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Bioinformatics 2008 24(13):i59-i67; doi:10.1093/bioinformatics/btn176
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

A robust framework for detecting structural variations in a genome

Seunghak Lee 1,*, Elango Cheran 1,* and Michael Brudno 1,2,*

1Department of Computer Science, 2Banting and Best Department of Medical Research and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3G4, Canada

*To whom correspondence should be addressed.


  Abstract

Motivation: Recently, structural genomic variants have come to the forefront as a significant source of variation in the human population, but the identification of these variants in a large genome remains a challenge. The complete sequencing of a human individual is prohibitive at current costs, while current polymorphism detection technologies, such as SNP arrays, are not able to identify many of the large scale events. One of the most promising methods to detect such variants is the computational mapping of clone-end sequences to a reference genome.

Results: Here, we present a probabilistic framework for the identification of structural variants using clone-end sequencing. Unlike previous methods, our approach does not rely on an a priori determined mapping of all reads to the reference. Instead, we build a framework for finding the most probable assignment of sequenced clones to potential structural variants based on the other clones. We compare our predictions with the structural variants identified in three previous studies. While there is a statistically significant correlation between the predictions, we also find a significant number of previously uncharacterized structural variants. Furthermore, we identify a number of putative cross-chromosomal events, primarily located proximally to the centromeres of the chromosomes.

Availability: Our dataset, results and source code are available at http://compbio.cs.toronto.edu/structvar/

Contact:seunghak{at}cs.toronto.edu,echeran{at}cs.toronto.edu,brudno{at}cs.toronto.edu


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