Case Summary¶
Opening a case from the case list, or the IP (when the product is released to beta) navigates to the case summary page by default.
This page provides the ability to:
- View case and patient information
- View any case warnings displayed across the top of the page
- Link out to the SNV, CNV, and STR pages
- Check the version of the tiering software used
- Check the release version of the New Interpretation Browser (New IB)
Case Warnings¶
Case warnings will appear at the top of the screen in a banner, as shown below.
Please refer to the Rare Disease Genome Analysis Guide for further information. The warnings could include the following:
Key
| Warning | Description |
|---|---|
| Potential low quality sample | Sample fails one or more sequencing quality control thresholds applied for evenness of coverage, GC dropout, AT dropout and average fragment size. As a result, there may be an increased risk of false positive or negative variants. |
| Consent status | The patient has changed their mind about consent for this test, please discuss next steps with the referring clinician |
| Closed case | This case has been closed and you cannot take actions such as commenting, flagging, classifying and exporting. To reopen and make changes to this case, the case status must be updated |
| Case permissions | You do not have the permissions to take actions, such as commenting, flagging, classifying and exporting. Talk to an administrator if you want to make changes to this case. |
| PID permissions | You don't have the permission to view patient identifiable information with your current permissions, if you think this is wrong, get in touch with Service Desk |
| No warnings | If there aren’t any warnings reported, there won’t be any shown on the case summary page |
Case Header¶
The case header contains basic case information. Additional patient and case information can be found on the top right of the banner by clicking the respective drop down menus.
Key
| # | Section | Description |
|---|---|---|
| 1 | First and last name | Patient’s first and last name as captured from TOMS |
| 2 | Year of birth | Patient’s year of birth as captured from TOMS |
| 3 | NHS number | Patient’s NHS number as captured from TOMS |
| 4 | Patient info | Click here for additional patient information |
| 5 | Case info | Click here for additional case information |
| 6 | Current user | Initials of current user. When clicked on, displays the current user's name, email and a log out button |
Patient Info¶
Key
| # | Section | Description |
|---|---|---|
| 1 | Name | Patient’s name as captured from TOMS |
| 2 | Date of birth | Patient’s date of birth as captured from TOMS |
| 3 | Genomic sex | Patient’s sex as captured from TOMS |
| 4 | NHS number | Patient’s NHS number as captured from TOMS |
| 5 | Patient ID | The patient’s ID as captured from TOMS |
| 6 | Clinical indication | Patient’s clinical indication from the Test Directory, defined during the test order. |
Info
Non-NHS users will be unable to see certain patient information, including the patient's name, date of birth and NHS number. Only the patient sex, patient ID and Clinical Indication will be visible.
Case Info¶
Key
| # | Section | Description |
|---|---|---|
| 1 | Referral ID | The Referral ID for the patient |
| 2 | Case status | Interpretation Status of the case, e.g. whether the analysis is in progress or the case is awaiting authorisation. See case management for more info |
| 3 | Update case status | This button can be used to update the case status (for more details, see case management) |
For information on the case status, please see case management.
Patient and Case Information¶
Key
| # | Section | Description |
|---|---|---|
| 1 | Patient ID | The patient’s ID as captured from TOMS |
| 2 | Proband choice | The patient’s consent status, e.g. Yes or No |
| 3 | Test order date | The date the test was ordered |
| 4 | Analysis issue date | The date the referral has successfully arrived in the New IB |
| 5 | Referral Priority | Priority for the case, e.g. “Routine” or “Urgent” |
| 6 | Referral ID | The Referral ID for the patient |
| 7 | Ordering hopsital | Requesting organisation defined during test ordering |
| 8 | Interpreting lab | Interpreter organisation defined during test ordering |
Interpretation Summary¶
Key
| # | Section | Description |
|---|---|---|
| 1 | Interpretation Summary | Summary of the tiered SNVs, CNVs and STRs identified by the Rare Disease interpretation pipeline |
Additional information¶
Here, you can find additional information on the case. For example, the tiering software version used for the case.
Key
| # | Section | Description |
|---|---|---|
| 1 | Tiering software version | The version of the tiering pipeline used to prioritise the variants into tiers. |