VarSight

VarSight is a software tool to assist in identifying and prioritizing genomic variants that may explain the phenotypes of rare disease patients. The tool addresses the challenges in variant prioritization arising from the high variability in phenotype presentation and the molecular sources of disease.

Key features and findings of VarSight:

It utilizes classification algorithms that input variant annotations and phenotype information to predict whether a variant will be clinically reported and returned to a patient.

The tool was tested through a retrospective study on variants clinically reported to 237 patients in the Undiagnosed Diseases Network.

VarSight's classifiers were compared to four variant prioritization algorithms and two single-measure controls, treating the classifiers as variant prioritization systems.

Topic

Rare diseases;Genotype and phenotype;Personalised medicine;Exome sequencing;Genetic variation

Detail

  • Operation: Variant prioritisation;Variant calling;Variant filtering;Variant classification

  • Software interface: Command-line user interface

  • Language: Python

  • License: Other

  • Cost: Free of charge with restrictions

  • Version name: v1.1

  • Credit: National Human Genome Research Institute, NIH Common Fund, Office of Strategic Coordination, Office of the NIH Director.

  • Input: -

  • Output: -

  • Contact: James M. Holt jholt@hudsonalpha.org

  • Collection: -

  • Maturity: -

Publications

  • VarSight: prioritizing clinically reported variants with binary classification algorithms.
  • Holt JM, et al. VarSight: prioritizing clinically reported variants with binary classification algorithms. VarSight: prioritizing clinically reported variants with binary classification algorithms. 2019; 20:496. doi: 10.1186/s12859-019-3026-8
  • https://doi.org/10.1186/S12859-019-3026-8
  • PMID: 31615419
  • PMC: PMC6792253

Download and documentation

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