Skip to Main content Skip to Navigation
Journal articles

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.
Document type :
Journal articles
Complete list of metadatas

Cited literature [36 references]  Display  Hide  Download

https://hal-pasteur.archives-ouvertes.fr/pasteur-01471706
Contributor : Anne Lassailly-Bondaz <>
Submitted on : Monday, February 20, 2017 - 12:53:52 PM
Last modification on : Monday, January 13, 2020 - 5:08:16 PM
Long-term archiving on: : Sunday, May 21, 2017 - 2:05:40 PM

File

journal.pone.0048314.pdf
Publication funded by an institution

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Collections

Citation

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⟩

Share

Metrics

Record views

645

Files downloads

689