Patent ID: 7361488

Claim:
A method of detecting a splice junction sequence in a plurality of target pre-mRNA sequences, said method comprising: a) hybridizing said plurality of target pre-mRNA sequences to a plurality of first splice junction specific probes and forming first hybrids wherein each of said plurality of target pre-mRNA sequences comprises a first target domain, a second target domain and a poly(A) sequence, said first target domain and said second target domain are adjacent each other and said first target domain comprises a splice junction sequence, and each of said plurality of first splice junction specific probes comprises: i) an upstream universal priming site (UUP), wherein each of said first splice junction specific probes has the same UUP; ii) at least one adapter; and iii) a first target-specific sequence substantially complementary to said first target domain, and said upstream universal priming site (UUP) locates in the upstream of said adapter and said first target-specific sequence; b) hybridizing said plurality of target pre-mRNA sequences of said first hybrids to a plurality of second probes and forming second hybrids wherein each of said second hybrids comprises a said target pre-mRNA sequence, a said first splice junction specific probe and a said second probe and each of said plurality of second probes comprises: iv) a second target-specific sequence substantially complementary to said second target domain; v) a downstream universal priming site (DUP), wherein each of said second probes has the same DUP, and said downstream universal priming site (DUP) locates in the downstream of said second target-specific sequence, and wherein, in each of said plurality of first and second hybrids, said poly(A) sequence remains single-stranded; c) contacting said second hybrids with a ligase and forming ligation complexes comprising ligated probes, each of said ligated probes comprising a said first splice junction specific probe and a said second probe; d) contacting said ligation complexes with a support comprising a poly(T) sequence, such that said poly(A) sequence hybridizes with said poly(T) sequence; e) removing unhybridized said first splice junction specific probes and unhybridized said second probes; f) denaturing said ligation complexes; g) amplifying the ligated probes using universal primers that hybridize to the UUP and DUP, or complement thereof, and generating a plurality of amplicons each comprising a said adapter; h) contacting said amplicons with an array of capture probes to form assay complexes, wherein said capture probes bind to said adapter; and i) detecting said assay complexes wherein the detection of said assay complexes is an indication of the presence of said splice junction sequence in the pre-mRNA sequences.