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Related Experiment Videos

Survey of allelic expression using EST mining.

Bing Ge1, Scott Gurd, Tiffany Gaudin

  • 1McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A, Canada.

Genome Research
|October 28, 2005
PubMed
Summary

This study identifies common cis-acting variants influencing gene expression by comparing human EST data with population allele frequencies. This approach enriches for genes with heritable polymorphisms affecting RNA allele distribution.

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Area of Science:

  • Genomics
  • Population Genetics
  • Molecular Biology

Background:

  • Cis-acting allelic variation significantly contributes to phenotypic diversity.
  • Previous research aimed to catalog genes with cis-acting variants through experimental screening.

Purpose of the Study:

  • To leverage human EST data and HapMap database for identifying cis-acting variants.
  • To assess the concordance of allele frequencies between EST data and population samples.
  • To enrich for genes with common heritable cis-acting polymorphisms.

Main Methods:

  • Utilized human EST data from dbEST for allelic expression analysis.
  • Employed the HapMap database to obtain expected allele frequencies in diverse human populations.
  • Compared allele frequencies from ESTs with HapMap data, focusing on the CEPH sample (Europeans).

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  • Performed in silico and experimental validation.

    • Main Results:

    • Observed greater concordance of allele frequencies between dbEST and the CEPH HapMap sample compared to Asian and African populations.
    • Identified deviations in allele frequencies potentially due to heritable cis-acting variants affecting RNA allele distribution.
    • Demonstrated successful enrichment of genes with common heritable cis-acting polymorphisms.

    Conclusions:

    • Human EST data, when compared with population databases like HapMap, can effectively identify genes with cis-acting regulatory variants.
    • This strategy provides a powerful in silico method for discovering common heritable cis-acting polymorphisms linked to expressed alleles.