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Seattle SNPs
Colleen Davis
Genotyping Background

The International HapMap Project is developing a validated marker set using validated SNPs derived from dbSNP. The ultimate goal of this project is to genotype up to 5,000,000 SNPs (~1 SNP/600 bp) in diverse populations drawn from Europe, Asia and the Americas. This data will then be used to develop a linkage disequilibrium based map, divided into blocks, which define sets of correlated SNPs, to produce a common resource for genetic association studies.

We originally used a DNA sample panel of 90 individuals (see Sample Population Descriptions Panel 1). While the panel overall was representative of the U.S. population, the ethnicities of the individual samples were unknown. We converted to a panel of 95 DNA samples of known ethniticies (see Sample Population Descriptions Panel 2). These samples are included in the HapMap project. The NIEHS SNPs project is now generating comprehensive SNP data for HapMap derived samples from the European, Asian and African populations. In tandem with this effort, we have also implemented a large-scale genotyping effort, using Illumina BeadArray technology, to map highly informative tagSNPs from previously studied NIEHS SNPs candidate genes in the HapMap sample set (n = 60 unrelated, Yorubans; n = 60 unrelated, CEPH Europeans; and n = 45 unrelated samples from Beijing, China, and n = 45 unrelated samples from Toyko, Japan). This genotyping effort will serve to integrate our high-density SNP map (~1/300 bp) with the SNP dataset currently being produced by the International HapMap Project. In addition, we have also performed genotyping on non-HapMap samples from Hispanic (n = 50) and African-American (n = 62) populations, to represent other major groups in the United States.

National Institute of Environmental Health Sciences Environmental Genome Project National Institute of Environmental Health Sciences UW NIEHS