Summary

The focus of this release has been on fixing a number of issues in the CVA Portal front end and preparing the backend database to serve CNVs and Cancer cases to the Front End.

In addition, we have made a number of improvements to the "Search" to make it more concise and to the performance of case loading.

Finally, the syncing of cases between the Interpretation Portal and CVA has been fixed so as cases are updated in the Decision Support Systems and Interpretation Portal the updates are synced across to CVA automatically

New features / improvements:

• The syncing of cases with the CIP-API has been fixed
• Showing the count of cases where each variant has been observed
• CNV data has been added to the backend database. CNV support for the CVA Portal is planned
• Default order of variants in the case view is now: Reported variants at the top, then sorted by genomic coordinates
• Improved search conciseness e.g. cases can now be searched by Interpretation Request ID and version (123-1)
• Search for Genomic Region limited to <1Mb
• Page loading performance improvements including phenotypically similar cases
• Human Phenotype Ontology (HPO) are now normalised (i.e. old HPO terms are migrated to the current version)
• HPOs additional information are now fetched from CVA API instead of using the external EBI service
• Genes shown are now coming from the CellBase annotations and not from the annotations made at analysis time
• Gene filter search more concise

Fixed:

• CVA data intake improved to handle edge cases
• Pagination in phenotypic similarity sidebar
• Panel versions correspond now to the version applied to any given case and not the latest version of the panel
• Case creation and last modified dates are now correct, the day within the month was wrong before
• Fix link to cases from phenotypic similarity sidebar
• Incorrect error messages shown after filters applied

Known issues:

• Many filters in the case view are broken (gene, tier, consequence type, compound heterozygous)
• Summary of Findings side bar does not include variants - we are working to fix this, in the mean time variant details can be found in the Reporting Outcomes Questionnaire Side Bar
• Filters are persistent between different searches affecting usability
• ClinVar link out for variants is not shown
• 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