Introduction

UNLABELLED: Next-generation sequencing technologies expedited research to develop efficient computational tools for the identification of structural variants (SVs) and their use to study human diseases. As deeper data is obtained, the existence of higher complexity SVs in some genomes becomes more evident, but the detection and definition of most of these complex rearrangements is still in its infancy. The full characterization of SVs is a key aspect for discovering their biological implications. Here we present a pipeline (PeSV-Fisher) for the detection of deletions, gains, intra- and inter-chromosomal translocations, and inversions, at very reasonable computational costs. We further provide comprehensive information on co-localization of SVs in the genome, a crucial aspect for studying their biological consequences. The algorithm uses a combination of methods based on paired-reads and read-depth strategies. PeSV-Fisher has been designed with the aim to facilitate identification of somatic variation, and, as such, it is capable of analysing two or more samples simultaneously, producing a list of non-shared variants between samples. We tested PeSV-Fisher on available sequencing data, and compared its behaviour to that of frequently deployed tools (BreakDancer and VariationHunter). We have also tested this algorithm on our own sequencing data, obtained from a tumour and a normal blood sample of a patient with chronic lymphocytic leukaemia, on which we have also validated the results by targeted re-sequencing of different kinds of predictions. This allowed us to determine confidence parameters that influence the reliability of breakpoint predictions. AVAILABILITY: PeSV-Fisher is available at http://gd.crg.eu/tools.

Publications

  1. PeSV-Fisher: identification of somatic and non-somatic structural variants using next generation sequencing data.
    Cite this
    Escaramís G, Tornador C, Bassaganyas L, Rabionet R, Tubio JM, Martínez-Fundichely A, Cáceres M, Gut M, Ossowski S, Estivill X, 2013-01-01 - PloS one

Credits

  1. Geòrgia Escaramís
    Developer

    Genetic Causes of Disease Group, Centre for Genomic Regulation (CRG), Spain

  2. Cristian Tornador
    Developer

  3. Laia Bassaganyas
    Developer

  4. Raquel Rabionet
    Developer

  5. Jose M C Tubio
    Developer

  6. Alexander Martínez-Fundichely
    Developer

  7. Mario Cáceres
    Developer

  8. Marta Gut
    Developer

  9. Stephan Ossowski
    Developer

  10. Xavier Estivill
    Investigator

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Summary
AccessionBT000407
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByXavier Estivill