The Clinical Reports page list all tests and clinical reports performed for any genome in the workspace. From here you can launch new tests, assign reports, interpret variants, and review and approve Clinical Reports.
Opal Clinical can be integrated with EMR systems (such as EPIC and CERNER), allowing the passing of patient information along with an order to Opal and the return of the resulting approved Clinical Report back to the EMR system. If you are interested in EMR integration, please contact firstname.lastname@example.org.
You can reach the Clinical Reports page from:
- Opal Home page >> Clinical Reporter link
- Opal Toolbar >> Clinical Reporter link
- Opal Toolbar >> Menu >> Clinical Reporter link
Clinical Reports Table
The Clinical Reports table lists all reports in the workspace that are accessible to the user based on the user's Workspace Role and Project Roles. The table is sorted chronologically with the newest tests at the top.
- Report ID
- A unique ID for the report.
- Accession ID
- The accession ID for the genome to be tested is usually provided at launch of the test.
- Submitted On
- Timestamp the test was launched.
- Project (ID)
- The name of the project the genome is organized in followed by a unique project ID in parentheses.
- Genome (ID)
- The Genome Label of the tested genome followed in parentheses by a unique ID for the genome. A test launched without a genome selected with display Pending.
- For a panel test the Panel Name is displayed. Clicking on the Panel Name opens the Panel Detail view. For all other tests the test type is indicated here. The list of tests is described under Actions New Report (below).
- Test Code
- For a panel test the Test Code associated with the Panel is shown here.
- Set the filter to display only those results with pending, passed, or failed QC status; or display all results regardless of their QC status.
- Assigned To
- A test can be assigned to a Workspace Member/Admin for variant interpretation and report review. Use the Manage Reports button to assign a report to someone in your workspace.
- The current status of the test or clinical report. The default Clinical Report Workflow uses a set of predefined status settings.
- Waiting for Genome
- When a test is launched with an accession ID but without specifying a genome the status for the test is Waiting for Genome until a genome with this accession ID is uploaded and attached to the report.
- Waiting to be Processed
- The test is queued for processing.
- The test is being processed.
- Ready for Interpretation
- The test is done processing and the variants can now be interpreted.
- Ready to Review
- The variant interpretation is completed and the report has been submitted for review. This status is part of a Clinical Reports Workflow customized by Fabric Genomics to include a review step in the report approval process.
- Waiting for Approval
- A report has been reviewed and can now be approved by a Lab Director or be retracted to edit or add variants.
- A report with the status Approved has been approved by a Workspace Member/Admin with Lab Director permissions. This report can no longer be deleted or edited. You can view the variant interpretation and download the PDF of the final report.
- This test has been cancelled.
- Additionally, custom Statuses and Clinical Report Workflows can be defined. Please contact email@example.com.
- The list of tests can be filtered and searched by the following fields:
- Report ID
- Accession ID
- Test Code
- Report Status
- Assigned To
Enter the search terms into the appropriate field and click Filter. The search terms need to be a full match, but are not case sensitive. Only test/reports matching the search terms are displayed in the table.
Filtering by Projects is also available. Filtering by Projects is a workspace setting that needs to be configured by Fabric Genomics support. If you want this feature turned on in your workspace, please contact firstname.lastname@example.org.
- Clicking the Clear button will clear all filters or search terms to display the full list of tests and reports.
- Test Templates
- Click here to open the Clinical Report Templates page to edit the default texts for Test Methodology, Test Limitations and Regulatory Disclosure for all tests other than panel tests. For panel tests this information is entered when creating or editing the Panel in the Panel Builder.
- Manage Reports
- You can approve or assign multiple clinical reports at once. This is designed to speed up processing and turnaround time.
Note: Batch approval is most useful for negative reports. A custom status can be used to separate Negative from Positive reports. Negative reports could have the special designation “Waiting for Approval (Neg)”, for example. Contact email@example.com if you want to implement custom statuses.You must have Lab Director responsibility to approve reports, though not to assign them.
- On the Clinical Reports page, first select each of the reports that you want to approve or assign, using the left column of checkboxes.
- Click on the Manage Reports button for a drop-down menu, and select either Approve Reports or Assign Reports.
- To Approve the selected report(s): in the dialog box that opens, review the report ID and accession ID of all reports selected for approval. Only reports with status “Waiting for Approval” may be approved, and selected reports in other statuses will not be listed in the Approve Reports dialog box; they cannot be approved. When you are satisfied with your review, click on the Approve Button.
- To Assign the selected report(s): in the dialog box that opens, select the name of the user to whom you want to assign the reports, and click on the Assign button.
- To launch a new test choose the appropriate test from the New Reports dropdown menu.
- A single genome is tested with an existing panel of genes to create a Panel Report. This test is designed for targeted tests, only variants that are in the panel genes and pass any applied filters are included in the test.
- A single genome is tested with VAAST to create a Solo report. All variants that pass any optional filters are included in the report.
- A proband with 2 unaffected parents is tested with VAAST to create a Trio report. All variants that pass any optional filters are included in the report.
- A proband with 2 unaffected parents and an unaffected sibling are tested with VAAST to create a Quad report. All variants that pass any optional filters are included in the report.
- Flexible Family
- A proband and up to 4 affected or unaffected relatives are tested with VAAST to create a Flexible Family report. All variants that pass any optional filters are included in the report.
- The Actions dropdown menu for each test/report provides a variety of options depending on the Status of the test/report. The relationship between Status and the available Actions are based on the default Clinical Reports Workflow.
- Select Genome(s)
- This option is only available when the Status is Waiting for Genome and opens the Select Genome page that allows you to manually select the genome(s) for this test. On the Select Genome page you can also change the Panel, Assay Type, the default Filter and Accession ID for the test.
- Edit Patient Information
- Select this option to open the Edit Patient Information page where you can upload, manually enter or update patient data to be added to the Clinical Report. This can be done at any Status except Approved.
- Quality Control Data
- Select this option to open the Quality Control Data page to enter or update quality control data for this test. This option is only available if an Assay Type was specified when launching the test.
- Tests/reports can be assigned and unassigned to a Workspace Member/Admin for interpretation and/or review.
- Import Candidate Variants
- Select this option to import variant interpretation information from an existing clinical report.
- Interpret Variants
- This option is available when the Status is Ready for Interpretation and opens the Variant Selection and Variant Interpretation pages where you can view, select and interpret the variants for this test/report.
- Export Variants To Be Confirmed
- Variants that have been marked for confirmation can be exported in csv format.
- Review Variants
- This option is available when the report has been submitted for review or approval and the Status is Ready to Review or Waiting for Approval.
- View Draft Report
- Before approving a report a PDF of the draft report can be downloaded and reviewed.
- Retract Report
- Retracting a report will set the status from Waiting for Approval back to Review Variants.
- Approve Report
- A Workspace Member/Admin with Lab Director permissions can approve a clinical report that has the Status Waiting for Approval. Once a report has been Approved it can no longer be deleted or modified.
- View Interpretation
- Once a Clinical Report is Approved the interpretation of the variants can only be viewed in the Review Variants page.
- View Final Report (PDF)
- Once a Clinical Report has the status Approved the PDF of the final report can be downloaded and viewed with this option. The file is named by the Accession ID.
- Report History
- A log of report events is displayed. For example, entries into the Report History are created when patient information or report fields are modified, variants are added to a report section, or quality control data are added to report.
- Delete Report
- A report can be deleted until its status is Approved. Once a report has been Approved, it can no longer be deleted.