Genomic Structural Variants

Volume 838 of the series Methods in Molecular Biology pp 291-310


Algorithm Implementation for CNV Discovery Using Affymetrix and Illumina SNP Array Data

  • Laura WinchesterAffiliated withWellcome Trust Centre for Human Genetics, Oxford University
  • , Jiannis RagoussisAffiliated withWellcome Trust Centre for Human Genetics, Oxford University Email author 

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SNP array data can be analysed for the purpose of calling SNP alleles but also for determining the absolute copy number of a certain genomic segment. Here, the method for detecting copy number (CN) change using intensity data from SNP arrays is focused on. Methods incorporating data from the two main genotyping platforms, Affymetrix and Illumina, are described and possible options and problems that may be faced are examined. We discuss the importance of the quality control when using this analysis method and present some guidelines for implementation, both prior and post to algorithm use. A discussion of algorithms available for CN detection is included as well as ideas for further analysis protocols.

Key words

SNP array Copy number Detection algorithm Copy number variant Illumina Affymetrix