IP integration¶
The New IB is connected to the Interpretation Portal via the CIP-API, similarly to Congenica. Compatible cases are dispatched from the Genomics England Rare Disease pipeline into the New IB by the CIP-API, and the case is then loaded (ingested) into the New IB system, ready for clinical analysis.
At the end of the interpretation, and upon closing a case in New IB, the relevant interpretation outcomes (reported variants, their associated interpretation data and the case overall comment) is passed on from the New IB to the CIP-API, and to CVA, as per the existing process.
All of these communications operate via updates to the IP Workflow Status, via the same operational model that exists with Congenica; through the IP Workflow Status, the CIP-API is informed of changes to case status in the New IB. Updating case status in the New IB results in a Workflow status update in the IP, as per this table:
Warning
The New Interpretation Browser button in the IP that launches a case in the New IB is always enabled, even before the New IB has completed ingestion. Please wait until the IP Workflow Status shows as Pending Review before attempting to view in the New IB.
| New IB Case Status | IP Workflow Status | Tab in IP |
|---|---|---|
| Ready for analysis | Pending Review | To Be Reviewed |
| In progress | In Progress | To Be Reviewed |
| Awaiting second review | In Progress | To Be Reviewed |
| Closed | Closed | Reported Cases |
Are cases still dispatched to the other systems (Interpretation Portal/IB and Congenica), in addition to the New IB?
Yes, all cases that have been dispatched to the New IB will still be present in the IP and dispatched to Congenica. Existing products and workflows are unchanged; these products can still be used in interpretation of RD GMS cases. In the longer term, the New IB is intended to replace the existing IP/IB.
If I analyse a case in the IP, will I be able to see my interpretations / selections in the New IB, and vice versa?
No. Whilst the New IB and Congenica both connect to the CIP-API, they are not connected to one another; interpretation done in one is not propagated to the other.
If I analyse a case in the New IB, can I re-analyse it (e.g. create new Summary of Findings) in another tool?
Yes. If you wish to re-analyse the case in another tool, you can re-open it, analyse it and create the Summary of Findings in the Portal IB or in Congenica, then complete the Exit Questionnaire to close it. The updated data will be sent to CVA, as per the existing process.
For further details on IP integration, please visit the Interpretation Portal user guide.
Case closure integration¶
Closing a case in the New IB will change the IP Workflow Status of the case to New IB: Closed in the Portal. The case will move directly onto the Reported Cases referral tab (skipping the Pending outcomes referral tab). Cases are no longer put in the Pending Outcomes tab because the Exit Questionnaire (EQ) is no longer required to be completed manually, as all the relevant interpretation and outcome data is now automatically collected by the New IB during case interpretation. An EQ and Variant Interpretation Logs (VILs) are still generated in the back-end and send to CVA for display, but this no longer requires manual intervention. The Summary of Findings (SoF) is also automatically generated in the Portal, for the case.
If a case is closed in the New IB or any other RD interpretation system (IP/IB or Congenica), is it also closed on all others?
No. A case that is closed in the New IB (IP Workflow Status = Closed) is automatically considered a Reported case in the IP, closing it off in the Portal, without the need for further intervention. It will automatically appear in the Reported Cases referral tab. Cases closed in Congenica, however, (IP Workflow Status = Closed), are not immediately closed in the Portal, as the Exit Questionnaire (EQ) still needs to be completed. The case is simply put in the Pending outcomes tab, requiring further manual intervention to move it to Reported Cases. Closing a case in the New IB has NO impact on the status of the case in Congenica (if the case is loaded and available there), and vice-versa. New IB and Congenica do not communicate.
Analysing and closing a case in the IP/IB does NOT lead to updated case statuses in the New IB nor Congenica. A case that is closed via the IP will remain open (IP Workflow Status = Pending Review) in New IB if the analysis wasn’t conducted there, despite being in the Reported Cases tab in the Portal. This is the same in Congenica at present, with the difference being that case archiving is in place in Congenica already. Case archiving is not yet in place in New IB, thus for now, cases will remain indefinitely present in the New IB even when analysed in other systems. We will be engaging with Clinical Scientists to define the optimal case archiving rules in the short future and this is a requirement to ensure that New IB continues to perform reliably at scale.
Would data be over-written if a case is closed in Congenica after it has been closed in the New IB?
No, data is not overwritten. The current behaviour of the Portal is that for a case to be marked as reported (Reported Cases), there needs to be an EQ created against the latest Summary of Findings (SoF). If the case is closed in Congenica after it has been closed in the New IB, a new SoF will be sent from Congenica to the Portal, which will place the case in Pending Outcomes and require an EQ to be completed against this latest SoF to move the case to the reported state. All SoFs are present in the IP, so you can see them all. CVA will display the latest one but all VILs, and EQs will be present in CVA too - nothing is overwritten.
Abbreviations
| Abbreviation | Definition |
|---|---|
| ACGS | Association for Clinical Genomic Science |
| ACMG | American College of Medical Genetics and Genomics |
| CDS | Coding DNA Sequence |
| CNV | Copy Number Variant |
| CVA | Clinical Variant Ark |
| New IB | New Interpretation Browser |
| GEL | Genomics England |
| GMS | Genomic Medicine Service |
| GLH | Genomic Laboratory Hub |
| HGVS | Human Genome Variation Society |
| HTML | Hyper Text Markup Language |
| HSCN | Health and Social Care Network (N3) |
| IGV | Integrative Genomics Viewer |
| IP | Interpretation Portal |
| NGIS | National Genomics Informatics System |
| PID | Patient Identifiable Data |
| QC | Quality Control |
| SO | Sequence Ontology |
| SNV | Single Nucleotide Variant |
| SV | Structural Variant |
| TOMS | Test Order Management Service |
| UAT | User Acceptance Testing |
| VCF | Variant Call Format File |
| WGS | Whole Genome Sequencing |