How to Use the Case Grid¶
This section provides details about the Case Grid within the GMS Interpretation Portal, including its main pages and functionalities. Users can access this interface from the landing page of the service or via the "Review Cases" button in the header of the GMS Interpretation Portal.
Video Tutorial¶
The following video offers an overview of the Case Grid, including instructions on how to use the status tabs, filter and sort data, and search for cases. You can also download a guide here.
Case Grid Guide¶
The following table provides an overview of the functionalities within the Case Grid. You can also download this guide here.
Key
| # | Section | Description |
|---|---|---|
| 1 | Review Cases | Navigates to the main cases page, sorted into different status tabs. |
| 2 | Service Desk | Directs to the Genomics England service desk portal to log tickets. |
| 3 | Identity Check Failures | In the Lyra release, the SNP check was removed from the case dispatch workflow. Therefore, the Identity Check Failures and Identity Check Pending statuses are no longer relevant, and no cases will appear under these tabs. |
| 4 | Identity Check Pending | See above. These statuses are no longer relevant. |
| 5 | Ready to Dispatch | Referrals in this tab have an interpreted genome generated by Genomics England but have not yet been sent to Decision Support Systems. For cancer cases, preliminary and supplementary reports are available to download. |
| 6 | To Be Reviewed | Referrals in this tab are ready to be reviewed by GLHs in their Decision Support System. |
| 7 | Pending Outcomes | Referrals in this tab have been reviewed in the Interpretation Portal or DSS, and a summary of findings has been generated (a preliminary report for cancer cases), but the reporting outcomes questionnaire has not yet been completed. |
| 8 | Reported Cases | Referrals in this tab have a summary of findings and a completed reporting outcomes questionnaire. These cases are considered "closed" but can be re-reviewed at any time using the Interpretation Browser. |
| 9 | Filter Options | Users can filter referrals by type (rare disease, cancer) or by GLH association. Unchecking “View My Cases” will list all cases from the GMS. |
| 10 | Search by Personal Identifiable Data | Search for interpreted referrals using NHS number or other PID. See Figure 2. |
| 11 | Search Case Grid | Search/filter the list of referrals by parameters such as Interpreting or Requesting Organisation, clinical indication, referral ID. |
| 12 | Case | Displays Referral ID and patient identifiable information of a referral. |
| 13 | Clinical Indication | Shows the clinical indication for a referral and the clinical indication code. |
| 14 | TOMS Order Date | Date of test ordering. |
| 15 | DSS Arrival Date | Date the referral has successfully arrived in the DSS. |
| 16 | Status | Status of the referral. |
| 17 | Case Type | Indicates whether the referral is for rare disease or cancer. |
| 18 | Requesting Organisation | Organisation that requested the test, defined during test ordering. |
| 19 | Interpreter Organisation | Organisation interpreting the test results, defined during test ordering. |
| 20 | Referral Priority | Priority set as “Urgent" or “Routine" during test ordering. |
| 21 | Patient Choice | Classification of patient consent: Green: All sequenced patients have positive genomic testing consent. Amber: At least one sequenced individual’s consent status is “n/a” and none have ambiguous or negative consent. Red: At least one sequenced individual has ambiguous or negative consent. Find more information here |
For each referral on the case grid, the application queries the Test Order Management Service (TOMS) to retrieve Patient Identifiable Data (PID) and inserts it into the case grid (Figure 1). If the application is unable to retrieve this data, an alert "Unable to retrieve patient data" is raised in the case grid. If this message is observed, the Portal remains functional, but PID will not be visible.
Shading of Referrals
Yellow-shaded referrals in the case grid indicate that some draft work has been saved for the case.
Referrals can be flagged with tags, such as "UPD" for cases where a family member is predicted to have Uniparental Disomy. For details of existing case tags, see the Referral Flags page.
Filter and Sort¶
The GMS Interpretation Portal provides an interactive interface for filtering and sorting referrals:
Filter Referrals by Sample Type
By default, the display shows all cases. To view only cancer or rare disease cases, untick the respective boxes.
Filter Referrals by Your Cases
By default, the “View My Cases” checkbox is selected. To view cases from outside your GLH, uncheck this box.
Sort Referrals by Dates
Sort referrals by the date the test was ordered (TOMS Order Date) or the date the referral arrived in the DSS (DSS Arrival Date).
Sort Referrals by Status
Referrals can be sorted by their status. Possible statuses include: [List of statuses].
Sort Referrals by Requesting Organisation
Sort referrals by the requesting organisation defined during test ordering.
Sort Referrals by Interpreter Organisation
Sort referrals by the interpreter organisation defined during test ordering.
Sort Referrals by Referral Priority
Referrals are assigned a priority of Routine or Urgent when ordered. This priority is visible in the Case Grid and on the overview pages of rare disease and cancer referrals.
Note that the priority for cases in the 100K Project was Low, Medium, High, or Urgent. This priority can still be seen in any raw JSON data downloaded from the Portal or CIP-API. For further information, see the CIP-API documentation.
Filter by Patient Choice
Patient Choice classification is visible for both Rare Disease and Cancer cases in the GMS Interpretation Portal. Each case is classified as:
- Green: All sequenced patients have positive primary genomic testing consent.
- Amber: At least one sequenced individual has consent status “n/a” and no sequenced individual has ambiguous or negative consent.
- Red: At least one sequenced individual has ambiguous or negative consent.
Search for Cases¶
Users can search for cases using various parameters such as Referral ID, Clinical Indication, Patient ID, Requesting Organisation, Interpreting Organisation, or NHS number.
To search from the Referral Grid, click the Search by Personal Identifiable Data button. A pop-up box will appear where you can search by NHS number & DOB or by DOB, First name, Last name, and Gender.
This search will filter the grid to show matching referrals.