Method for relative quantification of nucleic acid sequence, expression, or copy changes, using combined nuclease, ligation, and polymerase reactions

A kit for identifying a presence of one or more target nucleotide sequences in a sample comprising:

• an enzyme having 5′ nuclease activity;
• a ligase;
• and
• one or more oligonucleotide probe sets, each set comprising (a) a first oligonucleotide probe having a 5′ primer-specific portion and a first target specific portion, and (b) a second oligonucleotide probe having a 3′ primer-specific portion, a second target specific portion, and a 5′ nucleotide sequence, wherein said 5′ nucleotide sequence is complementary to at least a portion of the 3′ primer-specific portion and is configured to hybridize to said complementary portion of the 3′ primer-specific portion to form a hairpinned second oligonucleotide probe when said second oligonucleotide probe is not hybridized to a target nucleotide sequence, wherein the first and second oligonucleotide probes of a probe set are configured to hybridize adjacent to one another on a target nucleotide sequence with a junction between the first and second oligonucleotide probes, and wherein, in each of the one or more oligonucleotide probe sets, the second target specific portion has an overlapping identical nucleotide at the junction with the first oligonucleotide probe.