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Characterizing Complex Structural Variation in Germline and Somatic Genomes

Overview
Journal Trends Genet
Specialty Genetics
Date 2011 Nov 19
PMID 22094265
Citations 62
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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.

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References
1.
Jiang Z, Tang H, Ventura M, Cardone M, Marques-Bonet T, She X . Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet. 2007; 39(11):1361-8. DOI: 10.1038/ng.2007.9. View

2.
Stratton M . Exploring the genomes of cancer cells: progress and promise. Science. 2011; 331(6024):1553-8. DOI: 10.1126/science.1204040. View

3.
Medvedev P, Stanciu M, Brudno M . Computational methods for discovering structural variation with next-generation sequencing. Nat Methods. 2009; 6(11 Suppl):S13-20. DOI: 10.1038/nmeth.1374. View

4.
Artandi S, DePinho R . Telomeres and telomerase in cancer. Carcinogenesis. 2009; 31(1):9-18. PMC: 3003493. DOI: 10.1093/carcin/bgp268. View

5.
Campbell P, Yachida S, Mudie L, Stephens P, Pleasance E, Stebbings L . The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature. 2010; 467(7319):1109-13. PMC: 3137369. DOI: 10.1038/nature09460. View