How to use the Case Grid¶
This section details the main pages and functionality within the GMS Interpretation Portal application, the Case Grid. Users can access this interface from the landing page for this service, as well as from the Review Cases button in the header of the GMS Interpretation Portal.
Video Tutorial¶
The following video provides an overview of the Case Grid, including a description of how-to use the status tabs, filter and sort the data and search for cases. Find additional information in the following tabs. A downloadable guide is also available here.
Case Grid Guide¶
An overview of the different functionalities of the Case Grid is shown in the following table, and can also be downloaded here.
Key
| # | Section | Description |
|---|---|---|
| 1 | Review Cases | Takes you to the main cases page, sorted into different status tabs. |
| 2 | Service Desk | Takes you to the Genomics England service desk portal to log tickets. |
| 3 | Identity Check Failures | These are Rare Disease referrals for which the SNPs from array genotyping sent by GLHs to Genomics England via the Sample Matching Service (SMS) do not match the SNPs in the WGS result – i.e. there may be a patient mismatch or the SMS cannot calculate the match based on the SNP data submitted. |
| 4 | Identity Check Pending | Referrals in this tab have yet to have a SNP files uploaded to the Sample matching Service for all sequenced participants. |
| 5 | Ready to Dispatch | Referrals in this tab have an interpreted genome generated by Genomics England but have yet to be sent to the Decision Support Systems. For cancer cases, preliminary and supplementary reports are available to download when in “Ready to Dispatch” |
| 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 the DSS and have a summary of findings 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. Referrals in this tab are considered "closed" but can be re-reviewed at any time using the Interpretation Browser. |
| 9 | Filter options | Users can filter for referrals by rare disease, cancer, or whether they are associated with their GLH e.g. 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 e.g. Interpreting or Requesting Organisation, clinical indication, referral ID. |
| 12 | Case | Referral ID and patient identifiable information of a referral. |
| 13 | Clinical indication | Clinical indication for a referral and the clinical indication code in ( ). |
| 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 | Indication of whether the referral is a rare disease or cancer referral. |
| 18 | Requesting organisation | Requesting organisation defined during test ordering. |
| 19 | Interpreter organisation | Interpreter organisation defined during test ordering. |
| 20 | Referral priority | Referral priority set as “Urgent" or “Routine" during test ordering. |
| 21 | Patient choice | Green: All sequenced patients have a positive primary genomic testing consent. Amber: Consent status of least one sequenced individual is “n/a” and no sequenced individual has ambiguous or negative consent. Red: At least one sequenced individual has ambiguous or negative consent. |
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 is raised in the case grid “Unable to retrieve patient data”. If this message is observed the Portal is still functional, however, it will not be possible to see the PID.
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 e.g. if a family member is predicted to have Uniparental Disomy (UPD), the case could be tagged with “UPD”. For details of the existing case tags, please see the Referral Flags page.
Filter and Sort¶
The GMS Interpretation Portal offers this interactive interface, which enables the users to:
Filter referrals by Sample Type
By default, the dispay shows all the cases, if you wish to only view cancer or rare disease cases, untick the respective boxes.
Filter referrals by Your Cases
By default, the “View My Cases” checkbox above the case grid is selected. If you wish to view cases from an organisation outside of your GLH, uncheck this box.
Sort referrals by Dates
From the column names, you can sort referrals by the date of the test was taken (TOMS Order Date), as well as by the date the referral has successfully arrived in the DSS (DSS Arrival date)
Sort referrals by Status
The possible statuses of the referral could be ...
Sort referrals by Requesting Organization
Requesting organisation defined during test ordering
Sort referrals by Interpreter organisation
Interpreter organisation defined during test ordering.
Sort referrals by Referral Priority
Both Cancer and Rare Disease WGS Referrals in the GMS ordered through TOMS will have either a Routine or Urgent priority assigned to them when they are ordered.
The referral priority set in TOMS can be seen in the Interpretation Portal on the Case Grid and on the overview pages of rare disease and cancer referral.
It is possible to sort referrals on the Case Grid by their priority, however, it is not possible to edit the priority of a referral in the Interpretation Portal
Note
The priority for cases in the 100K Project was Low, Medium,High or Urgent. This priority enumeration can
still be seen in any raw JSON data downloaded from the Portal or CIP-API.
For further information please refer to the CIP-API documentation here
Filter by Patient choice
Patient Choice is a record of the patient choice decisions is visible for both Rare Disease and Cancer cases in the GMS Interpretation Portal, more information can be found in the Patient Choice tab. Each case is classified in one of the following categories:
-
Green: All sequenced patients have a positive primary genomic testing consent.
-
Amber: Consent status of least one sequenced individual is “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¶
From any of the tabs, the user can search for cases through the browser using:Referral ID, Clinical Indication, Patient ID, Requesting Organisation, Interpreting Organisation, or NHS number
When on the Referral Grid click the Search by Personal Identifiable Data button. This opens a pop-up box where you can search for a particular case using either the NHS number & DOB or using DOB, First name, Last name and Gender.
This will search for referrals that exist in the Interpretation Portal and filter the grid to show them.