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MTR-Viewer: identifying regions within genes under purifying selection.

Michael Silk1,2,3, Slavé Petrovski4,5, David B Ascher1,2,3,6

  • 1Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC 3052, Australia.

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Summary

The Missense Tolerance Ratio (MTR) viewer helps identify disease-causing genetic variants by highlighting regions intolerant to missense variation. This tool aids personalized medicine by revealing functionally important gene regions.

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Area of Science:

  • Genomics
  • Human Genetics
  • Bioinformatics

Background:

  • Genomic sequencing advances personalized medicine.
  • Distinguishing disease-causing from benign genetic variants is challenging.
  • Purifying selection removes unfavorable variation in human genomes.

Purpose of the Study:

  • Introduce the MTR-Viewer, a web-server for visualizing the Missense Tolerance Ratio (MTR).
  • Enable gene and variant level analysis of regional intolerance to missense variation.
  • Facilitate exploration of MTR scores across human genes, transcripts, and ethnicities.

Main Methods:

  • Calculated MTR using variation data from 240,000 exome and genome sequences.
  • Developed a web-server for visualizing MTR across >18,000 human genes and 85,000 transcripts.
  • Integrated display of population/disease variants and protein domain structures.

Main Results:

  • Identified highly intolerant regions enriched for pathogenic ClinVar and somatic COSMIC missense variants (P < 2.2 × 10-16).
  • Demonstrated MTR's ability to highlight functionally important regions independent of known domains.
  • Showcased MTR-Viewer's utility for exploring ethnicity-specific selective pressures.

Conclusions:

  • MTR-Viewer provides a novel method for identifying functionally critical gene regions.
  • The tool aids in distinguishing disease-causing variants for personalized medicine applications.
  • MTR-Viewer is a freely accessible resource for genetic variation analysis.