Cancer Referral Overview Page¶
Outline¶
To open a Referral and see an overview – click on the Referral ID in the Referral Grid for the case you wish to review.
Key
| # | Section | Description |
|---|---|---|
| 1 | Patient Summary | The Referral ID for the patient. |
| 2 | Referral Priority | Priority for the case, e.g. “Routine” or “Urgent”. |
| 3 | Case Status | Interpretation Status of the case, e.g. whether or not it is has a SoF ready. |
| 4 | Workflow status | The workflow status for the referral. |
| 5 | Patient | Link out to TOMS. If available, PID will be queried from TOMS and displayed here. |
| 6 | Interpretation Flags | This flag describes the TINC status of the sample. |
| 7 | Interpretation Services | List of the interpretation services that have been applied to the case. |
| 8 | Sex | The sex of the patient. |
| 9 | Patient Choice | Yes- patient has agreed to the test, No- patient has declined the test, NA- patient choice not relevant. |
| 10 | Interpreting Organisation | Defined during test ordering. |
| 11 | Requesting Organisation | Defined during test ordering. |
| 12 | Notes | Notes added to the case during Test Order. |
| 13 | DSS | For example, Illumina BaseSpace Variant Interpreter (BSVI) for cancer referrals. |
| 14 | Tumour Local ID | Information about the Tumour types; primary or metastatic; presentation and other details about the tumour. |
| 15 | Tumour Content | Tumour content is displayed as High, Medium or Low with an accompanying tumour content percentage. The thresholds for High, Medium and Low are as follows: Low is <40% tumour content. Medium is 40-60%. High is >60%. Please note that the tumour content displayed here in the Portal is the content entered by the GLH at the point of test order. |
New Feature: TINC
- TINC High: The germline sample for this patient is likely to be contaminated with DNA derived from the tumour. Consequently, the sensitivity of somatic variant detection may be reduced, potentially resulting in an increased risk of false negative findings. To mitigate the potential loss in sensitivity, the results of somatic variant calling with an unmatched germline sample are included in this analysis alongside subtraction with the patient’s germline sample.
- TINC Low: The germline sample for this patient is likely to be contaminated with DNA derived from the tumour. Consequently, the sensitivity of somatic variant detection may be reduced, potentially resulting in an increased risk of false negative findings. To mitigate the potential loss in sensitivity, the results of somatic variant calling with an unmatched germline sample are included in this analysis alongside subtraction with the patient’s germline sample.
- TINC Error: The results of the computational estimation of tumour in normal contamination (TINC) are not reliable for this patient (which may be due to low tumour content in the tumour sample, or very high tumour contamination in the germline sample). Consequently, TINC cannot be excluded and the sensitivity of somatic variant detection may be reduced, potentially resulting in an increased risk of false negative findings. To mitigate the potential loss in sensitivity, the results of somatic variant calling with an unmatched germline sample are included in this analysis alongside subtraction with the patient’s germline sample.
For further information on the TINC pipeline please refer to the Cancer Genome Analysis Guide
Functionality¶
The Cancer Referral Overview enables users to:
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View a summary of the domained somatic and tiered germline variants have been identified by the Cancer interpretation pipeline.
Unlike for Rare Disease referrals users cannot view the tiered variants in Cancer referrals in the Interpretation Portal.
All Cancer variant information, and links to IGV, are found in the Cancer Summary of Findings HTML and the Supplementary Findings HTML.
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Link out to Decision Support Systems (DSS)
In addition to the Primary and Supplementary HTML files, from the Cancer Referral Overview page users can link to the Decision Support System (DSS) to review variants.
A new Summary of Findings can be generated by the DSS and sent to the Interpretation Portal should users wish to do this.
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Download Feedback forms and Files
From the Cancer Referral Overview page users can access the Cancer Referral Feedback form
Any files associated with the referral can be downloaded from here, including the Primary and Supplementary HTML files
Cancer file download¶
From the main cancer case page the associated cancer files can be downloaded.
For additional technical details of the Cancer Reports please refer to Technical Documentation available for download here and the Cancer Genome Analysis Guide