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Pattern of sequence variation across 213 environmental response genes.

Robert J Livingston1, Andrew von Niederhausern, Anil G Jegga

  • 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195-7730, USA.

Genome Research
|September 15, 2004
PubMed
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The Environmental Genome Project identified common genetic variations in 213 environmental response genes. These findings help understand individual susceptibility to environmental exposures and related diseases.

Area of Science:

  • Genetics
  • Environmental Health
  • Molecular Biology

Background:

  • Human genetic susceptibility to environmental factors is crucial for understanding disease.
  • Environmental response genes (DNA repair, cell cycle, apoptosis, metabolism) are vital for genomic integrity.
  • Loss-of-function mutations in these genes are linked to severe diseases.

Purpose of the Study:

  • To identify single nucleotide polymorphisms (SNPs) in 213 environmental response genes.
  • To investigate the hypothesis that functionally significant polymorphisms increase susceptibility to genotoxic agents.
  • To provide a foundation for clinical and epidemiological studies on environmental exposures.

Main Methods:

  • The Environmental Genome Project (EGP) scanned 213 genes for variations.

Related Experiment Videos

  • Genomic sequence (20.4 kb/gene) from 90 individuals in the Polymorphism Discovery Resource panel was analyzed.
  • Bioinformatic tools (SIFT, Polyphen) were used to predict the functional impact of identified SNPs.

    • Main Results:

    • An average nucleotide diversity of 6.7 x 10(-4) was observed, with one SNP every 1500 bp.
    • Each gene averaged 26 haplotypes, 34 common SNPs, 6.2 coding SNPs (cSNPs), and 2.5 nonsynonymous cSNPs.
    • 57 potentially deleterious SNPs and 8 polymorphisms affecting protein translation were identified.

    Conclusions:

    • The study provides a comprehensive catalog of genetic variations in key environmental response genes.
    • These data can be extrapolated to estimate the total number of cSNPs and deleterious SNPs in the human genome.
    • The findings have significant implications for association studies of environmentally induced diseases.