Ligation-based methods and kits are disclosed for identifying at least two
target nucleotides in a mixed population sample, that is a sample that
contains or potentially contains target nucleic acid sequences from more
than one source. Typically, two ligation reaction compositions are
formed, ligation products generated, and the ligation products or their
surrogates are analyzed to identify target nucleotides in the mixed
population sample. In certain embodiments, the target nucleic acid
sequences, the ligation products, or both are amplified. In certain
embodiments, multiplex amplification and/or ligation reactions are
performed.