Curate Panel

Charlene Son-Rigby -

The Curate Panel page is the main page for the curation of panels. Here you can review and edit the panel details, add or delete genes, edit the gene description and associate conditions with the gene to enable automatic scoring of variants in clinical reports.

Navigation

You can reach the Curate Panel page from:
-  Opal Home page  >>  Panel Builder link >> Actions menu >> Curate Panel option
-  Opal Toolbar  >>  Menu  >>  Panel Builder option >> Actions menu >> Curate Panel option

Features

Panel Properties

The Panel Property fields above the Gene List allow you to edit the panel details and enter default text to populate the corresponding sections in the Clinical Report for Panel tests launched with this panel. For an individual Panel test these sections can be personalized in Preview Report.

Name
The name of a panel should be unique and short, but descriptive to identify the panels. The panel name is included in the header of panel tests in Clinical Reporter and the clinical report PDF.
Description
Enter a description of the panel. This description is for internal use only and is not included in the clinical report. It is good practice to include version information for the panel in the description.
Test Code
The Test Code should match the code used in the organizations LIMS/LIS system to order the test. This enables the API to launch Panel test with a specific panel.
Default Filter
Specifying a Filtering Protocol as a Default Filter here will pre-select that protocol in the New Panel Report page when the panel is chosen from the Choose Panel menu. The Default Filter supports standardization of test protocols. If needed the filter selection can be changed for an individual panel test in the New Panel Report page.
Panel tests launched via the API will ignore the Default Filter specified here. To use a Filtering Protocol when launching a Panel report via the API it must be specified in the API command line. 
The Default Filter also does not apply when the panel is used from the Filters Menu to filter variants in the Variants table.
Default Assay Type
Specifying a Default Assay Type will pre-select the Assay Type in the New Panel Report page when the panel is chosen from the Choose Panel menu. If needed this selection can be changed in the New Panel Report page for the individual panel test. 
Panel tests launched via the API will ignore the Default Assay Type specified here. To use an Assay Type when launching a Panel report via the API it must be specified in the API command line. 
Methodology
Enter the default text for the Methodology section in the Clinical Report.
Limitations
Describe here the test limitations for the Limitations section of the Clinical Report.
Regulatory Disclosures
Enter here the default text for the Regulatory Disclosures section in the Clinical Report
Recommendations
Enter a default content for the Recommendations section of the Clinical Report

Gene List

Below the panel properties is a table with all genes in the panel.

Symbol
Official symbol of the gene (HGNC). Clicking on the Symbol opens the Gene detail view providing a genome browser view of the gene, detailed information on the gene and related external links.
Name
Full name of the gene.
Condition
Associating a Condition with a gene here in the Panel enables Automatic Classification of previously classified variants in Clinical Reporter.

 Actions

Add Genes
This button opens the Add Genes to Panel page which provides several options to enter or select genes to add to the panel.
Save Panel Properties
This action will save any changes made to the Panel Properties.
Return to Panels
Click here to return to the Panels page.
Actions
The Actions dropdown menu provides editing options for an individual gene.
Edit Description
Selecting this option opens the Edit Gene dialog box where you can edit the default gene description which is populated from RefSeq. If a variant in the gene is included in the Clinical Report the gene description is used for the Primary/Secondary Findings Summary.
Associate with Condition
Select this option to add or edit the Condition-Gene Association used for Automatic Classification of variants in Clinical Reporter.
Edit Condition Associated with Gene
If the gene is already associated with a condition in the workspace this dialog box opens with the Workspace Condition-Genes tab and lists all condition-gene associations for this gene. Select the condition to be used for automatic classification and click the Save Changes button. You can also enter a new condition gene association by clicking on the New Condition-Gene tab.
Associate Condition with Gene
If the gene has not be associated with a condition in the workspace yet this dialog box opens with the New Condition-Gene tab. 
Delete
Selecting Delete will open the Delete Gene prompt to confirm the removal of this gene from the panel.
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