Workflow
Cancer referrals are registered and dispatched to Decision Support Systems as per the following workflow:
Unlike Rare Disease referrals, GMS Cancer referrals are registered in the Interpretation Portal with a Summary of Findings automatically generated by the Bioinformatics pipeline.
This Summary of Findings, in the form of the Primary HTML can be downloaded from the Cancer Referral Overview Page
Note
Because Cancer referrals already have a Summary of Findings (before they are sent to a DSS) they will automatically be in the “Pending Outcomes” tab until the referral is dispatched to BSVI. Upon loading of the case into the DSS (which should be automatic) the referral moves "back" to the “To Be Reviewed” tab.
It is at this stage at which GLHs are encouraged to begin reviewing the referral.
Using the Cancer DSS¶
From the Cancer Referral Overview page it is possible to view a summary of how many somatic and germline variants have been identified by the Cancer tiering pipeline.
Users cannot view the variants as they can with Rare Disease referrals within the Interpretation Portal, however they can view variant in IGV.js via the Summary of Findings HTML and the Supplementary Findings HTML. Users can also view tiered variant in the Decision Support System (DSS) for further analysis of the data. A new Summary of Findings can be generated by the DSS and sent to the Interpretation Portal should users wish to do this.
Creating a new Summary of Findings in the DSS will move the cancer referral back to the Pending Outcomes tab.
Completing the Cancer Feedback Form¶
Upon completion of the reporting outcomes questionnaire the referral will move to the “Reported Cases” tab.
This is the ‘completed’ state for a referral, unless a new Summary of Findings is generated, in which case, the referral will move to the “Pending Outcomes” tab once more until the questionnaire for that Summary of Findings has been completed.
Users can update their answers on an existing reporting outcomes questionnaire without creating a new Summary of Findings, and this does not change the status of a referral. It will remain in the “Reported Cases” tab.
Note
As with rare disease referrals, when cases have been dormant in the “Reported Cases” tab for over three months, the link out to the DSS will be disabled.