Panel Builder

Charlene Son-Rigby -

Fabric Genomics Curated Panels in Public Panels

Creating a Panel

Curating a Panel

Adding Genes to a Panel

Publishing Your Panels

Creating Pre-Test Reports

 

Panel Builder opens with a list of Panels in your workspace.

 PanelBuilder_ListView

  Panel View Columns
Name The name of Panel
ID Panel ID Number
Test Code Panel Test Code
Creator User who created Panel
Created On Date Panel was created
Published On Date Panel was published
Gene Count Number of genes in the Panel
Status Either In Development or Published. Published panels cannot be edited.
Actions Dropdown menu with commands that can be performed on each Panel.

 

Fabric Genomics Curated Panels in Public Panels

Panels created in your workspace will show up in the Workspace Panels. Fabric Genomics is also creating Public Panels to accelerate your panel development efforts. These panels have been curated based on strength of disease association and published guidelines.

Click on the Public Panel link to access the currently available public panels. More information on currently available panels is available here.

If you want to use any of these panels, click the Actions dropdown menu and select the “Clone Panel” option. Now, the panel will be available in your Workspace Panels, and can be edited and updated as needed. Note that a clinical report cannot be created off a public panel; you will need to clone the panel before you can use it.

Creating a Panel

Create a new Panel by clicking the “New Panel” button:

Create New Panel dialog

Enter the requested fields. Clearly identify the Panel as the Name will appear in your Clinical Reports. The Panel Methodology, Limitations, and Regulatory Disclosure field content will also be pulled into your reports, and where it can be updated as required.

Click on the “Create Panel” button to save your Panel.

 

Curating a Panel

Curating a Panel starts with selecting genes to add to Panel Genes and editing the Panel Properties. To do this, go to the Action drop down menu for your panel and select “Curate Panel”.

The resulting window displays Panel Properties as well as the list of genes in the panel. Under the Panel Properties you can edit all properties you added when creating the panel, as well as adding Recommendation to be printed in the clinical report and preselecting the Default Filter and Default Assay Type for this panel.

A new Panel will not contain any genes. To add genes to the Panel click the “Add Genes” button.

Adding Genes to a Panel

In the resulting “Add Genes” dialog enter your gene symbols separated by spaces or commas (you can also copy-and-paste the symbols). Alternatively, you can add genes from existing Gene Sets or Panels in Opal.

Click the “Add Genes” button to save the genes to your Panel.

Curate Panel window

The newly added genes are displayed in the Panel Genes section with their official gene names. You can edit or delete a gene by selecting the relevant command from the adjacent “Actions” dropdown menu.

 

Publishing Your Panels

After you have created your Panels in Panel Builder the next step is to test them against genomes using Clinical Reporter. Ideally you should have test genomes with the pathogenic variants you seek.

Once you have validated your panel, you can publish it. To do this, go to the Panels page and select “Publish Panel” from the dropdown menu.

Important Note: Once you have published a panel, it cannot be edited or moved back to In Development status, so be certain your panel is in its final ready state for your test.

Panels Page with Actions dropdown menu

Creating New Versions of Published Panels

You may want to create a new version of a published panel. To do this, choose “Clone Panel” from the Actions dropdown menu. This will create a copy of the published panel. Enter a name for your new panel.

If at any time you want to confirm which panel your new panel was cloned from, click “View History” in the Actions dropdown menu.

Retiring Panels

If you want to retire a published panel, select the “Retire Panel” option from the Actions dropdown menu. A retired panel cannot be used for new clinical tests.

Deleting Panels

If you want to delete a panel, select the “Delete Panel” option from the Actions dropdown menu. Published panels cannot be deleted; you should Retire published panels to remove them from usage.

 

Creating Pre-Test Reports

A lab may want to provide an ordering physician with coverage information of the genes in a panel, prior to confirming the order of a panel test for a patient. This is especially useful for custom panels, and allows a physician to validate that high priority target genes are well-covered. 

A pre-test report with this information can be generated for a panel curated in Panel Builder. A panel can cover all genes in an Assay, or it can be in silico panel that covers a subset of genes in the Assay. 

Prior to generating a pre-test report, an Assay Type needs to have been defined with gene coverage information. To do this, see Associate Genes to Assay Type

To generate a pre-test report, after adding the desired genes to the panel, in the Panel Builder list view, select the Actions dropdown menu for the desired Panel, and click "Export Pre-Test Report".

This will generate a PDF pre-test report that can be provided to the ordering physician.

 

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