Patent ID: 8389218

Claim:
A method comprising: a) contacting a sample comprising double-stranded genomic DNA with a site-specific nicking endonuclease that recognizes a nucleotide sequence that comprises a single nucleotide polymorphism (SNP) in said double stranded genomic DNA to provide a contacted genomic sample, wherein said endonuclease nicks said genomic DNA at a nick site that is proximal to said SNP only if a first allele of said SNP is present; b) denaturing said contacted genomic sample to provide a denatured genomic sample; c) contacting under hybridization conditions said denatured genomic sample with an array of probes comprising a first probe and a second probe, wherein: i) said first probe hybridizes to a nucleotide sequence in a first strand of said genomic DNA, wherein said nucleotide sequence comprises said SNP; and ii) said second probe hybridizes to a nucleotide sequence in a second strand of said genomic DNA, wherein said nucleotide sequence comprises said SNP; and iii) nicking at said nick site by said site-specific nicking endonuclease results in less binding of said denatured genomic sample to said first probe relative to a denatured genomic sample that is not nicked at said nick site; and d) comparing the amount of hybridization to said first probe to the amount of hybridization to said second probe, wherein decreased binding of said denatured genomic samples to said first probe relative to said second probe indicates that said first allele of said SNP is present.