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This article is part of the supplement: Proceedings of the 21st International Conference on Genome Informatics (GIW2010)

Open Access Research

Detection and reconstruction of tandemly organized de novo copy number variations

Dan He*, Nicholas Furlotte and Eleazar Eskin*

Author Affiliations

Dept. of Comp. Sci., Univ. of California Los Angeles, Los Angeles, CA 90095, USA

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BMC Bioinformatics 2010, 11(Suppl 11):S12  doi:10.1186/1471-2105-11-S11-S12

Published: 14 December 2010

Abstract

Background

The characterization of structural variations (SV) such as insertions, deletions and copy number variations is a critical step in the process of understanding the full genetic architecture of organisms. Copy number variations (CNV) have attracted much recent attention due to their effects on gene expression and disease status.

Results

In this paper, we present a method that utilizes next-generation sequencing technologies (NGS), in order to both detect and reconstruct CNVs. We focus on a special type of CNV, namely tandemly organized de novo CNVs, which have been shown to occur with high frequency in the mouse genome.

Conclusions

We apply our method to CNV regions randomly inserted into the reference mouse genome and show that our method achieves good performance for both detection and reconstruction of tandemly organized de novo CNVs.