Patent ID: 7662550

Claim:
A homogeneous detection assay method for identifying which variant among multiple variants of a short nucleotide sequence is present in a sample, said multiple variants differing from one another by one or more changes selected from the group of nucleotide substitutions, deletions and additions, comprising: (a) providing a reaction mixture containing the sample with at least three hybridization probes having different target binding sequences, said probes being capable of hybridizing to mismatched targets in the assay, and said probes being differently fluorescently labeled probes whose hybridization can be detected without separating unbound probes, wherein each of said probes is capable of hybridizing to more than one variant of said multiple variants with varying degrees of complementarity; (b) measuring the intensity of fluorescence signals resulting from hybridization of each of said probes; and (c) identifying which variant is present by determining a fluorescence fingerprint for the sample, said fluorescence fingerprint comprising ratios of the intensities of the fluorescence signals of the at least three probes.