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© Deriano Lab / Institut Pasteur
Chromosomes métaphasiques d’une cellule lymphoïde cancéreuse présentant une amplification des gènes Igh et c-myc
Publication : PloS one

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

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in PloS one - 29 Oct 2012

Mijušković M, Brown SM, Tang Z, Lindsay CR, Efstathiadis E, Deriano L, Roth DB

Link to Pubmed [PMID] – 23144753

PLoS ONE 2012;7(10):e48314

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.

http://www.ncbi.nlm.nih.gov/pubmed/23144753