Patent ID: 8288103

Claim:
A method for amplifying different target nucleic acid sequences of interest in a sample, each sequence comprising, from 3â€² to 5â€²: contiguous first, second, and third target domains, wherein the first target domain has a detection position one nucleotide from the 3â€² terminal base of the second target domain, and the second target domain is at least 100 nucleotides in length, 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 5â€² to 3â€²: a first priming sequence and a sequence that is substantially complementary to the first target domain and that has an interrogation position suitable for basepairing with the detection position; and a second probe comprising 5â€² to 3â€²: a sequence substantially complementary to the third target domain, and a second priming sequence, wherein at least one probe contains a distinct adapter sequence not native to the target sequence of interest; (c) immobilizing the hybridization complexes on a solid support; (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 primers to produce amplicons; and (g) immobilizing the amplicons on solid phase capture probes; thereby amplifying the different target sequences of interest in the sample.