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RD Workflow

Before a rare disease referral is registered in the CIP-API, the “patient choice” (consent) is checked for each patient in that referral. If consent for any patient in a referral is not available, the referral will be blocked and will not be visible to users in the portal. The referral will not be auto-dispatched to Congenica unless the patient consent is rescinded after dispatch.

See a Figure detailing this workflow:

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Lyra Release Update

In the Lyra release, the SNP check in the SMS has been removed from the case dispatch workflow. For detailed information and guidance on the updated workflow, please refer to the SMS Help Page.

When the referral arrives in the Interpretation Portal, it undergoes a Sample Matching Service (SMS) check. This check ensures that the identity of the patients in the referral are correct.

This can have 3 different outcomes:

  1. Pass SMS checks Referrals that pass the SNP check are deposited into the “Ready to Dispatch” tab on the Interpretation Portal. The case will be in the queue to be automatically dispatched to the DSS.
  2. Pending SMS checks Referrals can be missing the associated SNP VCF as it has not yet been uploaded by the GLH. In this scenario the SNP check is classed as “pending” and is deposited into the “Identity Check Pending” tab.
  3. Fail SMS checks Referrals that fail the SNP check are deposited into the “Identity Check Failures” tab. They will be flagged with a “cross” next to the sample LP number on the case page. A referral is this tab will not be dispatched to a DSS until the identify check issue is resolved e.g. a new SNP VCF is uploaded by the GLH.

Another SMS check will be automatic if a new SNP VCF has been uploaded in the case where there has been a failed SMS check previously. A successful SMS check is indicated by a tick icon next to the sample ID. If SMS checks pass for all samples in the referral, it should then proceed to the “Ready to Dispatch” tab and be in the queue to be automatically dispatched to the DSS.

Note

It is still possible to create a Summary of Findings (“Clinical Report”) from a referral if it is in either the “Identity Check Failures” or “Identity Check Pending” tabs using the Interpretation Browser. Creating a Summary of Findings from a referral which fails SMS checks is strongly advised against.

Upon successful loading of the referral in the DSS it moves to the “To Be Reviewed” tab and the DSS link from the case page is activated.

If the referral fails to load in the DSS it will remain in the “Ready to Dispatch” tab. Please inform the Genomics England Service Desk if you believe a case has failed to load in the DSS.

Movement of a referral into the next stage – from “To Be Reviewed” into “Pending Outcomes” (and into the next tab of the Interpretation Portal) - requires a Summary of Findings (known as a “Clinical Report” in the CIPAPI) to be generated in either the DSS or within the Interpretation Portal.

Without a Summary of Findings, the case will remain at “To Be Reviewed””.

When a Summary of Findings has been created, the referral will move to the “Pending Outcomes” tab of the Interpretation Portal.

If a “Reporting Outcomes Questionnaire” is completed for a Summary of Findings, the referral will move to the “Reported Cases” tab in the Interpretation Portal. Unless a new Summary of Findings is generated for the referral, the referral will remain in the “Reported Cases” tab and in three months of residing in this state, the URL linking out to the DSS will be retired. This is considered the “Completed” state.

Note

If a user wants to update a closed referral to correct a mistake or classification in CVA, they will have to create a new SoF in the Interpretation Portal or CVA. The referral will move back into the “Pending Outcomes” tab until a new Reporting Outcomes Questionnaire is completed. Note that when the report is downloaded, the “patient choice” is checked again.

Updating a Closed Referral

If a user needs to correct a mistake or update the classification in CVA (e.g. for a new Diagnostic Discovery Finding) for a previously reported referral, they should follow these steps:

  1. Create a New SoF:

    • In the Interpretation Portal or DSS, generate new SoF (see the workflow here for quick steps).
    • The closed referral will be moved back into the "Pending Outcomes" tab.
    • On the referral page you will see a new SoF version has been created

  2. Complete a New RoQ:

    • Users are required to complete a new RoQ for the new SoF version.
    • This step ensures that the referral is closed and the latest information is captured accurately.
    • See the workflow here for quick steps.

By following these steps, users can effectively update closed referrals in CVA, ensuring the accuracy and completeness of the information in the system.

It's important to note that when the report is downloaded, the "patient choice" is rechecked to ensure compliance with consent requirements.

Last update: 2024-01-30