Patent ID: 7267966

Claim:
A method of analyzing a first nucleic acid sample comprising: (a) submitting a computer query to an electronic sequence database to identify the sequence and size of the fragments that are predicted to result from digestion of said first nucleic acid sample with at least one selected restriction enzyme; (b) selecting a subset of said fragments that are within a selected size range from said computer query; (c) identifying known polymorphisms present on said fragments in said subset of fragments; (d) providing a nucleic acid array comprising a plurality of probes which are complementary to said polymorphisms identified in said subsets of fragments; (e) providing said first nucleic acid sample; (f) reproducibly reducing the complexity of said first nucleic acid sample to produce a second nucleic acid sample, wherein said reducing complexity step comprises: (i) fragmenting said first nucleic acid sample with said at least one selected restriction enzyme of step (a); and (ii) ligating adaptor sequences to said fragments of step (f)(i), and amplifying at least some of said fragments ligated with said adaptor sequences using a selected amplification method, thereby producing a second nucleic acid sample; (g) hybridizing said second nucleic acid sample to the nucleic acid of array of (d); and (h) analyzing a hybridization pattern resulting from said hybridizing step of (g).