Methods for Genotyping Selected Polymorphism

摘要

Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.

主权项

1. A method of genotyping a plurality of polymorphisms in an organism comprising:
(a) identifying a plurality of target sequences each comprising a polymorphic position, wherein each target sequence has the same common sequence within 1000 bases of the polymorphic position and wherein each target sequence has a consensus sequence immediately adjacent to the common sequence; (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; (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 polymorphisms.