Methods for genomic analysis
First Claim
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1. A method for determining disease-related genetic loci without a priori knowledge of a sequence or location of said disease-related genetic loci, comprising:
- determining SNP haplotype patterns from regions consisting essentially of coding regions of at least 16 individuals in a control population;
determining SNP haplotype patterns from regions consisting essentially of coding regions of individuals in a diseased population; and
comparing frequencies of said SNP haplotype patterns of said control population with frequencies of said SNP haplotype patterns of said diseased population, wherein differences in said frequencies indicate locations of disease-related genetic loci.
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Abstract
The present invention relates to methods for identifying variations that occur in the human genome, relating these variations to one another, and, ultimately, relating these variations to the genetic bases of phenotype such as disease resistance, disease susceptibility or drug response. The methods allow for, once variants have been identified, analysis of SNPs in coding regions of control and experimental populations.
50 Citations
20 Claims
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1. A method for determining disease-related genetic loci without a priori knowledge of a sequence or location of said disease-related genetic loci, comprising:
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determining SNP haplotype patterns from regions consisting essentially of coding regions of at least 16 individuals in a control population;
determining SNP haplotype patterns from regions consisting essentially of coding regions of individuals in a diseased population; and
comparing frequencies of said SNP haplotype patterns of said control population with frequencies of said SNP haplotype patterns of said diseased population, wherein differences in said frequencies indicate locations of disease-related genetic loci. - View Dependent Claims (2, 3, 4)
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5. A method of constructing a SNP haplotype block map from coding regions using multiple genomes comprising:
arranging SNPs found in at least about ten percent of said coding regions genomes into SNP haplotype blocks.
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6. A method of making associations between SNP haplotype patterns from coding regions of a genome and a phenotypic trait of interest comprising:
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building a baseline of SNP haplotype patterns from regions consisting essentially of coding regions of a genome;
pooling genomic DNA from a population having a common phenotypic trait of interest; and
identifying said SNP haplotype patterns that are associated with said phenotypic trait of interest. - View Dependent Claims (7, 8)
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9. A method for determining disease-related genetic loci without a priori knowledge of a sequence or location of said disease-related genetic loci, comprising:
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determining SNP haplotype patterns from nucleic acids derived from transcribed RNA of at least 16 individuals in a control population;
determining SNP haplotype patterns from nucleic acids derived from transcribed RNA of individuals in a diseased population; and
comparing frequencies of said SNP haplotype patterns of said control population with frequencies of said SNP haplotype patterns of said diseased population, wherein differences in said frequencies indicate locations of disease-related genetic loci. - View Dependent Claims (10, 11, 12)
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13. A method for identifying drug discovery targets comprising:
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associating SNP haplotype patterns from regions consisting essentially of coding regions with a disease;
identifying a chromosomal location of said associated SNP haplotype patterns;
determining a nature of said association of said chromosomal location and said disease; and
selecting a chromosomal location or a product of expression of that chromosomal location that is associated with said disease;
wherein said selected chromosomal location or a product of expression of that chromosomal location that is associated with said disease is a drug discovery target. - View Dependent Claims (14, 15)
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16. A method of determining a SNP haplotype pattern in regions consisting essentially of coding regions of an individual comprising:
assaying for at least one informative SNP.
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17. A method comprising:
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determining a sequence of an organism;
scanning additional individuals of said organism for variants from regions consisting essentially of coding regions of said sequence;
identifying some of said variants from said regions that occur with others of said variants from said regions in a first group;
identifying some of said variants from said regions that occur with others of said variants from said regions in a second group; and
using some, but not all, of said variants from said regions in said first and second groups to correlate said groups with a phenotypic state.
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18. A method for determining pharmacogenomic-related genetic loci in coding regions without a priori knowledge of a sequence or location of said pharmacogenomicrelated genetic loci, comprising:
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determining SNP haplotype patterns in regions consisting essentially of coding regions from at least 16 individuals in a control population;
determining SNP haplotype patterns in regions consisting essentially of coding regions from individuals that react in an altered manner to administration of a substance; and
comparing frequencies of said SNP haplotype patterns in said coding regions of said control population with frequencies of said SNP haplotype patterns in said coding regions of said individuals that react in an altered manner to administration of a substance, wherein differences in said frequencies indicate locations of pharmacogenomic-related genetic loci. - View Dependent Claims (19, 20)
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Specification