Patent ID: 7501266
Filing Date: 2009-03-10
Classification: C12Q,Y10S,Y10T

Abstract:
1. A method of differentiating homozygous, heterozygous and wild-type alleles in a target sample comprising mutant or polymorphic alleles or wild-type alleles using results obtained from a probe array, wherein individual probes in the array are designed to detect designated mutant or polymorphic alleles or wild-type alleles through hybridization of said probes and targets, where the results compensate for hybridization between probes and targets other than their designated targets, comprising: amplifying the genomic regions in the target sample that are predicted to include said mutant or polymorphic alleles or said wild-type alleles, thereby producing a first set of labeled amplicons having a region complementary to a subsequence of said mutant or polymorphic alleles (if said mutant or polymorphic alleles are present in said target sample) and a second set of labeled amplicons having a region complementary to a subsequence of said wild-type alleles (if said wild-type alleles are present in said target sample); providing an array of probe pairs, the first member of each pair being complementary, in whole or in substantial part, to a subsequence of a first-set amplicon and the second member of each pair being complementary, in whole or in substantial part, to a subsequence of a second-set amplicon; contacting under hybridizing conditions said array of probe pairs with said amplicons; detecting hybridization between probes and said amplicon sets based on the presence of signals from the labeled, hybridized amplicons, said signals being corrected to adjust for hybridization between probes and amplicons other than their designated amplicons as follows: defining three relative ranges of values for said ratios such that: (i) the lowest range of ratio (a) indicates that said target sample is homozygous for wild-type alleles and the lowest range of ratio (b) indicates that said target sample is homozygous for mutant or polymorphic alleles, (ii) a middle range of either ratio (a) or (b) indicates that said target sample is heterozygous, and (iii) the highest range of ratio (a) indicates that the said target sample is homozygous for mutant or polymorphic alleles and the highest range of ratio (b) indicates that said target sample is homozygous for wild-type alleles.