Affymetrix® Genotyping Console™ Software

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CNP analysis is a specialized method for determining copy number state in genomic CNP regions. CNP regions are observed to be more variable in copy number state than the genome as a whole. Because the copy number state in CNP regions is more likely to deviate from the normal copy number state of two, previous copy number analysis methods were less accurate when applied to CNP regions. Therefore, a new analysis algorithm called Canary was developed for copy number analysis within CNP regions. It was developed by researchers at the Broad Institute. See Appendix G in the GTC 3.0.1 User Manual for more information on CNP analysis and the Canary algorithm.