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:

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.
Link out to Cancer Decision Support System (cDSS)

In addition to the Primary and Supplementary HTML files, from the Cancer Referral Overview page users can link to the Cancer Decision Support System (cDSS) to review variants.

Note

Users will no longer be able to generate a new Summary of Findings in the cDSS. The HTML report generated by the bioinformatics pipeline will be used as a summary of findings, interpretations can be captured in the cDSS at a variant level. Please see the cDSS user guide for further information.
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

Last update: 2023-09-18