Patent ID: 7083929

Claim:
A method of sequencing in parallel at least one nucleotide of a plurality of polynucleotide sample fragments, the method comprising: (a) providing a plurality of polynucleotide sample fragments, (b) from said sample fragments, forming a mixture of sequencing fragments, wherein (1) each sequencing fragment terminates at a predefined end with a known base, and (2) each sequencing fragment contains an identifier tag sequence which identifies the sample fragment to which the sequencing fragment corresponds and optionally, the terminating base-type of the fragment, wherein said forming includes the steps of: (1) hybridizing to each sample fragment, a tagged primer containing (i) an identifier tag sequence, and (ii) a primer sequence located on the 3′-side of the tag sequence wherein each tagged primer has a primer sequence that is complementary to a unique sample fragment in said plurality of sample fragments, to form a plurality of tagged primer-sample fragment hybrids, where at least one different identifier tag sequence is used to identify each sample fragment, (2) performing a chain extension reaction on each hybrid to form sequencing fragments extended by at least one base, and (3) combining the sequencing fragments generated from the hybrids, to form a sequencing fragment mixture, (c) contacting the sequencing fragment mixture with an array of immobilized different-sequence tag probes, each tag probe (1) being capable of hybridizing specifically with one of said identifier tag sequences, and (2) having an addressable location in said array, where said contacting is conducted under conditions effective to provide specific hybridization of the identifier tag sequences, or tag sequence complements, with the corresponding immobilized tag probes, to form a hybridization pattern on said array, and (d) from the hybridization pattern formed, determining a nucleotide sequence for at least one base in at least one sample fragment.