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 filte

SUBMITTER: Mijuskovic M 

PROVIDER: S-EPMC3483208 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature