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Updated: Dec 9, 2025
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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
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A vast resource of allelic expression data spanning human tissues
Stephane E Castel1,2, François Aguet3, Pejman Mohammadi4,5,6,7
1New York Genome Center, New York, NY, USA. scastel@nygenome.org.
Genome Biology
|September 11, 2020
Summary
We created the largest allele expression (AE) dataset, covering 54 human tissues. This resource enables new research into gene regulation and cis-regulatory variants across the human body.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Allele expression (AE) analysis is a key method for studying cis-regulatory effects.
- Understanding gene regulation is crucial for deciphering complex biological processes and diseases.
Purpose of the Study:
- To present a comprehensive AE resource derived from the GTEx v8 dataset.
- To introduce an extension of the phASER tool for estimating cis-regulatory variant effects using haplotype-level AE data.
- To facilitate future research on regulatory variation in human tissues.
Main Methods:
- Generation of a large-scale AE resource from 15,253 GTEx v8 samples across 54 human tissues.
- Analysis of AE data at both single nucleotide polymorphism (SNP) and haplotype levels.
- Development of an enhanced phASER tool for estimating effect sizes from haplotype-level AE data.
Main Results:
- Creation of the largest AE dataset to date, with 431 million SNP-level and 153 million haplotype-level measurements.
- Public availability of haplotype-level AE data.
- Demonstration of the utility of the AE resource and the extended phASER tool.
Conclusions:
- The presented AE resource is a valuable asset for the scientific community.
- This resource will significantly advance the study of regulatory variation across diverse human tissues.
- The publicly available data and enhanced tools will empower future genomic research.
