Phenotype Matching

VarSome Clinical users can attach phenotypes to germline samples. When provided, a new column in the variant table (Phenotypes) is displayed showing the number of associations between the genes and the phenotypes provided. Consistently to our VarSome platform, we have also merged diseases into phenotypes so the users can now attach phenotypes (using HPO terms like before) and diseases (using MONDO and OMIM® terms). 

How can I add phenotype(s) to my sample?

Launch analysis page

In the "Launch analysis" page you can start typing a phenotype (select "All" or "Only OMIM®") in the respective field and include this information when launching a new analysis.

To select the phenotypes of interest, start typing the term and select the phenotypes from the dropdown list. Phenotypes shown in the dropdown list can be limited based on their source. When selecting “All” you will get terms from HPO, MONDO and OMIM® databases:

When selecting “Only OMIM®”, the dropdown terms will be retrieved solely from the OMIM® database:

Sample page - Analysis actions

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

Or you can edit the Phenotype information from the results page of an analysis by clicking on the "Analysis actions" button:

You will then be directed to a new screen where you can add the phenotype information and then click on "Save" to apply the changes. After a few minutes, the "Phenotypes" column will be updated 

There will be a column named "Phenotypes" in the variant table with a value per each variant. This column will contain the number of user input phenotype(s) associated with the variant gene.

Hover over the number with the mouse to see the name of the matched phenotypes.

This column can be used to sort the table in descending/ascending order.

You can also create a dynamic filter to filter variants based on these values following the steps below:

How are the phenotypes matched with the variants?

The phenotype names can come from The Human Phenotype Ontology (HPO), Online Mendelian Inheritance in Man (OMIM®) or Mondo Disease Ontology (MONDO), depending on the user selection. This will affect the way the gene-phenotype associations are retrieved since we will use different sources for each phenotype term: 

  • HPO: in this case the HPO database is used to get the phenotype (HPO term) - gene associations.
  • MONDO: the Monarch data source is used here to get the disease (MONDO term) - gene associations.
  • OMIM®: the disease (OMIM®) - gene associations are retrieved directly from the OMIM® database.