This Quick Start is a step-by-step guide for new Opal Clinical Users designed to assist you as you sign up for your Opal account through to approving your first Clinical Report.
The Opal Clinical features covered in this Guide:
Signup - Creating your Opal account
Upload Genome - Uploading your first genome into a new project
Create Panel - Creating your first disease panel
Set Up Test - Setting up your first clinical report
Interpret and Score Variants - Classifying variants using ACMG 2015 Guidelines
Review Report - Reviewing the report
Approve Report - Approving the final report
For a detailed description of all Opal Clinical features and functions, refer to the User Guide.
You should have received an invitation email to join a workspace on Fabric Genomics' Opal Platform. If you have not, contact firstname.lastname@example.org. Open the invitation email and use the following steps to create an account in Opal:
- Click on the Sign up link in the invitation email to display the Sign Up dialog box.
- Enter your First Name and Last Name, create a secure Password and click Sign Up.
- Review the Fabric Genomics Opal License Agreement and accept the Fabric Genomics Opal Research Use Acknowledgment by clicking Accept. The Dashboard of your workspace will be displayed.
- From the Opal Toolbar select Admin Settings in the Workspaces dropdown menu to display the Manage Settings page.
- In the Edit Info tab update your workspace information by entering Lab Name and Contact information to populate the header of your clinical reports.
- Click on the Home link in the Opal Toolbar to go to the Dashboard.
You are now ready to upload a genome and create a new project:
- On the Opal Dashboard click on the Upload Genomes icon to display the Upload Genome page.
- Click on the + New Project button to display the New Projects dialog box.
- Enter a Name and Description for the project and click on Create Project.
- Click Choose File to open a file picker dialog box and locate your variant file.
- Enter a Genome Label to name the genome uniquely within this project.
- Enter your organization’s unique sample ID as External ID.
- Select the appropriate option from the Sex dropdown menu.
- Confirm your Assembly Version as GRCh37/hg19 by checking the check box.
- Click Upload.
The genome is queued to the annotation pipeline and after completion of the annotation the genome is accessible in Clinical Reporter.
Before you can launch your first panel test you need to create a panel containing the genes you want to include in your clinical test:
- On the Opal Dashboard click on the Panel Builder icon to display the Panels list view.
- Click on + New Panel to display the Create Panel dialog box.
- Enter a Name, a short Description, and a Test Code to identify your panel. If desired, enter information for the Methodology, Limitations and Regulatory Disclosures to be included on the clinical report generated for this panel.
- Click Create Panel.
- In the Panels list view select Curate Panel from your panel’s Actions dropdown menu to display the Curate Panel page.
- Click on + Add Genes to display the Add Genes to Panel page.
- In the By Symbol tab enter the symbols for the genes to be included in this panel.
- Click Add Genes.
- When done adding all genes, click on < Back to go back to the Curate Panel page.
Set Up Test
Now you can launch you first panel test:
- Go to the Dashboard by clicking on the Home link in the Opal Toolbar.
- Click on the Clinical Reporter icon to display the Clinical Reports page.
- Click on + New Report to display the New Panel Report page.
- From the Choose Panel dropdown menu choose your panel.
- From the Choose Project dropdown menu choose your project.
- Then, select your Genome.
- Click Save.
This will launch the test and the Clinical Reports page will list the test with status Waiting to be processed.
Interpret and Score Variants
When the status changed to Ready for Interpretation (refresh your browser page) you can begin interpreting variants:
- On the Clinical Reports page select Interpret Variants from the Actions dropdown menu of your test to display the Interpret Variants page.
- Click on the column header Review Priority to sort the displayed variants by review priority. Mousing over the Review Priority circles displays an explanation of the color coding.
- Mouse over the row for the top variant to display the Score Variant tab. Click on the tab to open the Variant Detail view with the Condition-Gene tab displayed. Opening the Variant Detail view changes the Scoring Status to Scoring.
- Click on + New Condition-Gene to display the New Condition Gene dialog box.
- Enter the Gene symbol, the Condition, and any Notes about the condition gene association.
- You can also add PMIDs for relevant articles and Prevalence information, choose an Inheritance model, Penetrance level and Age of Onset from dropdown menus.
- Click Save to store the condition gene association.
- Select the condition gene association you want to evaluate this variant for. This switches the Variant Detail view to the Score Variant tab.
Now you begin the scoring the variant using the ACMG Scoring Criteria which follow the ACMG Standards and Guidelines:
- The Score Variant tab is displaying the first ACMG Scoring Criteria.
- The Scoring Tools section will display the relevant data for this variant to help you decide whether the criteria is met. Selecting Yes or No will advance to the next criteria. You can also skip criteria.
- As you are going through the 28 ACMG scoring criteria the Inferred Class, initially displayed as Uncertain Significance in the header bar of the Score Variant tab, will change based on your responses. In the Scoring Summary a summary of the scoring criteria is displayed.
- You can set the classification at any time for this variant. Click on Set Classification to open the Set Classification dialog box.
- Confirm the inferred class by clicking Set Classification or override the inferred class by selecting your desired classification in the dropdown menu, then click on Set Classification. The classification and condition will now be displayed in the Class (Condition) field for this variant. A record of this scoring session will also be entered in the Scoring History and is visible for any future Interpretations of this variant in this workspace.
- To accept this classification as the final class for this variant click Finalize as Scored to open the Set as Scored dialog box and confirm by clicking Set as Scored. Now this classification cannot be changed any more for this test.
- In the Report Section field select where to report this variant in the clinical report, Primary Findings or Secondary Findings, or choose Not Reported to omit the variant from the clinical report.
Repeat this process for all variants you want to score for this test.
When all relevant variants are scored you are ready to review and approve the report:
- On the Interpret Variants page click on Review Report to open the Review Report page.
- Enter patient specific information:Last Name, First Name, Patient DOB, Patient Age, Accession ID, Patient Sex, Patient Ethnicity, Indication for Testing, Date Specimen Collected, Date Specimen Received, Specimen Type. High-volume labs can use the Fabric Genomics API to input this information programmatically.
- Enter your desired text for the result of this test in the Result section of the report.
- The Summary field is prepopulated with the Scoring Summary for each reported variant and the Gene Description for the respective genes, the Recommendations, Test Methodology, Test Limitations and Regulatory Disclosures fields are prepopulated from the report template and the Lab Contact from the Workspace Settings. If desired, you can update these fields for this report here.
- When done with all edits select Submit for Approval from the Set Status dropdown menu. The Confirm Submission dialog box is displayed.
- Check the checkbox to verify that you reviewed the test results and click Confirm.
The Clinical Reports page will list the test now with status Waiting for Approval.
The report is now ready for final approval. To approve a report you need Lab Director permission in the workspace:
- On the Clinical Reports page select Approve Report from the Actions dropdown menu of your test to display the Approve Report dialog box.
- Check the checkbox to verify that you reviewed and approved the test results and click Approve. The Clinical Reports page will list the test now with status Approved.
- Select View Final Report (PDF) from the Actions dropdown menu to download the final report in PDF format.
Congratulations, you have created your first clinical report with Opal!