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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
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CompMap: an allele-specific expression read counter based on competitive mapping.

Santiago Sanchez-Ramirez1, Asher Cutter1

  • 1Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.

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|June 19, 2025
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Summary

CompMap accurately infers allele-specific expression (ASE) from hybrid transcriptomes by analyzing read mapping, overcoming common analysis challenges. This method improves the study of gene regulation across species and populations.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Allele-specific expression (ASE) analysis is crucial for understanding gene regulation.
  • Interspecies and inter-population hybrids offer unique systems for studying regulatory divergence.
  • Existing analysis pipelines for ASE can suffer from mapping bias and information loss.

Purpose of the Study:

  • To introduce CompMap, a novel Python-based method for generating allele-specific expression counts.
  • To address limitations in current methods for inferring gene regulatory changes from hybrid transcriptomes.
  • To provide a robust tool for analyzing genotype-specific alignments.

Main Methods:

  • CompMap utilizes genotype-specific alignments to generate allele-specific expression counts.
  • The method compares read-mapping statistics within homologous regions to parental alignments.
  • Ambiguous alignments are resolved statistically using a binomial distribution or proportionally.

Main Results:

  • CompMap effectively sorts and counts reads, not just single nucleotide polymorphisms (SNPs).
  • Simulations demonstrate low error rates in assessing regulatory divergence using CompMap.
  • The method provides accurate allele-specific expression counts from complex hybrid samples.

Conclusions:

  • CompMap offers a self-contained and efficient solution for ASE analysis in hybrid systems.
  • The method mitigates mapping bias and information loss common in other pipelines.
  • CompMap facilitates a more accurate assessment of cis- and trans-regulatory changes.