v1.1.80 Release Notes

01 July 2019

Summary

Clinical Variant Ark (CVA) Portal is the visual gateway into the knowledge base built from rare disease cases and variants within the Genomics England Interpretation Platform.

You can access CVA Portal, using your existing Genomics England username and password here, cva.genomicsengland.nhs.uk

In this release we have been focused on fixing and improving the existing filters in CVA Portal.

Users can now filter cases in their search results based on the case resolution

e.g. as a user searching for cases in CVA with "Intellectual disability" I can now filter the search results to those that have been closed with "positive primary findings" i.e. one or more variants included in the Summary of Findings for the case

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GMS-BETA CVA Portal

In addition, we have been building a new "GMS-BETA" environment in preparation for the launch of NGIS for UAT.

The CVA-GMS BETA site can be found on HSCN network here: https://cva-gms-beta.genomicsengland.nhs.uk

We will be switching on the AD authentication over the coming weeks so GMS BETA testers of NGIS will be able to login. Currently this instance of CVA is empty of cases but as GMS BETA test cases flow through the NGIS platform they will appear here.

New features / improvements:

  • User can now filter cases based on whether they have "positive" or "negative" primary findings (CZFE-351)
  • Summary of Findings side bar now includes the reported variants (CZFE-501)
  • Upon performing a new search, any existing filters from previous search are now removed (CZFE-454)
  • The colour of the case resolution "tags" have been updated so those with positive primary findings are now red, where previously they were green Image

Fixed:

  • The filters and sorting on the list of variants in the case view have been fixed (CZFE-472, CZFE-473, CZFE-495, CZFE-506, CZFE-517)
  • Issue where the zygosity columns in the case viewer were not aligned correctly with the table heading (CZFE-553)

Known issues:

  • In some web browsers (e.g. Edge) the "Created date" is not loading on some pages
  • The link out to the Interpretation Portal is pointing to an internal URL
  • External Evidences link out for variants is still broken
  • The summary count of variants by interpretation service on the CVA variant view is not counting variants identified by tiering
  • GRCh37 variants without lift over to GRCh38 are never returned in search results
  • Cases with > 1,000 variants are not being sent automatically through to CVA from CIP-API

Access:

  • CVA Portal BETA can be accessed on the HSCN network here: cva.genomicsengland.nhs.uk

Providing feedback

We have been developing the CVA Portal with input on requirements from a number of different users from GMCs and GeCIPs, if you would like to be involved please contact the Genomics England Service Desk .