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Allele-specific expression (ASE)

Definition
AI-generated

Allele-specific expression (ASE) is unequal output of the two parental alleles at a transcribed locus—detected when heterozygous sites show biased read or UMI counts for reference versus alternate haplotypes after phasing or within-sample inference.

Topics
Sequencing Data Analysis
Synonyms
ASE
Related
Allele balance Expression Quantitative Trait Locus (eQTL) Genotype

Why it matters in GWAS

ASE links cis-regulatory variation or editing to functional readout without requiring population-level eQTL power; it helps interpret coding and noncoding GWAS candidates when RNA-seq is available and can reveal context-specific effects missed by bulk expression averages.

Example usage

"ASE at the GWAS index SNP was tested with binomial models on phased RNA-seq alignments."

Allele balance Expression Quantitative Trait Locus (eQTL) Genotype Phasing RNA Sequencing (RNA-seq) Transcriptome
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References

  • Castel SE, et al. (2015). Tools and best practices for data processing in allelic expression analysis. Genome Biol.
  • Degner JF, et al. (2009). Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics.
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