Patent ID: 8133667
Filing Date: 2012-03-13
Classification: C12Q

Abstract:
1. A method for analyzing a genomic DNA sample comprising: reducing the complexity of the sample by: (a) fragmenting the sample with a restriction enzyme that has a recognition sequence that comprises at least one fixed position and has a variable region consisting of one or two variable positions, wherein the at least one fixed position and the variable region are in the single-stranded overhang generated by cleavage with the restriction enzyme and cleavage generates a plurality of single-stranded overhangs of different sequence including at least a first overhang and a second overhang; (b) ligating a first selective adaptor comprising a single-stranded overhang that is perfectly complementary to the first overhang and a second selective adaptor comprising a single-stranded overhang that is perfectly complementary to the second overhang to a subset of the fragments to generate adaptor-ligated fragments, wherein the first selective adaptor is perfectly complementary to and ligates with a first subset of the single-stranded overhangs generated in step (a) and is not perfectly complementary to and does not ligate with a second subset of the single-stranded overhangs generated in step (a), wherein the second selective adaptor is perfectly complementary to and ligates with a third subset of the single-stranded overhangs generated in step (a) and is not perfectly complementary to and does not ligate with a fourth subset of the single-stranded overhangs generated in step (a) and wherein the first and second selective adaptors comprise a common priming sequence; and (c) amplifying at least some of the adaptor-ligated fragments by polymerase chain reaction using a primer that is complementary to the common priming sequence in the first and second selective adaptors to obtain amplified fragments that are a subset of the fragments; and analyzing the amplified fragments by hybridization to an array of probes.