Patent ID: 8685642

Claim:
A method for sample analysis, comprising: a) contacting a first DNA sample with a first restriction enzyme to provide a digested sample, wherein: i) said DNA sample may comprise a target sequence comprising a SNP site; and ii) said first restriction enzyme cleaves said target sequence at a cleavage site only if a first allele of a SNP is present at said SNP site; b) hybridizing said digested sample to a surface-bound polynucleotide comprising a probe sequence that hybridizes to said target sequence wherein: i. the surface-bound polynucleotide is up to 200 nucleotides in length, ii. the probe sequence comprises said cleavage site, and iii. the probe sequence is designed such that cleavage of the target sequence at said cleavage site by said first restriction enzyme results in less hybridization of the digested sample relative to a sample in which the target sequence is undigested by the first restriction enzyme; c) comparing the hybridization signal between the digested sample and the probe sequence to a reference signal, and d) determining whether the first allele of the SNP is present in the DNA sample, wherein the hybridization signal of the digested sample to the probe sequence as compared to the reference signal indicates whether the first allele of said SNP is present in the DNA sample.