Patent ID: 8283121

Claim:
A method for identifying one or more different target nucleotide sequences comprising: providing a sample potentially containing one or more target nucleotide sequences comprising sequence differences; providing one or more oligonucleotide probe sets, each probe set comprising (a) a first oligonucleotide probe comprising a target-specific portion, a further portion, and a 5′ upstream primer-specific portion and (b) a second oligonucleotide probe comprising a target-specific portion and a 3′ downstream primer-specific portion, wherein the first and second oligonucleotide probes in a particular set are suitable for ligation together when hybridized on a corresponding target nucleotide sequence, but have a mismatch which interferes with such ligation when the first and second oligonucleotide probes are hybridized to any other nucleotide sequence present in the sample; providing a ligase; blending the sample, the one or more oligonucleotide probe sets, and the ligase to form a ligase reaction mixture; subjecting the ligase reaction mixture to one or more ligase reaction cycles to form a ligation product sequence comprising (a) the 5′ upstream primer specific portion, (b) the further portion, (c) the target-specific portions, and (d) the 3′ downstream primer-specific portion, when the respective target nucleotide sequence of the corresponding oligonucleotide probe set is present in the sample; providing one or a plurality of oligonucleotide primer sets, each set comprising (a) an upstream primer and (b) a downstream primer; providing a polymerase; blending the ligase reaction mixture with the one or a plurality of oligonucleotide primer sets, and the polymerase to form a polymerase chain reaction mixture; subjecting the polymerase chain reaction mixture to one or more polymerase chain reaction cycles to form extension products comprising the ligation product sequence and/or complements thereof; and detecting the extension products to identify one or more target nucleotide sequences in the sample.