Patent ID: 7615350

Claim:
A method for determining cis linkage of alleles to a genomic locus haplotype, comprising: (a) providing a solid surface comprising a covalently bound plurality of oligonucleotide probes having a nucleotide sequence complementary to said genomic locus haplotype; (b) contacting the oligonucleotide probe with a sample of genomic DNA under conditions conducive to specific hybridization of the genomic DNA to the oligonucleotide probe to form a genomic DNA/oligonucleotide complex; (c) removing excess genomic DNA; (d) denaturing the genomic DNA/oligonucleotide complex; (e) separating the genomic DNA by haplotype; (f) amplifying selectively a region of interest in the haplotype separated genomic DNA using asymmetric PCR and labeled primers to form a labeled, single stranded DNA sample; (g) contacting the labeled, single stranded DNA sample with a microarray comprising a plurality of oligonucleotide probes under conditions conducive to hybridization; and (i) detecting a hybridization pattern for the DNA sample and assigning the allele type with cis linkage to the locus haplotype of the genomic DNA sample.