Patent ID: 8637248

Claim:
A method of determining the haplotype of a target nucleic acid having a first heterozygous polymorphic site on the 3′ side and a second heterozygous polymorphic site on the 5′ side, comprising: (i) carrying out PCR of the target nucleic acid using one of the forward primers (a-1) listed below, (a-1-1) a forward primer that contains a base sequence complementary to the first polymorphic site and can extend the target nucleic acid if the first polymorphism is the mutant type, and does not extend the target nucleic acid if the first polymorphism is the wild type, and (a-1-2) a forward primer that contains a base sequence complementary to the first polymorphic site and can extend the target nucleic acid if the first polymorphism is the wild type, and does not extend the target nucleic acid if the first polymorphism is the mutant type, and (b-1) a reverse primer that contains a base sequence complementary to a certain base sequence that does not contain the second polymorphism, and is located on the 3′ side of the second polymorphism, on the complementary strand of the target nucleic acid; and (ii) hybridizing the product obtained as a result of (i) with a first probe that has a base sequence identical with a certain segment of the base sequence of the target nucleic acid, which contains the wild-type nucleotide(s) of the second polymorphism, and a second probe that has a base sequence identical with a certain segment of the base sequence of the target nucleic acid, which contains the mutant nucleotide(s) of the second polymorphism, and detecting the signals of hybrid formation with the first and second probes, wherein the hybridization (ii) with the product obtained as a result of (i) comprises hybridizing a probe carrier on which the first probe and the second probe are fixed at respective different locations, and wherein the haplotype is determined irrespective of the locations of the first and second polymorphisms by using only one primer pair, the primer pair consisting of the forward primer (a-1-1) or (a-1-2) and the reverse primer (b-1).