Changelog

Release Notes for the CIP-API

Find more details in the NGIS release notes.

We value your input. If you have feedback on the Interpretation Portal or want to request new features, please do so by raising an NGIS Feedback request via our Jira Service Desk.

Regulus December 2025

• Numerical CNV Tiers: The CIP-API now supports numerical CNV tiers (Tier 1/2) instead of alphabetical tiers (Tier A/B), in line with updates to the bioinformatic pipelines.
• Migration of Existing Cases: Pre-existing CNV tier assignments have been migrated from alphabetical to numerical for smooth adoption.

Example:

Example of a Tier 1 CNV in the report events of an interpreted genome in SAP-2600-1 (r22046251634):

Orion 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"
                      }
                  ]
  

• Congenica (CIPAPI-2618): Following a bug fix in the CIP-API, the value returned from the "get workflow status" endpoint (and any related data views) will now use lowercase "congenica" instead of "Congenica". Please note that older cases may still return "Congenica" until they are reprocessed. You can view this change on the referral 2588-1.

• 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 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.

• 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 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 December 2023

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

Kraz November 2023

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

Izar 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.
• 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 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!

See below our roadmap, describing upcoming features we are working on!