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

Area of Science:

• Genomics
• Human Genetics
• Bioinformatics

Background:

• Single nucleotide polymorphisms (SNPs) are crucial for understanding human genetic diversity.
• Previous SNP discovery efforts have generated substantial but fragmented datasets.
• Integrating these datasets is essential for a comprehensive genomic view.

Purpose of the Study:

• To create a high-density map of single nucleotide polymorphisms (SNPs) across the human genome.
• To integrate all publicly available SNP data with genomic features like genes.
• To provide a resource for haplotype analysis and gene discovery for medical purposes.

Main Methods:

• Data compilation from The SNP Consortium and the International Human Genome Sequencing Consortium.
• Integration of SNP data with publicly available gene and genomic feature annotations.
• Analysis of SNP distribution and proximity to exonic regions.

Main Results:

• A map of 1.42 million SNPs with an average density of one SNP per 1.9 kilobases.
• Integration of SNPs with genes, with 60,000 SNPs in exons and 85% of exons within 5 kb of a SNP.
• Demonstration of variable nucleotide diversity across the genome, consistent with population genetics models.

Conclusions:

• The high-density SNP map is a valuable public resource for genomic research.
• This map facilitates the definition of haplotype variation across the human genome.
• The resource is expected to aid in the identification of genes relevant to human disease diagnosis and therapy.