Title |
A Streamlined Method for Detecting Structural Variants in Cancer Genomes by Short Read Paired-End Sequencing
|
---|---|
Published in |
PLOS ONE, October 2012
|
DOI | 10.1371/journal.pone.0048314 |
Pubmed ID | |
Authors |
Martina Mijušković, Stuart M. Brown, Zuojian Tang, Cory R. Lindsay, Efstratios Efstathiadis, Ludovic Deriano, David B. Roth |
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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