Introduction

BACKGROUND: Chromothripsis, a newly discovered type of complex genomic rearrangement, has been implicated in the evolution of several types of cancers. To date, it has been described in bone cancer, SHH-medulloblastoma and acute myeloid leukemia, amongst others, however there are still no formal or automated methods for detecting or annotating it in high throughput sequencing data. As such, findings of chromothripsis are difficult to compare and many cases likely escape detection altogether. RESULTS: We introduce ShatterProof, a software tool for detecting and quantifying chromothriptic events. ShatterProof takes structural variation calls (translocations, copy-number variations, short insertions and loss of heterozygosity) produced by any algorithm and using an operational definition of chromothripsis performs robust statistical tests to accurately predict the presence and location of chromothriptic events. Validation of our tool was conducted using clinical data sets including matched normal, prostate cancer samples in addition to the colorectal cancer and SCLC data sets used in the original description of chromothripsis. CONCLUSIONS: ShatterProof is computationally efficient, having low memory requirements and near linear computation time. This allows it to become a standard component of sequencing analysis pipelines, enabling researchers to routinely and accurately assess samples for chromothripsis. Source code and documentation can be found at http://search.cpan.org/~sgovind/Shatterproof.

Publications

  1. ShatterProof: operational detection and quantification of chromothripsis.
    Cite this
    Govind SK, Zia A, Hennings-Yeomans PH, Watson JD, Fraser M, Anghel C, Wyatt AW, van der Kwast T, Collins CC, McPherson JD, Bristow RG, Boutros PC, 2014-01-01 - BMC bioinformatics

Credits

  1. Shaylan K Govind
    Developer

  2. Amin Zia
    Developer

  3. Pablo H Hennings-Yeomans
    Developer

  4. John D Watson
    Developer

  5. Michael Fraser
    Developer

  6. Catalina Anghel
    Developer

  7. Alexander W Wyatt
    Developer

  8. Theodorus van der Kwast
    Developer

  9. Colin C Collins
    Developer

  10. John D McPherson
    Developer

  11. Robert G Bristow
    Developer

  12. Paul C Boutros
    Investigator

    Ontario Institute for Cancer Research, M5G 0A3

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Summary
AccessionBT002625
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByPaul C Boutros