FAQs¶
Accessing cases¶
How can I access the New IB?
Please visit the gettting access page to learn how to access the New IB.
Which cases can be analysed in New IB?
Currently, the New IB, allows for the review of GMS cases that are SNV-only, i.e. those without Tiered CNVs nor Tiered STRs. This represents ~18% of all GMS cases (based on analysis of past cases). Support for CNVs and STRs will be added shortly. CNV development is already underway.
Where can I select cases for analysis in New IB?
Please visit the Opening a referral in the New IB section in the user guide.
Can I open / review cases in the New IB without needing to use the IP?
No - to view cases in the New IB you will need to visit the referral page for that case via the IP. For further details, please visit the Opening a referral in the New IB section in the user guide.
Do I receive email notifications about cases being ready for analysis in the New IB?
No, email notifications are currently sent via CIP-API and are not yet implemented via the New IB, as case admin and management still happens at the IP level. We will introduce email notifications in the future, when we port over the case list functionality from the IP into the New IB.
Can I request a training session for my GLH/lab?
Yes - please visit the training page for further details.
Development of existing products¶
Will the existing IB/Portal still be undergoing development, now that New IB is released?
There will be minimal (if any) development effort put into the existing (historical) RD interpretation products - Interpretation Portal and the Interpretation Browser (which is the section within the Portal that contains the list of variants). Development effort in existing systems will solely be focused on ensuring that there are no breaking changes and no regression in existing functionality. New feature requests for RD interpretation will be assessed on a case-by-case basis but will most likely only be actioned in the New IB. Ultimately, the New IB will replace these existing systems.
The New IB addresses all user needs currently fulfilled by the IP/IB, minus support for CNVs and STRs. It also fulfilfs extra needs for SNVs not currently covered by the IP/IB, and has a more intuitive, responsive and future-proof user interface than the existing systems. Remaining areas (e.g. case list, BAF plots, gene panel coverage, download of VCF files) will be ported over in due course.
Data storage / flow¶
Can I download the Summary of Findings for my case (e.g. which includes the coverage report) when analysed via New IB?
Yes, all cases that are analysed in the New IB will have a SoF created in the Portal, as per the existing process. SoFs are not yet available in the New IB - this will be a future enhancement.
Are analysed and closed cases in the New IB sent to CVA? What information goes into CVA?
Yes, cases in the New IB are sent to CVA, as well as their interpretation and outcome data, as per the usual process. The New IB automatically generates the Summary of Findings (SoF) for the case upon case closure in the New IB. The SoF is then made available in the Portal. The Exit Questionnaire is also automatically created (without user input) for the case. Both the SoF and EQ are sent to CVA, as per usual, alongside Variant Interpretation Logs.
At the variant level, the following information is sent to CVA, from New IB: - Variant classification (or exclusion) - Variant comment - Variant contribution to phenotype - Transcript associated with the classification
All of the above are mandatory for variants classified as Pathogenic or Likely Pathogenic, and optional for all other variants.
At the case level, the overall case comment (which is typically filled in to summarise the findings of the analysis), is sent to CVA too.
Can an analysis log be exported for traceability and local storage?
Please visit the audit logs page for details.
Are Diagnostic Discovery results shown in the New IB? Is there an Add variants from VCF button like in the existing IP/IB?
Not yet. The New IB supports the whole-genome, showing all variants that are part of the Interpreted Genome (as output by the Genomics England Rare Disease pipeline), plus all variants included in the VCFs of the case. Therefore, one does not need to utilise a Add variants from VCF functionality, as the variants are all already present in the interface, so there is nothing to add. However, at present, the New IB still does not have filters in place, meaning the ability to search for a specific Diagnostic Discovery finding (e.g. intronic variant in gene X) is limited and sub-optimal.
We are working to introduce filters and presets, which will allow fast identification of such variants. In parallel, we’re working with the Diagnostic Discovery team to define how might we share and surface Diagnostic Discovery findings directly from the New IB.
If this is important to you or you have ideas on this, let us know by visiting the help and feedback page.
Re-analysis¶
Can I request re-analyses via the New IB? Where do I request re-analysis/re-issues if I analysed a case in the New IB?
The process for requesting re-analysis is unchanged for now and thus needs to be requested via the Service Desk here.
Is the re-analysis process still the same (via JIRA ticket), and what effect will this have on the stored comments/logs in New IB?
Yes, the process for requesting re-analysis is unchanged for now and thus needs to be requested via the Service Desk here. A new referral ID will be created, as usual, and the case will be re-dispatched to the New IB. Although only the latest version of the case will exist in IP, both versions of the case will be visible in the New IB (please ensure the latest version of the case is analysed and closed, so that the corresponding case in the IP is marked as reported and data sent to CVA). VILs for all past reviews will be visible in CVA, so no data is lost.
Feedback and limitations¶
Where can I submit feedback or new ideas?
Please visit the help and feedback page and follow the links provided.
Where can I log bugs or incidents?
Please visit the help and feedback page and follow the links provided.
Where can I get support?
Please visit the help and feedback page and follow the links provided.
Are there any limitations that impact the interpretation process that I should know about? What are the mitigations or workarounds?
For details on known limitations of the product, please visit the product limitations page.
Where can I see what is being considered for future releases?
Please visit the roadmap page and view the interactive roadmap.
Is HGMD Pro supported in New IB?
No, HGMD Pro isn’t supported as Genomics England does not hold a licence for it.
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 |