J. Comput. Biol. - An algorithm for detecting high frequency copy number polymorphisms using SNP arrays.

Tópicos

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Resumo

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.

Resumo Limpo

present general algorithm detect genom variant use illumina iselect platform illumina iselect platform design detect snps algorithm allow detect general form variat includ copi number polymorph microsatellit algorithm reli priori inform type polymorph studi design genotyp call larg number individu simultan algorithm proceed initi normal intens correct batch effect marker cluster use modifi gaussian mixtur model account varianc express individu varianc measur bead level intens probemark pair final cluster use determin genotyp algorithm run dataset iceland individu

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