Introduction

The NIEHS Environmental Genome Project is a multi-disciplinary, collaborative effort focused on examining the relationships between environmental exposures, inter-individual sequence variation in human genes and disease risk in U.S. populations. The NIEHS SNPs Program at the University of Washington is targeted on the systematic identification and genotyping of single nucleotide polymorphisms (SNPs) in environmental response genes. The first phase of the effort is focused on finding common sequence variation (SNPs) in human genes involved in DNA repair and cell cycle pathways (see links under Gene Targets in the navigation menu on the left). Ultimately, the project will provide dense genetic maps of human genes that can be applied in evaluating human disease risk with environmental exposures.

GeneSNPs Database

NIEHS SNPs are available in the GeneSNPs database as well as the national database resource, dbSNP. GeneSNPs provides a gene-centric map of the genome structure, coding sequences, and identified allelic variation in genes being targeted for a role in disease susceptibility by the NIEHS. This database provides a graphical view of all available SNP data including allele frequencies and genotypes in select populations. This information is key in selecting the polymorphic sites needed to examine disease risk in human population studies.

Polymorphism Analysis

Automated DNA sequencing is being used to identify and genotype SNPs in human candidate genes (see PolyPhred). Candidate genes are being sequenced to identify common sequence variation for functional analysis and population-based studies. Candidate genes were formerly sequenced across a panel of 90 individuals representative of the U.S. population (see Sample Population Descriptions Panel 1). Candidate genes are now being sequenced across a panel of 95 individuals of known ethniticies (see Sample Population Descriptions Panel 2). All SNPs have been identified using only high quality sequence data (Q > 25) and each SNP reported from the NIEHS SNPs program has been confirmed in multiple individuals and/or in multiple reactions.