Patent ID: 8204695

Claim:
A method of estimating a fraction of a first allele and a second allele for each of a plurality of SNP locations, in a sample of nucleic acids, comprising: inputting for each SNP location, a first hybridization value indicative of hybridization affinity of the sample of nucleic acids to nucleic acid probes that are complementary to the first allele, wherein the first hybridization value is a sum of hybridization values for a plurality of nucleic acid probes that are a perfect match to the first allele; inputting for each SNP location, a second hybridization value indicative of hybridization affinity of the sample of nucleic acids to nucleic acid probes that are complementary to the second allele, wherein the second hybridization value is a sum of hybridization values for a plurality of nucleic acid probes that are a perfect match to the second allele; selecting for each SNP location, a third hybridization value that is indicative of hybridization affinity of the sample of nucleic acids to nucleic acid probes that include at least one nucleotide that differs from both the first and second alleles; providing a normalized first and second hybridization value by subtracting the third hybridization value from the first and second hybridization values; and calculating an estimation of the fraction of the first allele and the second allele in the sample of nucleic acids by dividing the normalized first hybridization value by a sum of the normalized first and second hybridization values, wherein the calculation is performed by a computer comprising a computer software product.