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GCI & VCI Updates
Christine Preston edited this page Sep 24, 2024
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- The REVEL scores displayed in the Variant Type tab have been updated. The VCI now displays all transcripts which have a REVEL score, with their associated score and MANE status. The data is sourced from ClinGen's Linked Data Hub LDH.
- Phase status can now be specified in the gene curation evidence for AR and semidominant conditions (see Help Documentation for details)
- The Variant Curation Interface now supports the criteria strength "Very Strong" for PM6, PS3, and PS4.
- ClinVar submissions can now be used as gene curation evidence (see Help Documentation for details)
- More model organisms have been added as experimental evidence options: Ferret (Mustela putorius furo) 9669; Hydra (Hydra vulgaris) 6087; Anole (Anolis carolinensis) 28377; Aspergillus (Aspergillus nidulans) 162425; Neurospora (Neurospora crassa) 5141; Marmoset (Callithrix jacchus) 9483)
- Additional scoring options now available in dropdown menu for scoring individual homozygous probands
- Final approval date is now required to be set by the curators to match GCI functionality.
- Updated XML parsing to support ClinVar changes. ClinVar updated their XML files and changed element names that we access for variant data. We updated our variant parsing function to support this change
- Updated Hypothesis linking. Changes the page that we link to from the VCI. Instead of the first annotation in a list of annotations, we display a list of annotations via the search page for that tag (ClinVar ID or CAID). We have also added a tooltip next to the link for context/help
- Updated BRCA Exchange smart link. The VCI links to BRCA Exchange needed to be updated to due to their resource changing their output structure
- Variant IDs (both ClinGen Allele Registry and ClinVar when available) are now part of the dashboard .csv download
- The test interface underwent the annual data wipe, this does not impact any of the curations in the production version
- CIViC links have been updated to be compatible with the CIViC v2 REST API
- Curation URls are now a part of the dashboard .csv download
- The gnomAD links now correctly link to the variants in gnomAD v2
- There is a more streamlined process for adding evidence repository publishing rights to approved ClinGen VCEPs
- There is a warning and further information next to the displayed REVEL scores
- Curators can capture their curation reasons and publish them to the ERepo
- Curators can capture their curation reasons and publish them to the ClinGen website
- Duplicated PMIDs warning in Case/Seg -- a warning is now displayed to users in the case/segregation evidence table; when two PMIDs are from the same source they are both highlighted
- Disease now required in order to publish
- Text updates to the GCI
- Fixed display issue for non-affiliation dashboards
- Gene Tracker precuration ID required to start GDM
- OLS v4 update -- updating the modals for bringing in MONDO terms to get data via EBI's OLS version 4 API (was v3)
- Enable the scoring and publishing of CNVs during Gene Curation -- support the use of the ClinGen Allele Registry's CACN IDs for copy number variants added into the GCI.
- Preview Evidence Summary links -- the labels for each evidence type within the Preview Evidence Summary table now provide a link back to where the data associated with that evidence can be edited. This improves the navigation within the UI. Now, if you discover an error or typo, it can be corrected easily by clicking on the "Label" name in the leftmost column in the table; this will open a new tab where that evidence can be edited.
- Case/Control Contradictory/Review options -- ability added to select Review and Contradicts as options for Case/Control evidence, and if Contradicts is selected, contradictory evidence will be indicated on the classification matrix page, as well as in the Evidence summary.
- LitVar link -- variants with hits in LitVar now have a link to that resource displayed in the external resources table of the basic info tab and the number of hits is shown in parentheses.
- support for versioned CSpec links in VCI (links to specific document version)
- new genes available in the Variant Prioritization (VP) feature in the VCI (increased from 36 genes to 107 genes)
- Generate all variant titles using the Community Standard Title provided by the ClinGen Allele Registry
- ClinVar bulk submission, allowing grouping of ClinVar submissions within the VCI to generate a batch output - alpha version released for VCI stakeholder testing
- Added 9 new organisms to the non-human model organism pulldowns for both Model Systems and Rescue Experiment types
- Updated non-human model organism pulldowns to allow for type-ahead search functionality
- Acknowledgements panel updated with contextual help
- Improved links to Help support in header, including links to the new Help documentation in GitBook
- Send full status update message to Data Exchange whenever a GDM transfer and/or disease change occurs
- 'Notes' field added for GDM transfers
- Display MANE Select and MANE Clinical labels on the Basic Information tab transcript tables
- Added APP_STAGE environment so can create user with different properties
- Affiliations sorted in ascending alphabetical order
- Disable allow obsolete disease to be selected and associated with any objects.
- Add obsolete disease icon to dashboard tables, GDM curation page header and details sections
- Updated to React v16.14
- Display obsolete disease icon if VCI interpretation associated with obsolete disease
- CSpec backend changes and link in VCI header
- Changes to hypothes.is linkout logo and text changes
- 'Add in New Format' button to VCI Case Segregation page
- PM3 tracking report
- UI changes to handle CSpec link with criteria panels
- Minor comment fix in AuditTrail, revert config to gcsop8
- Added VP wiki page to external linkout in header
- Added better error handling/UI when requests fail on GeneSearch
- When add/edit/view GCI evidence, disallow copy obsolete disease and display obsolete disease icon if appropriate
- Do not allow to approve or publish classification if GDM associated with obsolete disease
- When directing user through approval process after saving classification, only guide up to provisional if GDM is associated with obsolete disease
- For Animal Model Only tag, check there's no altered/modified classification
- Default SOP version switched to version 9 (SOPv9)
- Final Approval Date is now a required field
- 0.25 increments added to scoring pulldowns
- New "Test Site Example Affiliation" attached to all users in the Test Interface, thus allowing all users to access the test version of the GCI and to try out how affiliations work
- Curation restricted within the UI for obsolete MONDO IDs
- Improved the "Saved Provisional and Approved" UI experience
- Improved dashboard performance
- Published and disseminated VCI paper
- Workflow updates to Variant Prioritization (VP)
- GCI records updated so that each GDM only has one GCEP owner
- Restricted gene curation to GCEPs only
- Curation restricted within the UI for obsolete MONDO IDs
- Affiliation data now available via API
- Improved affiliations field in users table
- All sections of the VCI now display the term "Classification" when referring to the 5 ACMG classification categories (Benign/Likely Benign/ Variant of Uncertain Significance/Likely Pathogenic/Pathogenic)
- Text formatting in evidence summaries via markdown editor -- comprehensive text editing capabilities (e.g. paragraph/line breaks, bold, italics, etc.) in GCI evidence summaries can now be saved, displayed and published
- Specification document support -- users can now add a specification document to VCI curations, as well as link to the CSpec specifications for each individual ACMG criteria code
- Hypothes.is link -- variants with Baseline C3 Community annotations now have a link to those annotations within the Hypothes.is resource displayed in the header
- BRCA Exchange link -- variants with BRCA Exchange data now have a link to that resource displayed in the external resources table of the basic info tab
- CIViC link -- variants with CIViC data now have a link to that resource displayed in the external resources table of the basic info tab
- Alphabetize pulldown lists -- Affiliations, Contributors, and Secondary Approvers pulldown lists are now all alphabetized
- Evidence Summary linking improvement -- UI updated to make links to provisional and approved evidence summaries clearer
- Preview Evidence Summary -- restricted access to display only for GCEP owner
- Experimental info texts updated -- 'yellow box' texts updated by GCWG
- SCV automatic updates -- SCV data updated via ClinGen's ClinVar submitter service to allow automatic updates of SCV data in user-generated ClinVar submission files
- Dashboard speed improvement -- now loads over twice as fast due to re-indexing of affiliations, access to bulk snapshots, and preinstantiation of microservices
- Custom API -- each GCEP affiliation can access and export a customized set of their own gene curation data in JSON format
- Variant Prioritization (VP) -- This feature supports curators in exploring all variants in ClinGen's Allele Registry for select genes, providing curators with filters for specific associated variant data including some ClinVar statuses, gnomAD v2.1.1 subpopulation allele frequencies, REVEL predictor scores, and VCI curation statuses. This first version of the VP supports the following genes: CDH1, GAA, GJB2, HRAS, MAP2K1, MAP2K2, MYH7, PAH, PTEN, PTPN11, RAF1, RUNX1, SHOC2, SLC26A4, and SOS1. The data for the VP is supplied by ClinGen's Linked Data Hub (LDH).
- SOPv8 update -- the GCI now supports SOPv8 (https://www.clinicalgenome.org/docs/gene-disease-validity-standard-operating-procedure-version-8/), such as the scoring of individual variants instead of probands
- Earliest clinical publication -- users can select which paper(s) represents the earliest clinical publication(s) to assist with determining 'Replication Over Time'
- Comprehensive audit trail -- view the full edit history for each interpretation
- SOPv8 test site -- released for testing new GCI SOPv8 scoring framework
- Age units -- extended to include options for "Hours", and "Weeks gestation"
- Dashboard tables -- loading speeds up to three times faster
- LOVD link -- displayed on basic info tab when data is available at that genomic position
- Mitochondrial inheritance -- ability to score, approve, and publish gene-disease classifications with mitochondrial inheritance
- Variant Prioritization -- beta release (5 genes: PTEN, CDH1, GAA, PAH, and RUNX1)
- Header buttons texts updated:"Preview Evidence Summary" changed to "Preview Evidence Scored", and "Classification Matrix" changed to "View Classification Summary"
- Demo site registration is now self-service
- VCI dashboard table "pathogenicity" updated to "classification" and only show final classifications for provisional/approved classifications
- GCI dashboard table updated to only show final classifications for provisional/approved classifications
- Evidence summary text now required to save a classification
- Variant selection UI improved (ClinGen Allele Registry IDs and ClinVar Variation IDs are now automatically recognized)
- 5 new Affiliations (81 total)
- Users able to change MONDO IDs on unpublished Gene-Disease records
- 2 new searchable fields added to GCI dashboard table (Classification and Last Modified)
- SOP version 8 added as an option upon Approval (updates to GCI to fully support SOP v8 in the gene curation process will be released in early 2021)
- Medaka added as an option for non-human model organism
- Links to the GeneTracker updated
- 3 new searchable fields added to VCI dashboard table (Classification, Met Criteria, and Last Modified)
- Links added to 2 splice tools: SpliceAI and varSEAK
A comprehensive list of all the updates to the 1.0 Platform, that was replaced with 2.0 in December 2020, can be found HERE