Release Notes
Full NGIS release notes can be found here
Coming Up Next!¶
Nimbus - Update CNV tiers to Tier1, Tier2, etc. rather than TierA
In the future Nimbus release (date TBC) the tiering component of the bioinformatics pipeline is being upgraded.
As part of the upgrade the tier value in report events for structural variants (i.e. CNVs) called by Genomics England tiering will be changing from using TierA / Tier Null to using Tier1, Tier2, Tier3
This brings the tiering values for CNVs in line with those for small variants.
Any TPI that is pulling interpreted genome variants into their application should check their application can still load CNVs and, if used, handle the different tier value e.g. after Nimbus the tier value for a CNV that would previously be top priority would have and had the TierA tier will now have the Tier1
There is no change for GeL Report Models for this as the same tier enumeration is being used.
An example case with the updated tiering has been put 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 tier value for CNVs in report events is going to be TierA or Tier1 you can use the rd-tiering
version that is found in the softwareVersions of the Interpreted Genome.
Please note the exact version that will be used in Nimbus is still TBC
Support for Known Pathogenic Variant Prioritisation (KPVP)
Genomics England are planning to update the rare disease tiering algorithm of the bioinformatics pipeline to support Known Pathogenic Variant Prioritisation (aka KPVP).
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
If you have any further questions or concerns about the impact on these changes on your application, please come along to CIP-API surgery call (Fridays at 1pm) in the new year