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Nonsense-mediated mRNA Decay02:27

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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 15201, United States.

Bioinformatics (Oxford, England)
|September 9, 2023
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Summary
This summary is machine-generated.

A new software, aenmd, identifies human DNA variants that cause premature termination codons (PTCs) and escape nonsense-mediated mRNA decay (NMD). This helps understand dominant-negative or gain-of-function alleles in diseases.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Premature termination codons (PTCs) are common in pathogenic genomic variation.
  • Nonsense-mediated mRNA decay (NMD) typically leads to loss-of-function from PTCs.
  • Some PTCs escape NMD, causing dominant-negative or gain-of-function (DN/GOF) effects.

Purpose of the Study:

  • To systematically identify human PTC-causing variants.
  • To predict the susceptibility of PTC-containing transcripts to NMD.
  • To investigate the role of DN/GOF alleles in human disease.

Main Methods:

  • Development of aenmd, a user-friendly, self-contained software.
  • Implementation of established and experimentally validated rules for NMD escape prediction.
  • Application of aenmd to large-scale genomic databases (gnomAD, Clinvar, GWAS catalog).

Main Results:

  • aenmd annotates PTC-containing transcript-variant pairs for NMD escape prediction.
  • The software integrates seamlessly with existing analysis workflows and operates at scale.
  • Prevalence of human PTC variants and potential DN/GOF variants was reported across major databases.

Conclusions:

  • aenmd provides essential functionality for identifying PTC variants and predicting NMD escape.
  • The findings contribute to understanding the contribution of DN/GOF alleles to human disease.
  • The software is available as an R-package and a command-line interface.