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aenmd: Annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants.

Jonathan Klonowski1, Qianqian Liang1, Zeynep Coban-Akdemir2

  • 1Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

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Summary

New software, aenmd, identifies genetic variants causing premature termination codons (PTCs) that escape nonsense-mediated mRNA decay (NMD). This helps uncover potential dominant-negative or gain-of-function alleles driving human diseases.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Premature termination codons (PTCs) are common in pathogenic genomic variations.
  • PTCs typically lead to loss-of-function alleles via nonsense-mediated mRNA decay (NMD).
  • Some PTCs escape NMD, causing dominant-negative or gain-of-function (DN/GOF) effects, crucial for disease investigation.

Approach:

  • Introduced aenmd, a user-friendly, scalable software for annotating PTC-containing transcripts.
  • aenmd predicts NMD escape based on validated rules, integrating with existing workflows.
  • Applied aenmd to large-scale genomic databases (gnomAD, Clinvar, GWAS Catalog).

Key Points:

  • aenmd systematically identifies human PTC-causing variants and their NMD escape potential.
  • Quantified the prevalence of PTC variants and potential DN/GOF alleles in major human genetic databases.
  • The software offers unique functionality for NMD escape prediction at scale.

Conclusions:

  • aenmd facilitates the study of DN/GOF alleles by predicting NMD escape.
  • Understanding NMD escape is vital for interpreting PTC variants in human disease.
  • The software is available as an R package and a command-line interface.