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. 2014:45:15.6.1-11.
doi: 10.1002/0471250953.bi1506s45.

BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping

Xian Fan  1 , Travis E Abbott  2 , David Larson  2 , Ken Chen  1
Affiliations

BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping

Xian Fan et al. Curr Protoc Bioinformatics. 2014.

Abstract

The advent of the next-generation sequencing data has made it possible to cost-effectively detect and characterize genomic variation in human genomes. Structural variation, including deletion, duplication, insertion, inversion and translocation, is of great importance to human genetics due to its association with many genetic diseases. BreakDancer is a bioinformatics tool that relates paired-end read alignments from a test genome to the reference genome for the purpose of comprehensively and accurately detecting various types of structural variation.

Keywords: BreakDancer; Discordant Read Pair; Genomics; Next Generation Sequencing; Structural Variation.

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References

    1. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Sonkin D. The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity. Nature. 2012;483(7391):603–607. doi: 10.1038/nature11003.The. - DOI - PMC - PubMed
    1. Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Getz G. Absolute quantification of somatic DNA alterations in human cancer. Nature biotechnology. 2012;30(5):413–21. doi: 10.1038/nbt.2203. - DOI - PMC - PubMed
    1. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, Mardis ER. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature methods. 2009;6(9):677–81. doi: 10.1038/nmeth.1363. - DOI - PMC - PubMed
    1. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Fulton LL. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature. 2010;464(7291):999–1005. doi: 10.1038/nature08989. - DOI - PMC - PubMed
    1. Fan X, Nakhleh L, Chen K. BreakDown: integrative estimation of allele fraction from structural variation breakpoints n.d

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