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Deep phenotyping for patients by patients: a lay-friendly version of the Human Phenotype Ontology

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posted on 08.11.2017 by Melissa Haendel, Nicole Vasilevsky, Mark Englestad, Julie McMurry, Erin Foster, Tudor Groza, Chris Mungall, Catherine Brownstein, Ingrid Holm, Cornelius Boerkel, Kayli Rageth, Michelle Moore, Peter Robinson
The Human Phenotype Ontology (HPO) has become the de facto standard representation of clinical “deep phenotype” data for computational comparison of abnormalities and for use in genetic disease diagnostics. The HPO enables non-exact matching of sets of phenotypic features (phenotype profile) against known diseases, other patients, and model organisms. The algorithms have been implemented into many variant prioritization tools and are used by the 100,000 Genomes project, the NIH Undiagnosed Diseases Program/Network, and thousands of other clinics, labs, tools, and databases.

Patients themselves are an eager and untapped source of accurate information about symptoms and phenotypes - some of which may go unnoticed by the clinician. However, medical terminology is often perplexing to patients, making it difficult to use resources like the HPO. Here, we systematically added layperson synonyms with approximately 60% being translatable into layperson terminology. Analyses suggest that the lay-HPO has the features required to be useful in a diagnostic setting, in that lay terms are: a) sufficiently specific and, b) well-represented in our disease-to-phenotype database that is utilized by the aforementioned tools for differential diagnostics. A new patient-centered tool aims to help patients assist clinicians in creating robust computational phenotype profiles to improve molecular diagnostic rates and be active participants in their diagnostic odysseys.

Funding

PCORI ME-1511-33184; 1R24OD011883

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