GeneSNPs Database

Program Description

The GeneSNPs database has been developed primarily as web-based, publicly-available graphical display of the newly identified SNPs discovered through resequencing environmentally responsive genes (ERGs) by the University of Washington. In addition, high-quality, well-validated SNP data relevant to the NIEHS-listed ERGs are imported from other publicly available web resources. The imported data are converted to a graphical display developed by the University of Utah and made available to the public through the web-accessible GeneSNPs database (http://www.genome.utah.edu/genesnps/) .

Program Contact Elizabeth A. Maull, Ph.D. maull@niehs.nih.gov

Grantee - Gene SNPs Database Robert B. Weiss, Ph.D. University of Utah Development of GeneSNPs as a Web-accessible Highly Annotated Relational Database of Human and Mouse Environmental Responsive Genes bob.weiss@genetics.utah.edu Grantee/Center Website: http://www.genome.utah.edu/genesnps/

Select Program Highlights – GeneSNPs Database

The goals of the Environmental Genome Project are to facilitate the discovery and characterization of environmentally responsive genes; understand their structure and function; gain insight into their cellular interactions; and identify important polymorphisms that may determine differences in disease risk/susceptibility resulting from exposure(s) to environmental agents. The GeneSNPs contract makes available, in a graphical format, single nucleotide polymorphism (SNP) information for a discrete set of environmentally responsive genes. While most of the information comes directly from the University of Washington Resequencing effort, the database searches a variety of SNP databases for SNP information relevant to this set of genes. This information will be invaluable in informing epidemiologic studies focused on understanding the relationship between gene, exposure, and disease etiology. There is an expectation that understanding the genetic contribution to disease will revolutionize diagnosis, treatment and prevention, ultimately leading to improved public health.

In 2006, dbSNP/HapMap updates were added to the site to capture and incorporate the major releases of genome-wide SNP data (including validated genotypes) from the HapMap efforts. These included two significant data releases of HapMap genotypes during early Sept. and late Oct. 2005. Validation and incorporation of the new NCBI dbSNP dataset (Build 126, ftp release on May 22, 2006) and HapMap Public Release #21 (July 20, 2006) was accomplished in 2006. Population-specific identifiers from the custom DNA panel sample set were extended into the haplotype calculation and display features.

In 2007, Open Helix, under the direction of the University of Washington, developed a flash media based tutorial to describe all of the tools available to the scientific community through GeneSNPs.