New Interpretation Browser user guide¶
Accreditation
The New IB is UKAS accredited against ISO 15189:2022 as detailed in Genomics England’s Schedule of Accreditation.
The New Interpretation Browser (New IB) can only be accessed by users connected to the HSCN network and using their NHS Smart card. Your credentials will have been set up by the Genomics England Service Desk.
Currently, the New IB, allows for the review of GMS cases that are SNV-only, i.e. those without Tiered CNVs nor Tiered STRs. These are defined here for simplicity as “compatible” cases. Support for copy number variants and short tandem repeats will be coming soon.
Disclaimer
The clinical interpretation of referrals and variants should follow your local best practice guidelines
Only compatible cases are dispatched to the New IB, in addition to also being dispatched to Congenica (existing processes for Congenica and IP/IB are unchanged).
The New IB is only available to use for cases analysed from the launch date; past cases will require analysis using the alternative existing systems.
Opening a referral in the New IB¶
Non-compatible cases
Non-compatible cases will not display a New IB workflow status, and the New Interpretation Button in the Referral Page will be greyed out. This means the button is non-functional and will not link out to the New IB, as the referral does not exist in the New IB system.
Your interpretation journey starts in the Interpretation Portal (IP), where the case/referral list is located. To log in to the IP, click the button below and use your credentials:
Access the GMS Interpretation Portal
The IP features six tabs, each representing different referral statuses. Within each tab, you will find a referrals grid, which is the primary interface for locating specific referrals. Here, you can select a case to analyse.
Cases that are ready for analysis will be displayed in the To be Reviewed tab, identifiable by their Workflow Status in the referrals grid: "New IB: Pending Review" (this workflow status is also visible on the case referral page). For further details on IP integration, including workflow status, please visit the IP integration page.
After clicking on a compatible case, an active New Interpretation Browser button will be visible in the Referral Page. Clicking on this button will open the case summary page for the relevant case in the New IB, ready for your interpretation.
Site navigation¶
Navigate between the case summary page, variant grid page, and reporting page using the navigation sidebar. An info overlay is also available, providing linkouts to additional resources (e.g. release notes, roadmap, feedback form, etc). You can view the info overlay by clicking on the i icon at the bottom of the side navigation.
Side navigation¶
When viewing a case, the navigation sidebar can be used to navigate to different pages in the New IB. For further details on each page, see the key below.
Key
| # | Section | Description |
|---|---|---|
| 1 | Case summary | Navigates to the Case Summary page. |
| 2 | Small variants | Navigates to the Small variants list. This page can also be navigated to from the case summary page by selecting View List under the interpretation summary. |
| 3 | Copy number variants | Navigates to the Copy number variants list. This functionality is currently under development and is not yet available. |
| 4 | Short tandem repeat variants | Navigates to the Short tandem repeats variants list. This functionality is currently under development and is not yet available. |
| 5 | Reporting | Navigates to the Reporting page, where a summary of variants to report, other reviewed variants, and excluded variants is provided. |
| 6 | Info | Opens an overlay with link-outs to various resources |
Info overlay¶
This overlay provides link-outs to various resources. For further details on each resource, see the key below.
Key
| # | Section | Description |
|---|---|---|
| 1 | Contact support | Link-out to Service Desk where bugs or incidents can be submitted |
| 2 | New IB user guide | Link-out to the New IB user guide |
| 3 | New IB release notes | Link-out to the New IB release notes |
| 4 | Pipeline user guide | Link-out to the rare disease pipeline user guide |
| 5 | What's new | Opens an overlay which summarises the new features in the current release |
| 6 | See our roadmap | Links out to details of upcoming features in the New IB |
| 6 | Submit new ideas | This takes you to a page where you can submit ideas for upcoming releases of the New IB |
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 |