Now within Opal, you can capture and track quality control metrics as part of your workflow.
First you need to set up the quality control metrics you want to track using an Assay Type in your workspace.
In Opal, an Assay Type is typically a combination of a sequencer and technical assay, where the quality metrics and expected performance characteristics are the same. An Assay Type can be used for one or multiple tests in a workspace.
From the Home Page, click on the Assay Type icon.
A workspace admin sets up and manages assay types. Other users in the workspace can view existing assay type definitions.
To create an Assay Type as workspace Admin:
- Click on the green "New Assay Type" button
- Enter a name and a description. As a best practice, the name should be the name of your sequencer and/or your technical assay. For example "MiSeq" or "HiSeq - TruSight One"
- Click the blue "Save"button.
Now, add the Quality Control metrics to the Assay Type:
- From the Actions drop down menu, select "Quality Control Fields"
- Enter the Quality Control metric you want to track, and the field type:
- Text: Numerical or text values
- Multi-line text: Longer text information
- Date: Date values
Associate Genes to Assay Type
A lab may want to provide an ordering physician with coverage information of the genes in a panel, prior to ordering a panel test for a patient. To support this, genes with low coverage information can be entered in Opal, and a pre-test report generated for a panel that covers all genes in the assay, or for an in silico panel that covers a subset of the assay.
To upload genes and low coverage information, on the Assay Types page, click the Actions drop-down menu for the selected assay and select "Upload Genes". In the dialog box, upload an Excel or csv file. Downloadable templates are provided in the dialog box.
To generate a pre-test report, see Creating Pre-Test Reports.
Managing Quality Control Metrics in Clinical Reporter
Once an Assay Type has been created in a workspace, an Assay Type drop down menu will be displayed in the New Report pages. When an Assay Type is selected for a report, quality control metrics can be added.
To add quality control metrics:
- Select "Quality Control Data" from the Actions drop down menu in a report.
- In the New Quality Control Data modal, enter the values for the sample.
- You can also include information in the Notes field.
- Click the blue "Save" button
Now, on the Clinical Reports page a white and black "QC" icon will be displayed next to the Status of the report.
Note that genomes can be associated with new reports at any time. This is not dependent on passing quality control.
Reviewing and Approving Quality Control Data
To review and approve quality control data:
- Select "Quality Control Data" from the Actions drop down menu in a report. The quality control metrics for a sample will be displayed on the page. Quality control data that falls outside of minimum or maximum thresholds will be highlighted in red.
- From the Actions dropdown menu, select "Pass" or "Fail".
- In the dialog box, you will need to confirm your action for audit purposes.
Now, on the Clinical Reports page next to the report status, there will be a green QC icon if the sample passed, or a red QC icon if the sample failed.
If a sample fails quality control and you re-run it, you can create a new Quality Control Data record to capture the metrics from the new run. Approval of this new quality control data will change the QC Status to green / approved, but the previous run data will still be recorded for audit and shown in the Quality Control Data page for the sample.