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Trends Genet. 2012 Jan;28(1):43-53. doi: 10.1016/j.tig.2011.10.002. Epub 2011 Nov 15.

Characterizing complex structural variation in germline and somatic genomes.

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Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.


Genome structural variation (SV) is a major source of genetic diversity in mammals and a hallmark of cancer. Although SV is typically defined by its canonical forms (duplication, deletion, insertion, inversion and translocation), recent breakpoint mapping studies have revealed a surprising number of 'complex' variants that evade simple classification. Complex SVs are defined by clustered breakpoints that arose through a single mutation but cannot be explained by one simple end-joining or recombination event. Some complex variants exhibit profoundly complicated rearrangements between distinct loci from multiple chromosomes, whereas others involve more subtle alterations at a single locus. These diverse and unpredictable features present a challenge for SV mapping experiments. Here, we review current knowledge of complex SV in mammals, and outline techniques for identifying and characterizing complex variants using next-generation DNA sequencing.

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