Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Identifying Simultaneous Rearrangements in Cancer Genomes

Layla Oesper, Simone Dantas, Benjamin J. Raphael
doi: https://doi.org/10.1101/164855
Layla Oesper
1 Department of Computer Science, Carleton College, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simone Dantas
2 Institute of Mathematics and Statistics, Fluminense Federal University, Brazil.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Benjamin J. Raphael
3 Department of Computer Science, Princeton University, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

The traditional view of cancer evolution states that a cancer genome accumulates a sequential ordering of mutations over a long period of time. However, in recent years it has been suggested that a cancer genome may instead undergo a one-time catastrophic event, such as chromothripsis, where a large number of mutations instead occur simultaneously. A number of potential signatures of chromothripsis have been proposed. In this work we provide a rigorous formulation and analysis of the “ability to walk the derivative chromosome” signature originally proposed by Korbel and Campbell (2013). In particular, we show that this signature, as originally envisioned, may not always be present in a chromothripsis genome and we provide a precise quantification of under what circumstances it would be present. We also propose a variation on this signature, the H/T alternating fraction, which allows us to overcome some of the limitations of the original signature. We apply our measure to both simulated data and a previously analyzed real cancer dataset and find that the H/T alternating fraction may provide useful signal for distinguishing genomes having acquired mutations simultaneously from those acquired in a sequential fashion. An implementation of the H/T alternating fraction is available at https://bitbucket.org/oesperlab/ht-altfrac.

Footnotes

  • ↵∗ loesper{at}carleton.edu

  • ↵† sdantas{at}im.uff.br, Partially supported by CAPES Project ID 18316-12-3, CNPq and FAPERJ

  • ↵‡ braphael{at}princeton.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted July 26, 2017.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Identifying Simultaneous Rearrangements in Cancer Genomes
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Identifying Simultaneous Rearrangements in Cancer Genomes
Layla Oesper, Simone Dantas, Benjamin J. Raphael
bioRxiv 164855; doi: https://doi.org/10.1101/164855
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Identifying Simultaneous Rearrangements in Cancer Genomes
Layla Oesper, Simone Dantas, Benjamin J. Raphael
bioRxiv 164855; doi: https://doi.org/10.1101/164855

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4095)
  • Biochemistry (8793)
  • Bioengineering (6495)
  • Bioinformatics (23406)
  • Biophysics (11769)
  • Cancer Biology (9173)
  • Cell Biology (13304)
  • Clinical Trials (138)
  • Developmental Biology (7426)
  • Ecology (11392)
  • Epidemiology (2066)
  • Evolutionary Biology (15127)
  • Genetics (10419)
  • Genomics (14029)
  • Immunology (9154)
  • Microbiology (22132)
  • Molecular Biology (8797)
  • Neuroscience (47470)
  • Paleontology (350)
  • Pathology (1423)
  • Pharmacology and Toxicology (2486)
  • Physiology (3712)
  • Plant Biology (8073)
  • Scientific Communication and Education (1434)
  • Synthetic Biology (2217)
  • Systems Biology (6023)
  • Zoology (1251)