Original Research Article

Clinical validity of phenotype-driven analysis software PhenoVar as a diagnostic aid for clinical geneticists in the interpretation of whole-exome sequencing data

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Accepted:
Published online:

Abstract

Purpose

We sought to determine the diagnostic yield of whole-exome sequencing (WES) combined with phenotype-driven analysis of variants in patients with suspected genetic disorders.

Methods

WES was performed on a cohort of 51 patients presenting dysmorphisms with or without neurodevelopmental disorders of undetermined etiology. For each patient, a clinical geneticist reviewed the phenotypes and used the phenotype-driven analysis software PhenoVar (http://phenovar.med.usherbrooke.ca/) to analyze WES variants. The prioritized list of potential diagnoses returned was reviewed by the clinical geneticist, who selected candidate variants to be confirmed by segregation analysis. Conventional analysis of the individual variants was performed in parallel. The resulting candidate variants were subsequently reviewed by the same geneticist, to identify any additional potential diagnoses.

Results

A molecular diagnosis was identified in 35% of the patients using the conventional analysis, and 17 of these 18 diagnoses were independently identified using PhenoVar. The only diagnosis initially missed by PhenoVar was rescued when the optional “minimal phenotypic cutoff” filter was omitted. PhenoVar reduced by half the number of potential diagnoses per patient compared with the conventional analysis.

Conclusion

Phenotype-driven software prioritizes WES variants, provides an efficient diagnostic aid to clinical geneticists and laboratories, and should be incorporated in clinical practice.

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Acknowledgements

The study was supported by institutional funds of the Université de Sherbrooke, La Fondation du Grand Défi Pierre Lavoie, and La Fondation des Étoiles. We are thankful to Génome Québec and Fulgent for the exome sequencing. Moreover, we thank Marie Edmont and Laura Dempsey-Nunez for the genetic counseling. We are also grateful to the patients and their families for their participation in this study.

Author information

Affiliations

  1. Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada

    • Fanny Thuriot
    • , Caroline Buote
    • , Elaine Gravel
    • , Sébastien Chénier
    • , Valérie Désilets
    • , Bruno Maranda
    • , Paula J Waters
    •  & Sébastien Lévesque
  2. Department of Biology, Faculty of Sciences, Université de Sherbrooke, Sherbrooke, Canada

    • Pierre-Etienne Jacques
  3. Department of Computer Science, Faculty of Sciences, Université de Sherbrooke, Sherbrooke, Canada

    • Pierre-Etienne Jacques

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Competing interests

The authors declare no conflict of interest.

Corresponding author

Correspondence to Sébastien Lévesque.

Supplementary information

Supplementary material is linked to the online version of the paper at http://www.nature.com/gim