Methods for genomic analysis
First Claim
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11. A method for identifying pharmacogenomic-related loci without a priori knowledge of a sequence or location of said pharmacogenomic-related loci, comprising:
- identifying genetic variations in a plurality of individuals;
identifying at least some of said genetic variations that occur with at least some others of said genetic variations;
genotyping a subset of said at least some of said genetic variations that occur with at least some others of said genetic variations in both a case population and a control population to generate a data set of genotypes, wherein said case population consists of individuals who exhibit a particular response to a treatment and said control population consists of individuals who do not exhibit said particular response;
based on said data set of genotypes, computing a genotype frequency in said case population and a genotype frequency in said control population for each of said subset; and
identifying as pharmacogenomic-related loci a set of genetic variants for which said genotype frequency in said case population is different than said genotype frequency in said control population.
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Abstract
The present invention relates to methods for identifying variations that occur in the human genome and relating these variations to the genetic basis of disease and drug response. In particular, the present invention relates to identifying individual SNPs, determining SNP haplotype blocks and patterns, and, further, using the SNP haplotype blocks and patterns to dissect the genetic bases of disease and drug response. The methods of the present invention are useful in whole genome analysis.
47 Citations
25 Claims
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11. A method for identifying pharmacogenomic-related loci without a priori knowledge of a sequence or location of said pharmacogenomic-related loci, comprising:
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identifying genetic variations in a plurality of individuals;
identifying at least some of said genetic variations that occur with at least some others of said genetic variations;
genotyping a subset of said at least some of said genetic variations that occur with at least some others of said genetic variations in both a case population and a control population to generate a data set of genotypes, wherein said case population consists of individuals who exhibit a particular response to a treatment and said control population consists of individuals who do not exhibit said particular response;
based on said data set of genotypes, computing a genotype frequency in said case population and a genotype frequency in said control population for each of said subset; and
identifying as pharmacogenomic-related loci a set of genetic variants for which said genotype frequency in said case population is different than said genotype frequency in said control population. - View Dependent Claims (12, 13, 14, 15, 16, 17)
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18. A method for identifying pharmacogenomic-related loci without a priori knowledge of a sequence or location of said pharmacogenomic-related loci, comprising:
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determining a sequence of an organism;
scanning additional individuals of said organism for genetic variants from said sequence;
identifying a first subset of said genetic variants that occur with others of said genetic variants in a first group;
identifying a second subset of said genetic variants that occur with others of said genetic variants in a second group; and
using some, but not all, of said genetic variants in said first and second groups in an association study to identify which of said genetic variants is correlated with a phenotypic state, wherein said phenotypic state is a response to a pharmaceutical treatment, and further wherein genetic variants that are correlated with said phenotypic state are pharmacogenomic-related loci. - View Dependent Claims (19, 20, 21, 22, 23)
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24-1. The method of claim 25, further comprising using said pharmacogenomic-related genetic loci for a purpose selected from the group consisting of:
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testing of a candidate agent;
stratification of a population for clinical studies;
development of a gene therapy; and
use as a drug discovery target.
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25. A method for determining pharmacogenomic-related genetic loci without a priori knowledge of a sequence or location of said pharmacogenomic-related genetic loci, comprising:
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a) determining control genotypes, wherein said control genotypes are genotypes from at least 16 individuals in a control population for a set of genomic loci;
b) determining case genotypes, wherein said case genotypes are genotypes from individuals that react in an altered manner to administration of a substance for said set of genomic loci; and
c) comparing frequencies of said control genotypes with frequencies of said case genotypes, wherein members of said set of genomic loci that exhibit differences in said frequencies indicate locations of pharmacogenomic-related genetic loci. - View Dependent Claims (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24)
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Specification