Patent ID: 7459273

Claim:
A method of genotyping a plurality of polymorphic positions in an organism comprising: (a) identifying a plurality of target sequences each comprising one of said polymorphic positions, wherein each target sequence has the same common sequence within 1000 bases of the polymorphic position and wherein each target sequence has a degenerate priming site that is one species of a consensus sequence immediately adjacent to the common sequence, wherein the consensus sequence is 10-25 bases and at least 50% of the positions in the consensus sequence are the same in each target sequence and at least two of the bases in the consensus sequence vary between at least two of the target sequences, and wherein the common sequence and the consensus sequence are genomic sequences; (b) obtaining a plurality of capture probes, comprising a first universal priming region, a region that is complementary to the common sequence and a degenerate region that is complementary to the consensus sequence, wherein said degenerate region comprises at least two degenerate positions that comprise a mixture of different nucleotides that vary between different capture probes in the plurality of capture probes; (c) contacting a nucleic acid sample comprising genomic DNA from the organism with the plurality of capture probes; (d) extending the capture probes through the polymorphic positions; (e) amplifying the extended capture probes; (f) hybridizing the amplified extended capture probes to an array of probes comprising allele specific probes for a plurality of the polymorphic positions; and (g) analyzing the hybridization pattern to determine which alleles are present for at least two of the polymorphic positions.