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Related Experiment Videos

Sequence polymorphisms cause many false cis eQTLs.

Rudi Alberts1, Peter Terpstra, Yang Li

  • 1Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, Netherlands.

Plos One
|July 20, 2007
PubMed
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Many local expression quantitative trait loci (eQTLs) are falsely identified. Sequence polymorphisms affecting microarray probe hybridization, not cis-acting factors, cause these false positives, which can be detected and removed using a novel statistical method.

Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Quantitative trait loci (QTLs) mapping is crucial for understanding genetic influences on traits.
  • Local expression QTLs (eQQs) are of particular interest as direct candidates for physiological QTLs.
  • Previous studies have successfully mapped numerous eQTLs.

Purpose of the Study:

  • To investigate the accuracy of mapped local eQTLs in genetical genomics experiments.
  • To identify the underlying causes of potentially false positive local eQTLs.
  • To develop and apply a novel statistical method for detecting and correcting these false positives.

Main Methods:

  • A novel statistical approach was developed to analyze individual microarray probe signals.
  • This method accounts for sequence polymorphisms impacting probe hybridization.

Related Experiment Videos

  • The approach was applied to existing mouse and human eQTL datasets.

    • Main Results:

    • Many identified local eQQs are not due to cis-acting sequence polymorphisms affecting mRNA levels.
    • These "cis-acting" eQTLs often result from sequence variations within the probe-binding regions of mRNA.
    • The novel statistical method successfully detected and distinguished these hybridization-driven artifacts from true cis-eQTLs.

    Conclusions:

    • A significant number of reported "cis-acting" local eQTLs are artifacts of microarray probe hybridization.
    • Sequence polymorphisms affecting probe binding can mimic true cis-regulation.
    • The developed statistical approach provides a robust method for correcting eQTL datasets and improving the accuracy of genetic analyses.