Patent ID: 8029999

Claim:
A method for genotyping at least one individual comprising: reducing the complexity of a first nucleic acid sample, that is a genomic DNA sample from the individual, comprising a plurality of target sequences to produce a second nucleic acid sample by a method comprising amplifying a subset of the target sequences; generating a hybridization pattern by a method comprising hybridizing said second nucleic acid sample to an array of probes wherein said array of probes comprises at least one perfect match probe for each allele of each single nucleotide polymorphism in a collection of single nucleotide polymorphisms, said collection comprising between 10,000 and 1,500,000 single nucleotide polymorphisms, wherein a perfect match probe is exactly complementary to the polymorphic base of an allele and a region surrounding the polymorphic base; wherein greater than 80% of the single nucleotide polymorphisms in the collection are at least 10 kilo bases and less than 200 kilo bases from another single nucleotide polymorphism in the collection and the average minimum distance between single nucleotide polymorphisms in the collection is between 10 kilo bases and 400 kilo bases; and wherein each single nucleotide polymorphisms in the collection is located within a fragment that is within a selected size range when a genome is digested with a selected enzyme or enzyme combination; analyzing said hybridization pattern; and determining the genotype of the individual at a plurality of the single nucleotide polymorphisms in the collection of single nucleotide polymorphisms from the hybridization pattern.