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


RESULTS
We describe here a general model of structural variation that encompasses both balanced rearrangements and arbitrary copy-number variants (CNV).


CONCLUSIONS
In this model, we show that the space of possible evolutionary histories that explain the structural differences between any two genomes can be sampled ergodically.
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK. zerbino@ebi.ac.uk.|Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA. zerbino@ebi.ac.uk.
Daniel R
DR
Zerbino
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.|Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA.
Tracy
T
Ballinger
Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA.
Benedict
B
Paten
Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA.
Glenn
G
Hickey
Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA.
David
D
Haussler
Copy-number variation; DCJ; Rearrangement; Structural variation
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