A method for identifying, in a sample, one or more nucleic acid molecules potentially comprising distinct first target and second target regions coupled to each other, said method comprising: providing a sample potentially containing one or more nucleic acid molecules comprising distinct first target and second target regions coupled to each other; providing one or more oligonucleotide probe sets, each probe set comprising (i) a first oligonucleotide probe comprising a 5' first target-specific portion, a 3' second target specific portion, and a further portion, and (ii) a second oligonucleotide probe comprising a 5' second target specific portion, a 3' first target specific portion, and a further portion, wherein the further portion of the first or second oligonucleotide probes of a probe set comprises (i) a unique identifier sequence, (ii) a patient identifier sequence, (iii) one or more primer binding sequences, or any combination of (i), (ii), and (iii); contacting the sample and the one or more oligonucleotide probe sets under conditions effective for first and second oligonucleotide probes of a probe set to hybridize in a base specific manner to their corresponding first and second target regions of the nucleic acid molecule, if present in the sample; generating one or more ligation competent junctions suitable for coupling 3' ends of first oligonucleotide probes to 5' ends of second oligonucleotide probes of a probe set and for coupling 5' ends of first oligonucleotide probes to 3' ends of second oligonucleotide probes of a probe set when said probe sets are hybridized to complementary first and second target regions of a nucleic acid molecule; ligating the first and second oligonucleotides of a probe set at the one or more ligation competent junctions to form circular ligated products comprising a nucleotide sequence corresponding to the first and second distinct target regions of a nucleic acid molecule coupled to a further portion; and detecting and distinguishing the circular ligated products in the sample thereby identifying the presence, if any, of one or more nucleic acid molecules comprising distinct first target and second target regions coupled to each other in the sample. providing a sample potentially containing one or more nucleic acid molecules comprising distinct first target and second target regions coupled to each other; providing one or more oligonucleotide probe sets, each probe set comprising (i) a first oligonucleotide probe comprising a 5' first target-specific portion, a 3' second target specific portion, and a further portion, and (ii) a second oligonucleotide probe comprising a 5' second target specific portion, a 3' first target specific portion, and a further portion, wherein the further portion of the first or second oligonucleotide probes of a probe set comprises (i) a unique identifier sequence, (ii) a patient identifier sequence, (iii) one or more primer binding sequences, or any combination of (i), (ii), and (iii); contacting the sample and the one or more oligonucleotide probe sets under conditions effective for first and second oligonucleotide probes of a probe set to hybridize in a base specific manner to their corresponding first and second target regions of the nucleic acid molecule, if present in the sample; generating one or more ligation competent junctions suitable for coupling 3' ends of first oligonucleotide probes to 5' ends of second oligonucleotide probes of a probe set and for coupling 5' ends of first oligonucleotide probes to 3' ends of second oligonucleotide probes of a probe set when said probe sets are hybridized to complementary first and second target regions of a nucleic acid molecule; ligating the first and second oligonucleotides of a probe set at the one or more ligation competent junctions to form circular ligated products comprising a nucleotide sequence corresponding to the first and second distinct target regions of a nucleic acid molecule coupled to a further portion; and detecting and distinguishing the circular ligated products in the sample thereby identifying the presence, if any, of one or more nucleic acid molecules comprising distinct first target and second target regions coupled to each other in the sample.