Nucleic acid analysis by joining barcoded polynucleotide probes

A method for analyzing one or more target polynucleotides in one or more samples, the method comprising the steps of:

• (a) providing one or more samples, each sample comprising one or more target polynucleotides, each target polynucleotide comprising a first target sequence and a second target sequence;
• (b) providing a plurality of first and second complementary probes comprising a first and second complementary probe for each target polynucleotide,
• (i) each first complementary probe having two sequence portions that are complementary to a first target sequence of the target polynucleotide, and two sequence portions that are non-complementary to the first target sequence, wherein the non-complementary portions include an interrogation site bar code sequence and a universal sequence, and wherein a first complementary sequence portion is at 5′ of the interrogation site bar code and a second complementary sequence portion is at 3′ of the interrogation site bar code, wherein the universal sequence is 5′ to the first complementary sequence portion;
• and
• (ii) each second complementary probe having a sequence portion that is complementary to a second target sequence of the target polynucleotide and an immediately adjacent sequence portion that is non-complementary to said second target sequence;
• (c) incubating said plurality of first and second complementary probes with each sample under hybridization conditions such that first and second complementary probes hybridize to their complementary target polynucleotide in a sample to form a hybridization complex;
• (d) joining first and second complementary probes that are hybridized to first and second target sequences of a target polynucleotide in a sample to form a product polynucleotide;
• and
• (e) determining the presence, absence, amount or copy number of each target polynucleotide in said one or more samples by analyzing product polynucleotides or the complements thereof.