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AlphaMissenseR: an integrated framework for investigating missense mutations in human protein-coding genes.

Tram N Nguyen1, Tyrone Lee1, Nitesh Turaga1

  • 1Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, United States.

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AlphaMissenseR provides R/Bioconductor access to Google DeepMind's AlphaMissense predictions for human missense mutation pathogenicity. This package enables analysis, visualization, and benchmarking of variant effects.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Artificial Intelligence

Background:

  • Predicting missense mutation pathogenicity is crucial for understanding genetic diseases.
  • Existing tools often lack comprehensive analysis and visualization capabilities.
  • AlphaMissense offers AI-driven predictions for the entire human proteome.

Purpose of the Study:

  • To introduce AlphaMissenseR, an R/Bioconductor package for accessing AlphaMissense predictions.
  • To provide tools for analysis, visualization, validation, and benchmarking of variant pathogenicity.
  • To facilitate integration with genomic analysis and clinical variant databases.

Main Methods:

  • Development of an R/Bioconductor package (AlphaMissenseR).
  • Integration with Bioconductor genomic region analysis tools.
  • Implementation of multi-level visualization for genome browsers and 3D protein structures.
  • Integration with clinical and experimental variant databases.

Main Results:

  • AlphaMissenseR offers performant and reproducible access to AlphaMissense pathogenicity predictions.
  • The package enables interactive exploration of variant effects across genomic regions and protein structures.
  • Facilitates benchmarking of prediction methods against clinical and experimental data.

Conclusions:

  • AlphaMissenseR enhances the utility of AlphaMissense predictions for researchers.
  • The package supports comprehensive analysis, visualization, and validation of variant pathogenicity.
  • It serves as a valuable tool for the bioinformatics and genomics communities.