A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing.

Abstract : Defining the architecture of a specific cancer genome, including its structural variants, is essential for understanding tumor biology, mechanisms of oncogenesis, and for designing effective personalized therapies. Short read paired-end sequencing is currently the most sensitive method for detecting somatic mutations that arise during tumor development. However, mapping structural variants using this method leads to a large number of false positive calls, mostly due to the repetitive nature of the genome and the difficulty of assigning correct mapping positions to short reads. This study describes a method to efficiently identify large tumor-specific deletions, inversions, duplications and translocations from low coverage data using SVDetect or BreakDancer software and a set of novel filtering procedures designed to reduce false positive calls. Applying our method to a spontaneous T cell lymphoma arising in a core RAG2/p53-deficient mouse, we identified 40 validated tumor-specific structural rearrangements supported by as few as 2 independent read pairs.
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PLoS ONE, Public Library of Science, 2012, 7 (10), pp.e48314. 〈10.1371/journal.pone.0048314〉
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Martina Mijušković, Stuart M Brown, Zuojian Tan, Cory R Lindsay, Efstratios Efstathiadis, et al.. A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing.. PLoS ONE, Public Library of Science, 2012, 7 (10), pp.e48314. 〈10.1371/journal.pone.0048314〉. 〈pasteur-01471706〉

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