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Briefings in Functional Genomics and Proteomics Advance Access originally published online on September 8, 2009
Briefings in Functional Genomics and Proteomics 2009 8(5):353-366; doi:10.1093/bfgp/elp017
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© The Author 2009. Published by Oxford University Press. For permissions, please email: journals.permissions@oxfordjournals.org

This article appears in the following Briefings in Functional Genomics and Proteomics issue: Special Issue: Polymorphism, population genetics and natural variation [View the issue table of contents]

Special Issue Papers

Comparing CNV detection methods for SNP arrays

Laura Winchester, Christopher Yau and Jiannis Ragoussis

Corresponding author. Jiannis Ragoussis, Genomics, Wellcome Trust Centre For Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK. Tel: (01865) 287526; Fax: (01865) 287501; E-mail: ioannisr{at}well.ox.ac.uk

Data from whole genome association studies can now be used for dual purposes, genotyping and copy number detection. In this review we discuss some of the methods for using SNP data to detect copy number events. We examine a number of algorithms designed to detect copy number changes through the use of signal-intensity data and consider methods to evaluate the changes found. We describe the use of several statistical models in copy number detection in germline samples. We also present a comparison of data using these methods to assess accuracy of prediction and detection of changes in copy number.

Keywords: copy number, SNP array


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