Patent ID: 6884583

Claim:
A kit for identifying in a single 5′ nuclease assay which alleles at multiple different allelic sites are present in a sample of DNA, the kit comprising: a first set of oligonucleotide probes comprising first and second oligonucleotide probes for detecting which alleles are present at a first allelic site by single 5′ nuclease assay, the first and second oligonucleotide probes being designed to distinguish between at least two alleles at the first allelic site which differ from each other by at least one base position, wherein the first set of oligonucleotide probes is digestible by a 5′ to 3′ nuclease, and does not self-hybridize; a second set of oligonucleotide probes comprising third and fourth oligonucleotide probes for detecting which alleles are present at a second, different allelic site by the single 5′ nuclease assay, the third and fourth oligonucleotide probes being designed to distinguish between at least two alleles at the second allelic site which differ from each other by at least one base position, wherein the second set of oligonucleotide probes is digestible by a 5′ to 3′ nuclease, and does not self-hybridize; and a first primer that is capable of hybridizing to a sequence in the first allelic site 3′ relative to where the probes of the first set hybridize to the first allelic site and a second primer that is capable of hybridizing to a sequence in the second allelic site 3′ relative to where the probes of the second set hybridize to the second allelic site; wherein one of the first, second, third and fourth oligonucleotide probes lacks a fluorescer and the other three probes each include a different fluorescer, the three different fluorescers being selected such that the first and second sets of oligonucleotide probes can be used to determine which alleles are present at the first and second allelic sites in the single 5′ nuclease assay, and each of the three fluorescer-containing probes with a fluorescer includes a same quencher to quench the fluorescence of the fluorescer.