, we provide another simple statistical framework in which data across multiple profiles is standardized before segmentation. The proposed segmentation procedure is then applied to the standardized profiles one at a time to detect aberrant regions. Any such regions that are common across two or more profiles are probably real and may play important roles in the cancer pathogenesis process.

Conclusions

The main advantages of the proposed procedure are flexibility and simplicity.

【 授权许可】

   
2012 Yang; licensee BioMed Central Ltd.

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