Patent ID: 7132239

Claim:
A method for identifying which members of two or more sets of substantially homologous sequences are present in a sample of DNA, the method comprising: performing a nucleic acid amplification on a sample of DNA which includes (i) a first set of substantially homologous sequences and a second, different set of substantially homologous sequences, using a nucleic acid polymerase having 5′→3′ nuclease activity, (ii) one or more sets of forward and reverse primers capable of hybridizing to the sample DNA, in the presence of two or more sets of oligonucleotide probes, thereby amplifying the sets of substantially homologous sequences wherein: each set of substantially homologous sequences includes two or more members which each differ from each other at at least one base position, each set of oligonucleotide probes is for detecting the members of one of the sets of substantially homologous sequences, each set of oligonucleotide probes includes two or more probes which are complementary to different members of a set of substantially homologous sequences, each member being 5′ relative to a sequence of the sample DNA to which a primer of the corresponding set of primers hybridizes, and at least one of the oligonucleotide probes includes a different fluorescer than the other probes and a quencher positioned on the probe to quench the fluorescence of the fluorescer, and at least one of the oligonucleotide probes lacks a fluorescer; digesting those oligonucleotide probes which hybridize to the sample DNA during the amplification by the nuclease activity of the polymerase; detecting a fluorescence spectrum of the amplified DNA sample; calculating a fluorescence contribution of each fluorescer to the fluorescence spectrum; and determining a presence or absence of the different members of substantially homologous sequences based on the fluorescence contribution of each fluorescer to the fluorescence spectrum.