Phenotype Submission

You will be provided with a login for our secure online analysis portal, seqr, that provides collaborators with the ability to deeply analyze the genetic and phenotypic data from their samples. Each sample will be linked directly to PhenoTips, to ensure seamless entering, editing, and viewing of patient phenotype information.

PhenoTips is a software tool for collecting and analyzing phenotypic information for patients with genetic disorders (see https://phenotips.org/). This tool has been integrated with seqr to record phenotype information and pedigree structure. This platform allows for easier phenotyping by providing collaborators with a standardized language, the Human Phenotype Ontology (HPO), autocompletion/suggestion of phenotype terms, and customizable forms.

The Human Phenotype Ontology is developed by members of the Monarch Initiative and by the community at large. The HPO aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect, that are associated with hereditary and common diseases with over 115,000 annotations to known diseases. The HPO is built to be interoperable with other ontologies in support of data integration and comparison with model organisms. HPO profiles generated for rare disease patients form the basis of non-exact comparisons to known diseases and to model organisms, and Monarch algorithms using these data are used in numerous diagnostic tools and for matchmaking patients. An annotation sufficiency metric is used to assess the diagnostic capability of a given HPO profile by comparison against all the gold standard data available within Monarch. This results in the five star rating that is seen in PhenoTips, Patient Archive, and others tools.

Find out more about the monarch initiative at monarchinitiative.org, and HPO at www.human-phenotype-ontology.org. http://dx.doi.org/10.1093/nar/gkw1039.

If you already use PhenoTips to collect phenotypic information on your patients, please let us know and we can arrange to transfer this information into our system.

A minimum amount of phenotypic information is required for each participant. We will review your submission and may request that additional information be provided.

Introduction to seqr and Phenotips Training: Watch video tutorial

How to draw a pedigree in PhenoTips: Watch video tutorial