Haplotype map of the human genome and uses therefor
AssigneeWhitehead Institute for Biomedical Research
InventorsMark J. Daly, David M. Altshuler, Eric S. Lander, John D. Rioux, Stacey B. Gabriel, Stephen Schaffner
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Abstract
A method of producing a haplotype map which can be used to select an optimal set of single nucleotide polymorphic sites for examination in a subsequent genotyping study is disclosed, along with the map so produced.
Claims17
A haplotype map of a region of interest of the human genome comprising one or more discrete haplotype blocks bounded by one or more sites of recombination.
A method of producing a haplotype map of a region of interest of the human genome comprising determining the pattern of historical recombination across the region of interest and identifying one or more discrete haplotype blocks bounded by one or more sites of recombination, thereby producing a haplotype map of the region of interest.
A method of selecting a set of single nucleotide polymorphic sites (SNPs) for use in genotyping a genomic region of interest comprising the steps of:
- identifying at least one SNP which distinguishes each major haplotype in each discrete haplotype block in a haplotype map of the genomic region of interest of the human genome, wherein the haplotype map comprises one or more discrete haplotype blocks bounded by one or more sites of recombination;
- and
- selecting a sufficient number of the SNPs from each discrete haplotype block for use in a genotyping study;
- thereby selecting a set of SNPs for use in genotyping studies of the genomic region of interest.
A method of identifying an association between a phenotype and a haplotype comprising the steps of:
- identifying at least one SNP which distinguishes each major haplotype in each discrete haplotype block in a haplotype map of the genomic region of interest of the human genome, wherein the haplotype map comprises one or more discrete haplotype blocks bounded by one or more sites of recombination;
- selecting a sufficient number of the SNPs from each discrete haplotype block to form a set of SNPs suitable for use in a genotyping study;
- and
- assessing the the set of SNPs for an association between a phenotype and a haplotype
A method of identifying an association between a phenotype and a haplotype comprising the steps of:
- identifying a set of SNPs which uniquely distinguishes a haplotype by selecting the members of the set from the discrete haplotype blocks of a haplotype map consisting of one or more discrete haplotype blocks bounded by one or more sites of recombination;
- and
- assessing the set of SNPs to identify an association between a phenotype and a haplotype.
A method of identifying the location of a gene associated with a phenotype comprising the following steps:
- identifying a set of SNPs which uniquely distinguishes a haplotype by selecting the members of the set from the discrete haplotype blocks of a haplotype map of a chromosomal region associated with the phenotype consisting of one or more discrete haplotype blocks spanned by one or more sites of recombination;
- and
- assessing the set of SNPs to identify an association between a phenotype and a haplotype, wherein identification of the association between the haplotype and the phenotype is indicative of the location of the gene.
A method of localizing the position of a disease-susceptibility locus of a disease comprising the steps of:
- identifying a set of SNPs which uniquely distinguishes a haplotype by selecting the members of the set from a haplotype map of a chromosomal region associated with the phenotype consisting of one or more discrete haplotype blocks spanned by one or more sites of recombination;
- and
- assessing the set of SNPs to identify an association between the haplotype and the phenotype of the disease, wherein identification of the association between the haplotype and the phenotype is indicative of the position of the disease-susceptibility locus of the disease.
A method of diagnosis for susceptibility to a disease comprising the steps of:
- identifying a set of SNPs which uniquely distinguishes a haplotype in a chromosomal region associated with the disease by selecting the members of the set from the discrete haplotype blocks of a haplotype map of the chromosomal region consisting of one or more discrete haplotype blocks bounded by one or more sites of recombination;
- and
- assessing the set of SNPs to identify an association between the haplotype and the phenotype of the disease, wherein identification of the association between the haplotype and the phenotype is indicative of susceptibility to the disease.
Dependencies are inferred from the claim text.