Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics.

Journal: Current protocols in human genetics
Published Date: Sep 1, 2019

Abstract

The Human Phenotype Ontology (HPO) is a standardized set of phenotypic terms that are organized in a hierarchical fashion. It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnostics. The HPO is frequently used to create a set of terms that accurately describe the observed clinical abnormalities of an individual being evaluated for suspected rare genetic disease. This profile is compared with computational disease profiles in the HPO database with the aim of identifying genetic diseases with comparable phenotypic profiles. The computational analysis can be coupled with the analysis of whole-exome or whole-genome sequencing data through applications such as Exomiser. This article explains how to choose an optimal set of HPO terms for these cases and enter them with software, such as PhenoTips and PatientArchive, and demonstrates how to use Phenomizer and Exomiser to generate a computational differential diagnosis. © 2019 by John Wiley & Sons, Inc.

Authors

  • Sebastian Köhler
    School of ITEE, The University of Queensland, St. Lucia, QLD 4072, Australia, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, National Institute of Informatics, Hitotsubashi, Tokyo, Japan, Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK, LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, Genetic Services of Western Australia, King Edward Memorial Hospital, WA 6008, Australia, School of Paediatrics and Child Health, University of Western Australia, WA 6008, Australia, Institute for Immunology and Infectious Diseases, Murdoch University, WA 6150, Australia, Office of Population Health, Public Health and Clinical Services Division, Western Australian Department of Health, WA 6004, Australia, Academic Department of Medical Genetics, Sydney Children's Hospitals Network (Westmead), NSW 2145, Australia, Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, NSW 2006, Australia, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany and Berlin Brandenburg Center for Regenerative Therapies, 13353 Berlin, Germany.
  • N Christine Øien
    Freelance Genome Analyst, Berlin, Germany.
  • Orion J Buske
    Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada.
  • Tudor Groza
    The Garvan Institute of Medical Research, Sydney, Australia.
  • Julius O B Jacobsen
    Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
  • Craig McNamara
    Pryzm Health, Perth, Australia.
  • Nicole Vasilevsky
    Library, Oregon Health & Science University, Portland, OR 97239, USA.
  • Leigh C Carmody
    Monarch Initiative (monarchinitiative.org).
  • J P Gourdine
    Monarch Initiative (monarchinitiative.org).
  • Michael Gargano
    Monarch Initiative, monarchinitiative.org.
  • Julie A McMurry
    Monarch Initiative, monarchinitiative.org.
  • Daniel Danis
    Monarch Initiative, monarchinitiative.org.
  • Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Damian Smedley
    School of ITEE, The University of Queensland, St. Lucia, QLD 4072, Australia, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, National Institute of Informatics, Hitotsubashi, Tokyo, Japan, Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK, LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, Genetic Services of Western Australia, King Edward Memorial Hospital, WA 6008, Australia, School of Paediatrics and Child Health, University of Western Australia, WA 6008, Australia, Institute for Immunology and Infectious Diseases, Murdoch University, WA 6150, Australia, Office of Population Health, Public Health and Clinical Services Division, Western Australian Department of Health, WA 6004, Australia, Academic Department of Medical Genetics, Sydney Children's Hospitals Network (Westmead), NSW 2145, Australia, Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, NSW 2006, Australia, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany and Berlin Brandenburg Center for Regenerative Therapies, 13353 Berlin, Germany.
  • Melissa Haendel
    Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
  • Peter N Robinson
    The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA.

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