Amplicon preparation and sequencing on solid supports

A method for determining a true nucleic acid sequence variant, comprising:

• (a) contacting a nucleic acid sample comprising a plurality of target polynucleotides with gene specific forward and reverse primers under conditions sufficient for hybridization, each species of said gene specific forward primer comprising a unique sequence index and an adapter;
• (b) amplifying by polymerase chain reaction (PCR) said plurality of target polynucleotides to produce a plurality of amplicons;
• (c) directly contacting a plurality of target specific capture primers immobilized on a solid support with said plurality of amplicons under conditions sufficient for hybridization to produce a first plurality of immobilized amplicons, said solid support further comprising a plurality of universal capture primers;
• (d) extending said plurality of target specific capture primers to produce a plurality of immobilized extension products complementary to said target polynucleotides, wherein said immobilized extension products comprise a terminal adapter portion capable of hybridizing to said universal capture primers;
• (e) annealing said plurality of universal capture primers to said plurality of said immobilized extension products;
• (f) amplifying by PCR said plurality of immobilized extension products to produce a second plurality of immobilized amplicons, wherein said second plurality of immobilized amplicons comprises a uniformity of 85% or more;
• (g) sequencing said second plurality of immobilized amplicons, and
• (h) eliminating random sequence errors for one or more target polynucleotide by comparing three or more nucleotide sequences at a variant position for a target polynucleotide species, wherein said target polynucleotide species are identified by said unique sequence index to thereby determine a true nucleotide sequence variant in said one or more target polynucleotides.