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Updated: May 24, 2026
10:17
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data
Jean-Baptiste Veyrieras1, Daniel J Gaffney, Joseph K Pickrell
1Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America. jb.veyrieras@gmail.com
Plos One
|February 24, 2012
Summary
Expression quantitative trait loci (eQTLs) mapping reveals genetic variation
Area of Science:
- Genomics
- Population Genetics
- Molecular Biology
Background:
- Expression quantitative trait loci (eQTLs) analysis links genetic variation to gene expression.
- Previous studies indicated eQTL enrichment near transcription start sites (TSS) and end sites (TES).
Purpose of the Study:
- To re-evaluate the distribution of cis-eQTLs using diverse expression data.
- To investigate the discrepancy in transcription end site (TES) peak findings between different datasets.
Main Methods:
- Analysis of human lymphoblastoid cell line expression data from Illumina, Affymetrix, and RNA sequencing platforms.
- Comparative mapping of cis-eQTLs across different genomic features and data types.
Main Results:
- Confirmed enrichment of eQTLs near TSS and in transcribed regions, particularly exons.
- Observed a significant reduction or absence of the previously reported TES peak in Affymetrix and RNA-seq data.
- Identified that the Illumina TES peak was likely an artifact of exon-specific QTLs affecting 3' UTRs.
Conclusions:
- Exonic sequences play a crucial role in gene regulation, as supported by consistent eQTL enrichment.
- The distribution of eQTLs is influenced by the specific technology and probe positioning used in expression analysis.
- Revisiting eQTL distribution with multiple data types refines our understanding of genetic regulatory elements.
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