An algorithm for detecting high frequency copy number polymorphisms using SNP arrays

We present a general algorithm for the detection of genomic variants using the Illumina iSelect platform. The Illumina iSelect platform is designed to detect SNPs, but our algorithm allows for the detections of more general forms of variations, including copy number polymorphisms and microsatellites. The algorithm does not rely on a priori information of the type of polymorphism being studied and is designed to genotype call a large number of individuals simultaneously. The algorithm proceeds by initially normalizing intensity and correcting for batch effects. Then each marker is clustered using a modified Gaussian mixture model where we account for variances in the expression of an individuals and the variance measured in bead level intensities of a probe/marker pair. Finally, these clusters are used to determine genotypes. The algorithm was then run on a dataset of 35,000 Icelandic individuals.