Patent ID: 8003354

Claim:
A multiplex detection method, comprising (a) providing a first solid support comprising a plurality of different target nucleic acids, wherein each of said target nucleic acids comprises a locus having a single nucleotide polymorphism (SNP) allele; (b) providing a plurality of at least 100 different probe sets, wherein each of said probe sets comprises a first allele specific probe and a locus specific probe, wherein said first allele specific probe comprises a first universal priming sequence and a target specific portion that is complementary to a specific target nucleic acid of said plurality of different target nucleic acids and is capable of identifying the single nucleotide polymorphism allele of said specific target nucleic acid, and wherein said locus specific probe comprises a second universal priming sequence, an adapter sequence and a target specific portion that is complementary to at least a portion of said locus; (c) hybridizing said probe sets to said target nucleic acids and forming a plurality of hybridization complexes; (d) extending the first allele specific probe of each of said hybridization complexes in an allele specific manner under sufficient conditions so that only the first allele specific probe of each of said hybridization complexes that is perfectly complementary to the SNP allele of a target nucleic acid of said plurality of different target nucleic acids is extended, and forming extended probes; (e) ligating said extended probes to said locus specific probes and forming ligated probes; (f) amplifying said ligated probes and forming amplicons, each of said amplicons comprising said adapter sequence; (g) hybridizing said amplicons to capture probes on a second solid support having at least 100 different said capture probes, wherein each of said capture probes is complementary to said adapter sequence; and (h) detecting said amplicons that are hybridized to said capture probes; thereby detecting said single nucleotide polymorphism allele of each of said plurality of different target nucleic acids.