Patent ID: 6986992

Claim:
A method of determining the identification of a nucleotide at a detection position in a target DNA sequence comprising: a) amplifying the target DNA using random primers to generate DNA amplicons; b) transcribing said DNA amplicons to generate RNA target sequences; c) providing a solid support with a first surface comprising at least one extension probe wherein said extension probe includes an interrogation nucleotide; d) hybridizing said RNA target sequence to said extension probe to form a hybridization complex; e) contacting said surface with: i) a modified reverse transcriptase; and ii) at least one chain terminating nucleotide comprising a hapten; under conditions whereby if said chain terminating nucleotide is perfectly complementary to the base of the target sequence immediately adjacent to the 3′ end of extension probe in the hybridization complex, said chain terminating nucleotide is added to extension probe to form a modified extension probe; f) contacting said modified extension probe with the binding partner of said hapten, wherein said binding partner is labeled; and g) detecting the presence of said label to determine the nucleotide at said detection position.