Welcome to the OncoSNP Project

OncoSNP is an analytical tool for characterising copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data. It was originally developed at the Department of Statistics, University of Oxford in collaboration with the Genomics Group, Wellcome Trust Centre of Human Genetics, University of Oxford and the Ludwig Colon Cancer Laboratory, Ludwig Institute of Cancer Research.

Project at a Glance:

OncoSNP contains the following novel features:
  • SNPs classified into one of twenty-one tumour states, each tumour state describes a particular form of copy number alteration and LOH event. 
  • Robust mixture of Student t-distributions used to model the SNP data giving stability in the presence of complex noise processes.
  • Ability to model both normal DNA contamination and intra-tumour heterogeneity jointly.
  • Estimates baseline intensity level for polyploid samples.
  • Inference using Bayesian methods allowing uncertainty in estimates to be characterised.

OncoSNP is freely available for academic and non-commercial use. Users wishing to use OncoSNP for commercial activities should contact Isis Innovations for further details. See the About page for contact details.

Upcoming

DeliverablePriorityDate
OncoSNP v1.0 High 1 January 2010 
OncoSNP-Lite Critical 15 December 2011 
OncoSNP v1.1 High 31 May 2011 
OncoSNP v1.2 Critical 6 February 2012 
OncoSNP v1.3 High 15 July 2013 
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News

  • OncoSNP v2.1 (Beta) Minor updates to allow inter-operability with non-human datasets.New switches introduced to allow processing of non-human named probes, specification of prior base copy number and access to ...
    Posted 4 Jul 2014, 12:58 by Christopher Yau
  • OncoSNP v2.0 (Beta) A beta version of a major upgrade of OncoSNP is now online. This new version allows for analysis of non-human species.
    Posted 2 Apr 2014, 03:27 by Christopher Yau
  • OncoSNP v1.4 OncoSNP v1.4 features some bug fixes and some code restructuring to improve efficiency.
    Posted 4 Jan 2014, 03:51 by Christopher Yau
  • Post-processing scripts An example R script has been uploaded that illustrates some possible ways to manipulate the output files is in the FAQ.
    Posted 12 Aug 2013, 03:50 by Christopher Yau
  • Bug Update A file synchronisation error has caused some users to download a pre-release version of OncoSNP v1.3. In this pre-release version the single sample input mode is malfunctioning ...
    Posted 31 Jul 2013, 06:57 by Christopher Yau
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