QuantiSNP© is an analytical tool for the analysis of copy number variation using whole genome SNP genotyping data. In its first implementation it was developed for data arising from Illumina® platforms and this is fully described in Colella and Yau et al., 2007. At present we are in the process of further developing QuantiSNP© with a particular interest in adapting the algorithm for cancer sample analysis.

QuantiSNP Availability

The algorithm was developed in a collaboration between the Department of Statistics, University of Oxford and the Wellcome Trust Centre for Human Genetics. The QuantiSNP software can be obtained from here. A username and password will be required for download of the software. These can be obtained after the license agreement has been signed. Interested parties should contact: Ioannis Ragoussis.

A discussion forum site provides a support forum for the software.

For specific technical details regarding the software, please contact the principal investigators:

Mathematical Methods: Dr. Christopher C. Holmes

Experimental Methods: Dr. Jiannis Ragoussis

If you use data generated using QuantiSNP© please cite the following publication: Colella and Yau et al., 2007

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Additional Resources for QuantiSNP and CNV detection

Illumina BeadStudio v3.1 Plug-in

Our groups are part of the Illumina Connect network and we are collaborating with Illumina to further develop the integration of QuantiSNP© CNV analysis into the genotyping analysis in BeadStudio. The plug-in will be available soon for download from this page, please visit the page in the following weeks.

Results and SNP Array Browsers
The results of the QuantiSNP analysis can be parsed into a custom track suitable for upload into the UCSC Genome Browser. An example of this custom track displays the analysis presented in Colella and Yau et al., 2007.

Custom tracks for the 100, 240, 300, 550, and 650 Illumina® SNP genotyping arrays suitable for uploading to the UCSC Genome Browser. Also a combination of all of the above tracks is available here.
NB: The larger arrays can take several minutes to load.

QuantiSNP Discussion Forum
A general discussion forum for users to suggest new features, report bugs and interact with other users is available here.

Other Contact Information:

For requests to be included in the mail update on QuantiSNP availability please contact: Christopher Yau

For queries regarding this material please contact Jennifer M Taylor.

QuantiSNP©

© University of Oxford. Copyright 2008

Last Update: 13th February 2008