Patent ID: 8808995

Claim:
A method of genotyping a plurality of polymorphic positions in an organism comprising: contacting a nucleic acid sample comprising genomic DNA from the organism with a plurality of capture probes, with the genomic DNA comprising a plurality of target sequences each comprising a polymorphic position, wherein each target sequence of the plurality has the same common sequence and wherein each target sequence has a degenerate priming site that is one species of a consensus sequence immediately adjacent to the common 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, and with each capture probe of the plurality 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; extending the capture probes through the polymorphic positions; amplifying the extended capture probes; hybridizing the amplified extended capture probes to an array of probes comprising allele specific probes for a plurality of the polymorphic positions; and analyzing the hybridization pattern to determine which alleles are present for at least two of the polymorphic positions.