A haplotype map of the human genome

  title={A haplotype map of the human genome},
  author={Michael Olivier},
Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of… 

Completing the map of human genetic variation

A community resource project recently launched by the National Human Genome Research Institute to sequence large-insert clones from many individuals, systematically discovering and resolving these complex variants at the DNA sequence level is described.

Common deletion polymorphisms in the human genome

This work describes a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating deletion variants across the human genome.

A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

Although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HAPMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations.

Human genetics: Mapping the common variation

The HapMap data can be used to maximize the power of array-based association studies, in which tag SNPs cannot be chosen by researchers, and to evaluate statistical significance and interpret results of genome-wide association studies.

Natural genetic variation caused by small insertions and deletions in the human genome.

Almost 2 million small insertions and deletions (INDELs) that range from 1 bp to 10,000 bp in length in the genomes of 79 diverse humans are reported, indicating that small INDEL variation is likely to be a key factor underlying inherited traits and diseases in humans.

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

A pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions is observed and is consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa.

Single Nucleotide Polymorphisms in Human Disease and Evolution: Phylogenies and Genealogies

Genealogies and phylogenies are two ways to view the same evolutionary process, and each has specific applications to the discovery of genetic factors in human disease, especially relevant in the genomic era.

Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs

Two genes involved in the thyroid hormone pathway that show signals of selection in African Pygmies that may be related to their short stature are identified.

Genome-Wide Associations of Gene Expression Variation in Humans

The results suggest that regulatory polymorphism is widespread in the human genome and show that the 5-kb (phase I) HapMap has sufficient density to enable linkage disequilibrium mapping in humans.



The Structure of Haplotype Blocks in the Human Genome

It is shown that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed.

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.

Haplotype Variation and Linkage Disequilibrium in 313 Human Genes

Pairs of SNPs exhibited variability in the degree of linkage disequilibrium that was a function of their location within a gene, distance from each other, population distribution, and population frequency.

Linkage disequilibrium in the human genome

The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked demographic event about 27,000–53,000 years ago, implying that LD mapping is likely to be practical in this population.

A first-generation linkage disequilibrium map of human chromosome 22

This study demonstrates the feasibility of developing genome-wide maps of LD and shows a strong correlation between high LD and low recombination frequency in the extant genetic map, suggesting that historical and contemporary recombination rates are similar.

The Fine-Scale Structure of Recombination Rate Variation in the Human Genome

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Conserved worldwide linkage disequilibrium in the human factor XI gene.

Interestingly, haplotypes associated with the linked SNPs are conserved across all populations studied, despite significantly different allele frequencies between populations, which emphasizes the need for a better understanding of general patterns of LD to facilitate identification of genes for common disorders.

High-resolution haplotype structure in the human genome

A high-resolution analysis of the haplotype structure across 500 kilobases on chromosome 5q31 using 103 single-nucleotide polymorphisms (SNPs) in a European-derived population offers a coherent framework for creating a haplotype map of the human genome.

Extent and distribution of linkage disequilibrium in three genomic regions.

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Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots

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