Patent ID: 7670810

Claim:
A method for detecting at least 10,000 typable loci comprising single-nucleotide polymorphisms (SNPs) of genome fragments, comprising: (a) providing a plurality of genome fragments of a whole genome, wherein said providing comprises representationally amplifying a whole, native genome, and wherein said plurality of genome fragments comprises a concentration of at least 1 μg/μl of DNA; (b) contacting said plurality of genome fragments with an array of at least 10,000 predetermined nucleic acid probes immobilized to a substrate, wherein said probes comprise a region of at most 100 nucleotides in length that is complementary to typable loci of a genome, and wherein said probes hybridize with genome fragments to form probe-fragment hybrids; (c) modifying the probe of a probe-fragment hybrid while hybridized to said genome fragments by adding a detectable nucleotide or nucleotide analog by a polymerase; (d) exposing said modified probes to denaturing conditions, thereby removing hybridized genome fragments; and (e) detecting said modified probes, thereby detecting at least 10,000 typable loci comprising SNPs.