Phenotype Matching

In VarSome Clinical you can add known phenotypes or diseases linked to the sample you analyze.

Launch analysis page

In the "Launch analysis" page you can start typing a phenotype or a disease according to HPO in the respective field and include this information when launching a new analysis.

setup

Sample page - Analysis actions

You could also add phenotypes or diseases in an analyzed sample by clicking on the button of the Analysis actions menu either when viewing your sample in the Samples page:

Or you could edit the Disease/ Phenotye information from the results page of an analysis clicking on the "Analysis actions" button:

You will then be directed to a new screen where you can add your preferences regarding Disease or Phenotype information and then click on the "Save" button for the changes to take place:

In the Variant Table, a column named Phenotypes (or Diseases) will be visible and for each variant reported, it will include the number of phenotypes or diseases linked to the gene including the variant and matched to the phenotypes or diseases provided when launching an analysis. Then, you can sort by that column to prioritize variants accordingly.

phenotypes

 

How are the phenotypes and diseases matched with the variants?

The phenotype names and synonyms come from The Human Phenotype Ontology (HPO) and the disease names and synonyms come from Mondo Disease Ontology. We use HPO and Mondo to define the names but we get the gene associations to phenotypes and diseases from Monarch.

The Monarch initiative is fed by several data sources such as OMIM. Please, find here the link to the Monarch data sources list.

 

vclin-only-cropped