Patent ID: 7536263

Claim:
A genotyping method comprising designing a plurality of probe sets for a mutation site of a target nucleic acid in an amplicon of the target nucleic acid, wherein a probe set consists of a discriminating probe and an amplicon probe, wherein the discriminating probe is a mutant type probe or a wild type probe for the mutation site, and the amplicon probe has a sequence which perfectly matches a region of the amplicon excluding any mutation site in the amplicon and that hybridizes to a sequence which is absent from other amplicons of the target nucleic acid; immobilizing the plurality of probe sets on a substrate in order to manufacture an optimal probe set screening chip; hybridizing a standard nucleic acid to the optimal probe set screening chip, wherein the standard nucleic acid is a wild type standard nucleic acid or a mutant type standard nucleic acid; collecting quantitative hybridization intensity data; calculating a value for each probe set of the following equation: {Mean(ln(r wS ))−2SD(ln(r wS ))/√{square root over (N wS )}}−{Mean(ln(r HS ))+2SD(ln(r HS ))/√{square root over (N HS )}} wherein N denotes a number of times hybridization of the standard nucleic acid has been performed; r wS is a ratio between a hybridization intensity of a wild type standard nucleic acid to the amplicon probe and a hybridization intensity of the wild type standard nucleic acid to the discriminating probe; r HS is a ratio between a hybridization intensity of a mutant type standard nucleic acid to the amplicon probe and a hybridization intensity of the mutant type standard nucleic acid to the discriminating probe; and Mean and SD denote a mean value and a standard deviation, respectively, of N ln(r) values which are obtained by hybridizing the standard nucleic acid to the DNA chip N times; and selecting the probe set having the largest value as the optimal probe set; hybridizing a plurality of amplicons of a target nucleic acid to a DNA chip on which the optimal probe set for the mutation site is immobilized, determining the genotype of the mutation site of the target nucleic acid, and displaying the determined genotype to a user.