Upgrade to Cellbase v5: Impact on Portal¶
In the Nembus release, all applications in NGIS are being upgraded to use version 5 of our annotation system CellBase The updated CellBase introduces new and improved annotation datasets such as Ensembl, UniProt, and ClinVar.
The consequent upgrades in the Interpretation Portal aim to enhance functionality and data availability, ensuring a seamless transition for users.
Changes Impacting Portal Features:¶
'Show Variant Details'¶
All information retrieved from this section is now sourced from Cellbase v5, including:
- CellBase Location
- Cellbase Alleles
- HGVS
- Most Severe Consequence Type
- Most Severe Deleterious Score
- Consequence Types
- Population frequencies
- Variant Trait Association
Users may observe differences in information if their case was processed in the Genomics England Pipelines with Cellbase version < 5.
This section should still load if a variant has been retrieved using the 'Add Variants from VCF' option.
GRCh37 100K cases
Please note that the 'Show Variant Details' button is no longer available for GRCh37 cases.
'ClinVar Classifications'¶
Cellbase is also used in the Interpretation Browser to incorporate the latest ClinVar Annotations for displayed variants. After this upgrade, users will continue to be able to use this feature as expected.
'Add Variants from VCF'¶
The 'Add Variants from VCF' feature remains functional and will now retrieve the gene symbol using the latest version of the Cellbase databases. Users should be aware that if their case was processed in the Genomics England Pipelines with a version < 5, they may encounter a different gene symbol than expected, as the Portal uses the most up-to-date information. Please note that this feature will no longer be available for GRCh37 cases.
Max Allele Frequencies¶
The Interpretation Portal calculates the Max Allele Frequencies shown in the Interpretation Browser with the current list of Studies and Subpopulations used by the Rare Disease Pipelines. With the upgrade to Cellbase v5, the DiscovEHR and UK10K studies have been removed from our database. Users will then see the most up-to-date selection of studies, even if the cases were processed with a Cellbase version < 5.
Summary of Findings (SoF)¶
The Interpretation Portal relies on Cellbase to obtain Allele Frequency data for generating the SoFs. However, this data will no longer be accessible for cases based on the GRCh37 genome reference. Users attempting to retrieve this information will receive an error notification. Despite this, they will still have the option to download the SoF as usual.
Identifying Cases Processed with Previous Cellbase Versions¶
If your case was processed by the Genomics England Tiering pipeline before the Nembus release, it used an older version of Cellbase. To help you identify whether a case was processed with the current or an older version of Cellbase, we have introduced a new flag in the case information section of the Portal.
- Cases processed with an older version: The version number will be highlighted in red.
- Cases processed with the current version: The version number will be displayed without highlighting.
Additionally, all cases will include a link to this documentation page for further reference.
This flagging system ensures that you can quickly determine the version of Cellbase used for processing your case and access detailed information as needed.
