Panels

Charlene Son-Rigby -

The Panel Builder allows you to create virtual panels of genes. Panels are primarily used to launch a New Panel Report in Clinical Reporter but can also be used to filter variants by a group of genes in any report in Variant Miner and Clinical Reporter.

The Panels page lists all available panels, and from here you can create new panels and curate existing panels.

Navigation

You can reach the Panels page from:
-  Opal Home page  >>  Panel Builder link
-  Opal Toolbar  >>  Menu  >>  Panel Builder link

Features

Panels Tabs

The panels are organized in 2 groups, Workspace Panels and Public Panels. To view the panels in each group click on the respective tab above the Panel list.

Workspace Panels
Workspace Panels contain all panels created in this workspace. These panels are available throughout Opal to create panel reports or filter variants.
Public Panels
The panels listed here were curated by Fabric Genomics. To use any of the Public Panels in the workspace select Clone Panel from the Actions dropdown menu to copy the panel to the Workspace Panels tab. 

Panel List

Name
Click on the panel name to display the panel description and the list of genes in the panel.
ID
A unique ID for the panel.
Test Code
A Test Code can be assigned to the panel to link the panel to a test code in the organization's LIMS/LIS system. The Test Code will enable the launch of Panel tests with a specific panel using the Opal API.
Creator
Name of user who created the panel.
Created On
Date Panel was created.
Published On
Date the panel was published. See Status and Actions for more information on publishing panels.
Gene Count
Count of the genes in this panel.
Status
A panel can be in one of three different statuses reflecting the curation state of the panel. 
In Development
The panel is still in the process of curation, it can be modified by editing the panel information or adding/deleting genes. Panels with the status In Development can be used to create Panel Reports or filter variants, but the set of genes can differ between reports as the panel is modified.
Published
Validation of this panel is completed and the panel is curated. The panel is now locked and cannot be modified any more. This ensures that all reports generated or filtered with this panel use the same set of genes. It is recommended to use only published panels for the interpretation of clinical data.
Retired
If a Published panel needs to be modified a new panel is created by cloning the published panel, then the published panel is Retired. A retired panel cannot be selected any more to launch a new panel report or to filter variants, and cannot be modified any more. Retired panels can still be cloned into a new panel.

Actions

New Panel
The New Panel button opens the New Panel dialog box.
Curate Panel
Selecting Curate Panel opens the Curate Panel page where you can update the panel information and add/delete genes or chromosomal regions. You can curate only panels with the status In Development.
Publish Panel
Selecting Publish Panel opens the Publish Panel dialog box where you can add a note and are asked to confirm the publication of the panel.
Important: This action cannot be undone and will lock the panel. Before publishing a panel it should be tested with validation samples.
Retire Panel
Selecting Retire Panel opens the a dialog box where you are asked to confirm the retirement of this panel. 
Important: This action can not be undone.
View Panel
A panel with the status Published or Retired cannot be edited any more, but the details of the panel and its genes can be viewed by selecting View Panel.
Clone Panel
Select Clone Panel to copy any panel into a new panel with the Status In Development.
Delete Panel
Only a Panel with the Status In Development can be deleted.
View History
This option displays a history of the panel's modifications.
Export Pre-Test Report
Selecting Export Pre-Test Report generates a PDF pre-test report which can be used to provide an ordering physician with coverage information of the genes in the panel before ordering the test. In order to include coverage information in the Pre-Test Report an Assay Type with gene coverage information needs to be defined prior to generating the pre-test report. 

 

Have more questions? Submit a request

Comments