Identification of alleles
AssigneeAffymetrix, Inc.
InventorsXiaohua Huang, Thomas B Ryder, Paul Kaplan
Life of this patent
Estimating the term…
Abstract
A method for determining the genotype of one or more individuals at a polymorphic locus employs amplification of a region of DNA using primers containing tags and hybridization of the products to one or more probes on a solid support. The genotype or ratio of alleles is identified from the pattern of hybridization. The method can also be used to determine the frequency of different alleles in a population.
Claims32
A method to determine a nucleotide at a polymorphic locus in a nucleic acid sample, comprising the steps of:
- amplifying a region of DNA comprising a polymorphic locus in the sample to form amplified DNA products using a primer pair, wherein a first primer of the pair terminates at its 3′ end at the polymorphic locus, wherein the first primer comprises a 3′ portion which is complementary to the region of DNA and wherein the first primer terminates at its 5′ end with a 5′ portion which is identical in sequence to all or part of a probe on a solid support and not complementary to the region of DNA wherein the 5′ portion is of an appropriate length and sequence such that the 5′ portion complement hybridizes to the probe with high affinity and high specificity, to form a first strand and a second strand, wherein the first strand comprises a portion identical to all or part of the probe and the second strand comprises a 5′ portion complementary to all or part of the probe;
- labeling the amplified DNA products to form labeled amplified DNA products;
- hybridizing the labeled, amplified DNA products to the probe on the solid support such that the second strand hybridizes to the probe on the solid support;
- and
- detecting labeled, amplified DNA products hybridized to the probe on the solid support, wherein the presence of said labeled amplified DNA products on the solid support indicates that the nucleic acid sample contains at the polymorphic locus a nucleotide which is the same as the 3′ terminal nucleotide of the primer.
A method to prepare samples for analysis to determine a nucleotide at a polymorphic locus in a nucleic acid sample, comparing the steps of
- amplifying a region of DNA comprising a polymorphic locus in the sample to form amplified DNA products using a primer pair, wherein a first primer of the pair terminates at its 3′ end at the polymorphic locus, wherein the first primer comprises a 3′ portion which is complementary to the region of DNA and wherein the first primer terminates at its 5′ end with a 5′ portion which is identical in sequence to all or part of a probe on a solid support and not complementary to the region of DNA wherein the 5′ portion is of an appropriate length and sequence such that the 5′ portion complement hybridizes to the probe with high affinity and high specificity to form a first strand comprising a portion identical to all or part of the probe and a second strand which comprises a 5′ portion complementary to all or part of the probe;
- labeling the amplified DNA products to form labeled amplified DNA products;
- and
- hybridizing the labeled, amplified DNA product to the probe on the solid support such that the second strand hybridizes to the probe on the solid support, thereby forming prepared samples for analysis.
Dependencies are inferred from the claim text.