PhenoTips: Patient Phenotyping Software for Clinical and Research Use

Abstract

We have developed PhenoTips: open source software for collecting and analyzing phenotypic information for patients with genetic disorders. Our software combines an easy-to-use interface, compatible with any device that runs a Web browser, with a standardized database back end. The PhenoTips' user interface closely mirrors clinician workflows so as to facilitate the recording of observations made during the patient encounter. Collected data include demographics, medical history, family history, physical and laboratory measurements, physical findings, and additional notes. Phenotypic information is represented using the Human Phenotype Ontology; however, the complexity of the ontology is hidden behind a user interface, which combines simple selection of common phenotypes with error-tolerant, predictive search of the entire ontology. PhenoTips supports accurate diagnosis by analyzing the entered data, then suggesting additional clinical investigations and providing Online Mendelian Inheritance in Man (OMIM) links to likely disorders. By collecting, classifying, and analyzing phenotypic information during the patient encounter, PhenoTips allows for streamlining of clinic workflow, efficient data entry, improved diagnosis, standardization of collected patient phenotypes, and sharing of anonymized patient phenotype data for the study of rare disorders. Our source code and a demo version of PhenoTips are available at http://phenotips.org.

Axons to Exons: the Molecular Diagnosis of Rare Neurological Diseases by Next-Generation Sequencing

“…Thus, the most straightforward approach is large-scale data sharing of phenotypes and genotypes from unsolved patients. Phenotyping tools, such as PhenoTips [50], are now available that use Human Phenotype Ontology [51] to facilitate the rapid and accurate characterization of patients in a standardized fashion. This data can be linked with genotypic information and pushed to matchmaking databases to facilitate the diagnosis of affected individuals or families.…”

RD-Connect: An Integrated Platform Connecting Databases, Registries, Biobanks and Clinical Bioinformatics for Rare Disease Research

“…Phenotypic data contributed by the associated research projects, Neuromics and EURenOmics, is being captured using the HPO, enabling standardized cross-cohort comparisons and filtering, as well as implementation of algorithms for automated "matchmaking" to help find cases with clinically similar presentations and variants in the same gene. Collaboration between RDConnect, Neuromics, and the developers of the PhenoTips 30 software has enabled development of user-friendly Provide different stages of implementation of the common data element, starting form the most common element.…”

A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders

“…A core data set, including Human Phenotype Ontology terms to record each participant's key features, was collected at enrollment and recorded using PhenoTips. 10 All diagnostic investigations, including those planned, were collected from referring clinicians and from the medical records at enrollment.…”