Patent ID: 7427479

Claim:
A method for identifying at least one first target nucleotide and at least one second target nucleotide in a mixed population, comprising: forming a first ligation reaction composition comprising (a) at least one first target nucleic acid sequence, (b) at least one first ligation probe set comprising at least one first probe and at least one second probe, wherein the at least one first probe comprises at least one first target-specific portion and the at least one second probe comprises at least one second target-specific portion, and (c) at least one first ligase; forming a second ligation reaction composition comprising (a) at least one second target nucleic acid sequence, (b) at least one second ligation probe set comprising at least one first probe and at least one second probe, wherein the at least one first probe comprises at least one target-specific portion and the at least one second probe comprises at least one target-specific portion, and (c) at least one second ligase; subjecting the first ligation reaction composition to at least one cycle of ligation to generate at least one first ligation product; subjecting the second ligation reaction composition to at least one cycle of ligation to generate at least one second ligation product; and identifying the at least one first target nucleotide, the at least one second target nucleotide, or the at least one first target nucleotide and the at least one second target nucleotide in the mixed population.