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Allele-specific expression analysis: pipelines, applications, challenges, and unmet needs.

Stefania Mattevi1, Francesco Mazzarotto2, Paolo Martini1

  • 1Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.

Computers in Biology and Medicine
|August 4, 2025
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Summary

Allele-specific expression (ASE) analysis reveals gene regulation insights but current tools lack automation and multi-omics integration. Future pipelines need to enhance single-cell support and data integration for broader biological and clinical applications.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Diploid organisms normally show balanced maternal and paternal gene expression.
  • Allele-specific expression (ASE) occurs due to genetic/epigenetic variations, leading to biased allele output.
  • ASE analysis is crucial for understanding gene regulation with functional and clinical relevance.

Purpose of the Study:

  • To critically assess 26 current pipelines for allele-specific expression analysis.
  • To identify limitations in existing ASE analysis tools regarding automation, multi-omics, and single-cell data.
  • To guide future development of advanced ASE analysis pipelines.

Main Methods:

  • Review and critical assessment of 26 allele-specific expression analysis pipelines.
  • Categorization based on data type handling, haplotype phasing, statistical methods, and output visualization.
  • Evaluation of input requirements, capabilities, and application scope for each pipeline.

Main Results:

  • Most current ASE analysis pipelines lack end-to-end automation and robust multi-omics integration.
  • Limited support exists for high-throughput single-cell sequencing data in existing pipelines.
  • Significant variations in pipeline capabilities for data handling, phasing, and statistical approaches were observed.

Conclusions:

  • There is a critical need for automated, multi-omic ASE analysis workflows.
  • Future pipelines must enhance compatibility with single-cell technologies for comprehensive gene regulation studies.
  • Advancements in ASE pipeline development will deepen understanding of gene regulation mechanisms and their clinical significance.