Patent ID: 7745178

Claim:
A method for analyzing a nucleic acid sample comprising: fragmenting the nucleic acid sample using a first restriction enzyme and a second restriction enzyme and producing three different types of fragments comprising a first type of fragments cut by the first restriction enzyme but not by the second restriction enzyme, a second type of fragments cut by the second restriction enzyme but not by the first restriction enzyme and a third type of fragments cut by both the first restriction enzyme and the second restriction enzyme; ligating a first adaptor and a second adaptor to the three different types of fragments and producing adaptor-ligated fragments, wherein the first adaptor is blocked from ligation to the three different types of fragments at the 3′ end of one strand of the first adaptor, the first adaptor has a single stranded 3′ region comprising a first primer region on other strand of the first adaptor, and the complement of said first primer region is not present in said first adaptor, and wherein the second adaptor is blocked from ligation to the three different types of fragments at the 3′ end of the first strand of the second adaptor, the second adaptor has a single stranded 5′ region comprising a second primer region on the first strand of the second adaptor, and the complement of said second primer region is not present in said second adaptor, and wherein the first adaptor ligates to said first type of fragments and said third type of fragments and the second adaptor ligates to said second type of fragments and said third type of fragments; amplifying the adaptor-ligated fragments using a first primer complementary to said first primer region and a second primer comprising said second primer region and producing amplified fragments comprising said third type of fragments, wherein only the adaptor-ligated fragments formed by ligating said third type of fragments and both the first adaptor and the second adaptor are exponentially amplified; providing a nucleic acid array consisting essentially of probes designed to detect the bases present at a plurality of polymorphisms predicted to be present in said third type of fragments; hybridizing the amplified fragments to the array; and analyzing a hybridization pattern resulting from the hybridization thereby analyzing the nucleic acid sample.