A method for amplifying different target nucleic acid sequences of interest in a sample, each sequence comprising from 3' to 5', contiguous first, second, and third target domains, wherein the first target domain has a detection position one nucleotide from the 3' terminal base of the second target domain, and the second target domain is at least 1, and preferably from 1 to 100 nucleotides, comprising the steps of: (a) providing a sample having different target nucleic acid sequences of interest; (b) contacting the sample with a set of probes for each of the different target nucleic acid. sequences of interest to form hybridization complexes, each set comprising: a first probe comprising from 5' to 3': a first universal priming sequence and a sequence that is substantially complementary to the first target domain and that has an interrogation position suitable for base pairing with the detection position; and a second probe comprising 5' to 3': a sequence substantially complementary to the third target domain, and a second universal priming sequence, wherein at least one probe contains a distinct adapter sequence not native to the target sequence of interest; (c) providing a solid support, to which the hybridization complexes are immobilized; (d) contacting the hybridization complexes with an extension enzyme and dNTPs, wherein for each hybridization complex, if the base at the interrogation position is perfectly complementary to the base at the detection position, then the first probe is extended along the second target domain; (e) ligating the extended first probes to second probes to form amplification templates; (f) amplifying the amplification templates with first and second universal primers to produce amplicons; and (g) immobilizing the amplicons on solid phase capture probes that are specific to individual adapter sequences. (a) providing a sample having different target nucleic acid sequences of interest; (b) contacting the sample with a set of probes for each of the different target nucleic acid. sequences of interest to form hybridization complexes, each set comprising: a first probe comprising from 5' to 3': a first universal priming sequence and a sequence that is substantially complementary to the first target domain and that has an interrogation position suitable for base pairing with the detection position; and a second probe comprising 5' to 3': a sequence substantially complementary to the third target domain, and a second universal priming sequence, wherein at least one probe contains a distinct adapter sequence not native to the target sequence of interest; a first probe comprising from 5' to 3': a first universal priming sequence and a sequence that is substantially complementary to the first target domain and that has an interrogation position suitable for base pairing with the detection position; and a second probe comprising 5' to 3': a sequence substantially complementary to the third target domain, and a second universal priming sequence, wherein at least one probe contains a distinct adapter sequence not native to the target sequence of interest; (c) providing a solid support, to which the hybridization complexes are immobilized; (d) contacting the hybridization complexes with an extension enzyme and dNTPs, wherein for each hybridization complex, if the base at the interrogation position is perfectly complementary to the base at the detection position, then the first probe is extended along the second target domain; (e) ligating the extended first probes to second probes to form amplification templates; (f) amplifying the amplification templates with first and second universal primers to produce amplicons; and (g) immobilizing the amplicons on solid phase capture probes that are specific to individual adapter sequences.