4. Using a VSWarehouse Assessment CatalogsΒΆ

Assessment catalogs are modifiable annotation sources. By hosting an assessment on a VSWarehouse instance it makes it easy to share the changes to each variant in the catalog between multiple users. You can create assessment catalogs with custom fields which provides the flexibility to use them many different ways. The more common use cases center around using them as sets of white-listed or black-listed variants to speed up your variant interpretation. For this tutorial we will be using the Clinical Significance catalog that is already on the VSWarehouse.

  1. The catalog that we will be using in this tutorial can be found in the Catalogs tab of the Manage VSWarehouse tab.

    Catalogs in VSWarehouse

    Figure 4-1: Open the assessment catalog in VarSeq.

    Click Open to create an assessment catalog view in VarSeq.

  2. Next switch to the 50 Percent sample by selecting it from the current sample selector. This will update the filters allowing an additional variant into the final results.

    Assessment Sample Selection

    Figure 4-2: Selecting the current sample

    Select the third variant, and notice that the assessment catalog view updates to the record at that position.

  3. Fill out the assessment for this variant with a Pathogenic Classification and a Reported Classification as Confirmed somatic variant (see Figure 4-3). Click the Save button to update the VSWarehouse assessment catalog.

    This assessment will then be placed on VSWarehouse were anyone can view or add the catalog as an annotation.

    Assessment Sample Selection

    Figure 4-3: Selecting the current sample

    Additionally you will see that your change has been logged in the recent assessments section for that variant. This allows for tracking of users and their changes.

  4. To view the assessment catalog data on the VSWarehouse. Open the internet browser of your choice and navigate to the VSWarehouse address. After login in you should see the Clinical Significance Catalog in the Assessment catalog section of the home page.

    Catalog on VSWarehouse home page

    Figure 4-4: Catalog on the VSWarehouse home page

    Select the Assessment catalog and find the record that you changed in VarSeq. Click on the record that was just changed in VarSeq, the record will allow you to change the variant assessment. Change the Reported Classification to Unconfirmed somatic variant and click save.

    Editing catalog on VSWarehouse

    Figure 4-5: Editing the catalog the VSWarehouse.

  5. Now, switching back to VarSeq refresh the catalog to load the changes made from the browser.

    Refreshing the catalog in VarSeq

    Figure 4-6: Refreshing the catalog in VarSeq

    The reported classification has now changed, notice the additional edit in the Recent Assessments Log.