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Novel phenotype–disease matching tool for rare genetic diseases

Genetics in Medicinevolume 21pages339346 (2019) | Download Citation




To improve the accuracy of matching rare genetic diseases based on patient’s phenotypes.


We introduce new methods to prioritize diagnosis of genetic diseases based on integrated semantic similarity (method 1) and ontological overlap (method 2) between the phenotypes expressed by a patient and phenotypes annotated to known diseases.


We evaluated the performance of our methods by two sets of simulated data and one set of patient’s data derived from electronic health records. We demonstrated that the two methods achieved significantly improved performance compared with previous methods in correctly prioritizing candidate diseases in all of the three sets. Our methods are freely available as a web application ( to aid diagnosis of genetic diseases.


Our methods can capture the diagnostic information embedded in the phenotype ontology, consider all phenotypes exhibited by a patient, and are more robust than the existing methods when phenotypes are incorrectly or imprecisely specified. These methods can assist the diagnosis of rare genetic diseases and help the interpretation of the results of DNA tests.

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The authors would like to acknowledge Alka Chandel, Parth Divekar, and Diana Epperson for helping to query and organize clinical data from the i2b2 database. This study is partially funded by the Center for Pediatric Genomics, Cincinnati Children’s Hospital Medical Center, and National Institutes of Health (NIH) grant U01 HG008666.

Author information


  1. Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA

    • Jing Chen PhD
    • , Anil Jegga DVM, MRes
    •  & Pete S. White PhD
  2. Division of Biostatistics and Bioinformatics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA

    • Huan Xu MS
  3. Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA

    • Kejian Zhang MD, MBA
    • , Pete S. White PhD
    •  & Ge Zhang MD, PhD
  4. Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA

    • Kejian Zhang MD, MBA
    •  & Ge Zhang MD, PhD


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The authors declare no conflicts of interest.

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Correspondence to Jing Chen PhD or Ge Zhang MD, PhD.

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