title: Characterizing complex structural variation in germline and somatic genomes.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Quinlan
authors.forename: Ira M
authors.initials: IM
authors.lastname: Hall
mesh_terms: D000818:Animals; D056914:Genomic Structural Variation; D023281:Genomics; D005854:Germ Cells / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D009369:Neoplasms / Q000235:genetics
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