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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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DOMINO: Using Machine Learning to Predict Genes Associated with Dominant Disorders.

Mathieu Quinodoz1, Beryl Royer-Bertrand2, Katarina Cisarova1

  • 1Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1011 Lausanne, Switzerland.

American Journal of Human Genetics
|October 7, 2017
PubMed
Summary

Identifying dominant mutations for Mendelian disorders is challenging. DOMINO, a new tool, uses machine learning on gene features to accurately predict dominant disease genes, improving genetic analysis.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Distinguishing pathogenic dominant (monoallelic) mutations from benign variants in Mendelian disorders is difficult due to high background noise.
  • Next-generation sequencing (NGS) generates vast data, necessitating tools to filter false positives and identify causative genes.

Purpose of the Study:

  • To develop DOMINO, a novel computational tool to assess the likelihood of a gene harboring dominant mutations.
  • To enhance the accuracy of identifying genes responsible for Mendelian disorders using NGS data.

Main Methods:

  • DOMINO employs a machine-learning approach utilizing 432 gene-specific features (genomic, conservation, expression, interactions, structure).
  • The algorithm was trained on 985 genes with known inheritance patterns and validated using cross-validation and newly discovered pathogenic genes.

Main Results:

  • DOMINO achieved an excellent performance with an area under the curve (AUC) of 0.92 on validation data.
  • Unsupervised analysis identified known genes and predicted 9 novel candidate genes with high confidence in intellectual disability and epilepsy cohorts.

Conclusions:

  • DOMINO is a robust tool for inferring dominant candidate genes with high sensitivity and specificity.
  • It serves as a valuable complement to NGS pipelines for analyzing the human genome and identifying disease-causing genes.