Release Notes

Full NGIS release notes can be found here.

What's New in the CIP-API?¶

Orion Increment - April 2025

Panel Name Update (PRD-3385): analysisPanels.panelName now displays the descriptive panel name (e.g., "Hypotonic infant") instead of the numeric ID (e.g., "285"). This update applues only to the pedigree; other panelName fields were already correctly formatted. See this change in referral 2585-1 and 2587-1

Details

Before:

"analysisPanels": [
                    {
                        "panelId": "490",
                        "panelName": "490",
                        "panelVersion": "33.101",
                        "reviewOutcome": "",
                        "specificDisease": "Hypotonic infant",
                        "multipleGeneticOrigins": "No"
                    }
                ]

After:

"analysisPanels": [
                    {
                        "panelId": "490",
                        "panelName": "Hypotonic infant",
                        "panelVersion": "33.101",
                        "reviewOutcome": "",
                        "specificDisease": "Hypotonic infant",
                        "multipleGeneticOrigins": "No"
                    }
                ]

Orion - February 2025

B-Allele Frequency (BAF) Plots: Cases will now include the B-Allele Frequency (BAF) plots as part of the files linked to the payloads.

Tier B CNV report events: The pipeline logic that allocates a tier (level of priority for review) to CNVs has been updated.

Large (>100kb) rare CNVs that overlap a gene with a transcript that has a compatible biotype (see here) will be promoted to 'Tier B'. These CNVs would previously have been marked as 'Tier Null' as they do not overlap a gene that is green in PanelApp.

TPIs will observe that in genomics england tiering interpreted genomes, the "Tier" value of CNV report events may now contain the value "TIERB" if the CNV meets the criteria linked above.

An example case (SAP-2582-1) is available in the SIT environment here

Nembus Increment - November 2024

The CIP-API authentication process has been streamlined to align with other GEL applications and now uses single sign on. This update includes a improvements in the Swagger page UI as well as adjustments in its authentication process, where users now need to retrieve a token for access.

Nembus Release - September 2024

Cellbase v5 Integration: The CIP-API has been upgraded to support cases processed with Cellbase version 5 and data release version 3. This upgrade did not require any change in the Gel Report Models. More context on the databases upgrade will be found in the NGIS release notes.

Warning

During our integration testing with Congenica we identified a scenario where cases may fail to process in Congenica due to Ensembl versions no longer aligning between GeL and Congenica after the CellBase upgrade.

Immediately post Nembus release it has been agreed with NHSE that any impacted referrals will be dealt with manually, then as part of the Nembus Increment release, Congenica will add functionality to "tag" details of tiered variants that fail to load in their application.

Tag information, if required, will then be made available to TPIs from the exisiting "tags" field in interpretation request endpoint.

Further information will be provided when Nembus Increment is released on how users can understand the tags.
Unified Tiering for Compound Heterozygous Variants: The Rare Disease pipeline has been updated to include unified tiering of CNVs, STRs, and small variants. These variant groups are now defined in the Interpretation Genome through the groupOfVariants field in the ReportEvent object for all three types. More information can be found here. Additionally, the segregationPattern field will now include tags such as CompoundHeterozygous or XLinkedCompoundHeterozygous.

Mira Release - April 2024

Dragen v4: The CIP-API now supports cases processed with Dragen v4 (INTPORTAL-1744, CIPAPI-2145).
SVG Format for STR Plots: The STR plots for new cases are now in SVG format instead of PNG (INTPORTAL-1744).
GRM Integration for GMS RD and Cancer: The Portal has been upgraded to incorporate version 8.5.0 of GRM for GMS RD and 8.6.0 for Cancer referrals (IP-5416). This upgrade also includes support for Tumour Only referrals (CIPAPI-2011) once they are available.

Lyra Release - December 2023

SNP Check Removed: The SNP check functionality has been removed.

Kraz Release - November 2023

Cancer Case Workflow Update: The workflow for cancer cases has changed due to the initiation of dispatching to cDSS.

Izar Release - March 2023

KPVP updates: The CIP-API now supports the new Known Pathogenic Variant Prioritisation (KPVP) feature. updates to the Interpretation Browser (IP-4603). KPVP improves the sensitivity of the Genomics England rare disease pipeline by ensuring genomic variants that are known (e.g. present in specific databases) to be disease causing are not incorrectly filtered out by other tiering rules. To support KPVP - report events within "genomics_england_tiering" interpreted genomes will have some additional fields 'added' to them. The following Powerpoint deck highlights what the proposed changes are, along with an example interpreted genome.

Izar Release - March 2023

KPVP: The CIP-API now supports the new Known Pathogenic Variant Prioritisation (KPVP) feature. KPVP enhances the sensitivity of the Genomics England rare disease pipeline by ensuring that genomic variants known to be disease-causing (e.g., those present in specific databases) are not incorrectly filtered out by other tiering rules. To support KPVP, report events within "genomics_england_tiering" interpreted genomes will have additional fields added to them. For more details, you can refer to the following PowerPoint deck that outlines the proposed changes, along with an example interpreted genome.

Grace Release - November 2022

Tier Null STRs: The Interpretation Portal now displays Tier Null STRs. More information can be found here, including a demo video here. This change affects how these STRs are tiered in the IG/IR if accessed through the CIP-API.

Coming Up Next!¶

Numeric Tiering for CNVs

In an upcoming release, the tiering component of the bioinformatics pipeline is being upgraded. As part of this upgrade, the tier value in report events for structural variants (i.e., CNVs) called by Genomics England tiering will change from using TierA / Tier Null to using Tier1, Tier2, Tier3. This update aligns the tiering values for CNVs with those used for small variants.

Any TPI (Third-Party Integrator) that pulls interpreted genome variants into their application should ensure their application can still load CNVs and, if necessary, handle the different tier values. For example, after this feature is released, a CNV previously marked as TierA (top priority) will now be marked as Tier1. There is no change required for GeL Report Models since the same tier enumeration is being used.

An example case with the updated tiering has been placed in the SIT environment here: https://cipapi-beta.genomicsengland.co.uk/api/2/interpretation-request/2561/1/?format=json

Example of how this looks:

To determine if the tier value for CNVs in report events is going to be TierA or Tier1, you can use the rd-tiering version found in the softwareVersions of the Interpreted Genome.

Last update: 2025-04-03