A Streamlined Method for Detecting Structural Variants in Cancer Genomes by Short Read Paired-End Sequencing

作者：Mijuskovic Martina; Brown Stuart M; Tang Zuojian; Lindsay Cory R; Efstathiadis Efstratios; Deriano Ludovic; Roth David B^*

来源：PLos One, 2012, 7(10): e48314.

DOI：10.1371/journal.pone.0048314

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.

• 出版日期2012-10-29