Patent ID: 8190373

Claim:
A system for identifying regions of copy number variation in a test sample comprising: a computer readable storage medium having computer program logic recorded thereon, wherein said computer program logic comprises instructions comprising: (a) input instructions for (i) receiving a plurality of probe intensity values for each of a plurality of perfect match probes for a first allele and each of a plurality of perfect match probes for a second allele for each of a plurality of polymorphisms; (ii) instructing a processor to execute computer code to calculate a first summary intensity value for the first allele and a second summary intensity value for the second allele for each polymorphism in the plurality of polymorphisms using one or more of the probe intensity values received in (a); (iii) normalizing the first summary intensity value for the first allele for each polymorphism using a normalization value for the first allele obtained from a reference set of samples of known genotype; (iv) normalizing the second summary probe intensity value for the second allele for each polymorphism using a normalization value for the second allele obtained from a reference set of samples of known genotype; (v) estimating copy number for said first allele for each polymorphism; (vi) estimating copy number for said second allele for each polymorphism; and (vii) estimating the copy number for each of a plurality of genomic regions, wherein each genomic region contains at least one of the polymorphism in the plurality of polymorphisms by combining the estimated copy number for said first allele and the estimated copy number for said second allele for each polymorphism; (b) instructions for comparing the estimated total copy number for each genomic region in the test sample to the reference set of samples; and (c) instructions for outputing a copy number estimate for each of a plurality of genomic regions in the test sample and for outputting genomic regions in the test sample where the copy number estimate for that region varies from the copy number of that region in the reference set of samples.