Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs

BMC Bioinformatics

Methodology Article

Glenn Hickey¹  David Haussler¹  Benedict Paten¹  Daniel R. Zerbino²  Tracy Ballinger² 

[1] Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, 95064, Santa Cruz, CA, USA;European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD, Hinxton, UK;Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, 95064, Santa Cruz, CA, USA;

关键词: Rearrangement;    Structural variation;    Copy-number variation;    DCJ;   

DOI  :  10.1186/s12859-016-1258-4

 received in 2016-01-28, accepted in 2016-09-13,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich mathematical models. However, it has been observed that genomes are highly plastic, and that whole regions can be moved, removed or duplicated in bulk. These structural variants (SV) have been shown to have significant impact on phenotype, but their study has been held back by the combinatorial complexity of the underlying models.ResultsWe describe here a general model of structural variation that encompasses both balanced rearrangements and arbitrary copy-number variants (CNV).ConclusionsIn this model, we show that the space of possible evolutionary histories that explain the structural differences between any two genomes can be sampled ergodically.

【 授权许可】

CC BY   
© The Author(s) 2016

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