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GCI & VCI Updates (2015 to 2020)
Matt W. Wright edited this page Nov 25, 2020
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- 7 new Affiliations (76 total)
- Streamlined automated user registration
- Structured case/segregation data can now be captured for evidence from non-published sources (e.g. Clinical Lab)
- HPO term names can be automatically imported and displayed when adding Human Phenotype IDs (HP IDs)
- Labels added to transcripts in basic info tab to indicate MANE transcripts
- GCI JSON exports published to the streaming service have been expanded to contain comprehensive evidence
- HGNC REST-API now used as source for all gene symbols
- The new HGNC API application fixes several gene-disease records that had outdated gene symbols
- 6 new Affiliations (69 total)
- MANE transcripts now used to generate HGVS variant titles for variants without a ClinVar preferred title
- Terms of Use agreement now available for view from the Help pulldown in the header (text supplied by DAPC WG)
- PHI warning texts updated (text supplied by DAPC WG)
- Gene-Disease record creation is now restricted to only those users curating as part of a GCEP
- Provisional Classifications now viewable by all users in the GCI
- HPO term names can now be automatically imported and displayed when adding Human Phenotype IDs (HP IDs)
- No Reported Evidence now changed to No Known Disease Relationship
- No Known Disease Relationship automatically classified in Classification Matrix when there is no scored genetic evidence and no contradictory evidence
- Animal Model Only tag automatically applied to No Known Disease Relationship Classifications with only non-human experimental evidence
- ClinVar overall interpretation and submissions data are displaying again in the basic info tab in the VCI
- 1 new Affiliation for Thrombosis VCEP (63 total)
- Warning message added to Affiliation change modal because we recommend users close all GCI/VCI tabs they have open when they switch between different Affiliations during a session
- Granular functional assay data from PubMed articles can now be displayed for a variant in the Experimental tab in the VCI. VCEPs would need to enter these data via a structured format into a spreadsheet, as described here, and by submitting this format to ClinGen's Functional Data Repository (FDRepo) these data would then subsequently be viewable in the VCI.
- Updated text for "Submission Policy Agreement", that is triggered when a variant interpretation is initiated. Note: user agreement/disclaimer texts that were recently provided by ClinGen's Data Access, Privacy, and Confidentiality (DAPC) Working Group will appear in the next release (R32)
- Status changes to Gene-Disease Records (such as creating a record, and provisioning, approving, publishing, or unpublishing a classification) are now sent automatically to the ClinGen streaming service. The first receiver of this new data stream is the Gene Tracking System.
- General notes can now be associated with PubMed articles in Gene-Disease Records. Any PubMed articles marked as containing "Non-scorable evidence" now appear in a table at the bottom of the Evidence Summary.
- New affiliation transfer tool allows interfaces admin personnel (contactable via the helpdesk) to transfer ownership of VCI Interpretation Records and GCI Gene-Disease Records from individuals to affiliations, and from one affiliation to another.
- Approved Evaluation summaries are now viewable by any other user in the VCI. Previously these summaries were not populating with data for some users.
- Bug fixed that prevented some records with Semidominant Mode of Inheritance from being published
- 2 more Affiliations (62 total)
- Updated MaxEntScan link
- When approving a Classification an affiliation can now attribute an alternate affiliation as the Approver, and also recognize curation Contributors
- Specification of an SOP version number other than the default (currently version 7) for an approved Classification
- Updated HPO browser links
- Multiple UBERON IDs can now be added
- Developers edited multiple records based on user requests. Such curation edits, and other bug fixes, are given a special status in our development queue with the highest priority given to curation blockers.
- Filtering of All Variant Interpretations Table on dashboard by Variant, Disease, MOI, and/or status
- Download CSV list of filtered variant interpretations
- Link from Conservation Analysis table in Variant Type/Missense Tab to the comparison view in UCSC (-30nt to +30nt)
- Updated gnomAD population table to version 2.1.1
- Filtering of All Gene-Disease Records Table on dashboard by Gene, Disease, MOI, and/or status
- Download CSV list of filtered gene-disease records
- Variant interpretation records affected by the change in ClinVar XML format have now all been corrected, and so the GRCh37 warning messages will no longer appear
- Developers edited multiple records based on user requests. Such curation edits, and other bug fixes, are given a special status in our development queue with the highest priority given to curation blockers.
- 6 more Affiliations (60 total)
- 2 new Approved VCEPs now able to publish to Evidence Repository (TP53 and LSD)
- 2 VCEP guidelines versions updated
- Granular evidence capture of case/segregation evidence (PMIDs only; other evidence sources will follow in subsequent release)
- Link to standardized evidence summary text added to Classification Matrix
- ClinGen Allele Registry (CAid) now saved for variants added via ClinVar Variation IDs
- 1 new Affiliation (Peroxisomal Disorders)
- 7 more Affiliations, including DICER1 and miRNA-Processing Gene EP (54 total) (added as a patch, 2019.07.31)
- Mosaic as adjective option for AD and Other MOIs (added as a patch, 2019.07.31)
- ClinVar submission export format available for VCEPs
- Full provenance (curator & affiliation) shown for PMID evidence
- Warning message before deleting PMID evidence
- Legacy names displayed for variants with ClinVar entries
- Link to VCI SOP added to Help pulldown
- Added Semi-dominant mode of inheritance, which is publishable to the ClinGen website
- Allow copying of "not" phenotype information from Groups to Families and Individuals
- Allow Mammalian Phenotype Ontology MP IDs as additional option in Experimental/Model Systems
- Additional species (zebra finch) added to non-human model organism pulldown
- Updated ClinVar import to support the new VCV XML data structure (added as a patch, 2019.09.15)
- 1 new Affiliation added (46 total)
- Ability for VCEPs to publish Approved interpretations to the ClinGen Evidence Repository (ERepo)
- Number of hits shown in the All Interpretations table
- Sorting of Evidence Summary tables by column header
- Number of hits shown in the All Gene Disease Records table
- 13 new Affiliations added (45 total)
- ClinGen EP Affiliations split into Variant Curation Expert Panels (VCEPs) and/or Gene Curation Expert Panels (GCEPs)
- Versions for gnomAD and ExAC data displayed in the population tab
- Indel population data returned for gnomAD and ExAC
- Added Undetermined mode of inheritance, which is publishable to the ClinGen website
- 1 new Affiliation added (32 total)
- PHI (personal health information) disclaimer texts now displayed when starting a new Interpretation and at the top of the Case/Segregation tab
- Each ACMG criteria code now has its own explanation box
- Ability for curators to associate a PMID with a specific ACMG criteria code
- 2 new Affiliations added (31 total)
- Added hyperlinks to the UNC Gene Tracking System: http://clingen.sirs.unc.edu
- Added NCBI API keys to continue to allow fast access to E-utilities API
- Created GCI/VCI Admin Console for generating statistical reports
- Developed new tool for transferring classifications from individual curators to affiliations
- Multiple updates to the GCI to reflect the changes in segregation scoring in version 6 of the Gene-Disease Clinical Validity SOP. Notes about the segregation changes:
- If a curator selects "Include LOD score in final segregation..." they must now also select a sequencing method, either "Candidate gene sequencing", or "Exome/genome or all genes sequenced in linkage region".
- All existing LOD scores will by default be "Candidate gene sequencing" until revised by a curator.
- Curators should check all their existing Classifications and assess any changes (especially "Candidate..." vs "Exome...").
- The Classification Matrix, Evidence Summary and ClinGen website have all been updated to reflect the new segregation scoring.
- To publish a new (version 6) Classification, a curator will first need to save a new Classification Matrix, create a new Provisional, and create a new Approved.
- Classifications based on the previous SOP (version 5) will remain on the ClinGen website until they are unpublished or replaced by a new (version 6) Classification.
- Classification Matrix/Evidence Summary is now viewable by any logged in user once record is marked as Approved
- Expert Curation date published to website updated to match the Approval date in the GCI, with the manually added date taking precedence over auto-filled Approval date
- Link to the Gene Curation SOP added to the Help pulldown
- SOP version number added to Evidence Summary
- Additional options added to Genotyping Methods pulldown
- Faster load times for All Interpretations Table
- PVS1 and PM6/PS2 criteria sections now have links added to Sequence Variant Interpretation (SVI) Working Group guidance
- Evaluation Summary/Evidence Summary is now viewable by any logged in user once record is marked as Approved
- Basic Info tab updated to include table of "All Interpretations for this variant in the Variant Curation Interface (VCI)"
- 2 new Affiliations added (29 total)
- Removed the “Contributors” and “Last edited” columns from the “All Gene Disease Records” table to enable much faster load times (released as supplement on 2018-08-21)
- Upgraded Auth0 to Lock v11
- Affiliation names abbreviated to the new ClinGen agreed standard format (e.g. 'ClinGen' removed, and 'expert panel' abbreviated to 'EP')
- 1 new Affiliation added (27 total)
- Improved loading speed of Interpretations and Gene-Disease records tables on dashboard (Note: further loading speed improvements are planned for future releases)
- Ability for ClinGen expert panels to programmatically "Publish" Approved Classifications directly from the GCI to the ClinGen website (clinicalgenome.org). Please see the GCI Help doc for more information on this new "Publish" feature. Notes about publishing to the website:
- From this point on all submissions of Approved Classifications to the ClinGen website need to be done only via the "Publish" feature in the GCI.
- Only Classifications with an 'Autosomal Dominant', 'Autosomal Recessive', or 'X-linked' mode of inheritance (i.e. those supported by the Clinical Validity Classification framework) should be published to the ClinGen website.
- The disease for a Gene:Disease Classification must be annotated using a MONDO ID for that Classification to be successfully published.
- Warning text added to free text fields that upon publication will be displayed on the ClinGen website
- All data is now displaying correctly in the Evidence Summary in the GCI
- Bug fixed where "No Selection" option could not be saved for demographics data in the GCI
- CAIDs for large deletions can now be entered into the VCI (previously encountered problem due to the VEP's 5kb limit)
- Missing data in the gnomAD and ExAC tables for some variants in the VCI will be automatically fixed when the next version of MyVariant.info is released
- HGVS titles for non-ClinVar variants are now based on the canonical transcript, whenever possible
- 2 new Affiliations added (26 total)
- Affiliation names changed from "Working Group" to "Expert Panel"
- Uberon, CL and EFO IDs can now be added in either colon or underscore format
- Checkbox logic updated in experimental section
- Criteria bar ACMG codes now link to the relevant section in the Interpretation record
- "Predictors" tab renamed to "Variant Type" tab
- Germline only advisory text added to "Interpretations Submitted to ClinVar" table
- Impact threshold for REVEL predictor changed from >0.5 to >0.75
- Fixed incorrect display of Classification value on saved Provisional panel
- Fixed page freezing for Experimental/Functional Alteration
- Fixed bug whereby gnomAD data was not being returned for intergenic variants
- Fixed bug whereby Gene-centric tab stalled for intergenic variants
- Added error reporting service for Elasticsearch
- Ability for curators to save their Classifications as Provisional and Approved
- Summaries of Provisional and Approved Classifications are now permanently Saved
- History of saved Provisional and Approved Classifications with links to view the Saved Summaries
- Ability for curators to save their Interpretations as Provisional and Approved
- Summaries of Provisional and Approved Interpretations are now permanently Saved
- History of saved Provisional and Approved Interpretations with links to view the Saved Summaries
- 4 new Affiliations added (24 total)
- Bug fixed where the same gene impact data was displayed for all variants being edited by a curator
- Bug fixed where 0.1 increment points were displaying incorrectly in the Classification Matrix table
- Page rendering error fixed which was appearing when a curator scored an evidence in a given Gene-Disease record and then later removed the score
- 5 new Affiliations added (20 total)
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The LIMITED score range in the GCI has been updated 0.1 to 6 (previously it was 1 to 6). This reflects the recent introduction of 0.1 incremental scoring for probands
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Linkout added to proband Score section to enable curation of a variant's gene impact
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Curator now allowed to enter text in the "Explain reason(s) for change" free text field of Score section, even if they do not change the score from the default
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A 'replication over time' mouseover message in the Classification Matrix now provides a definition of what this means
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Multiple enhancements to the Evidence Summary:
- Proband's Description of Genotyping Method free text info is now included in the Methods column
- Author reference information shortened to first author's last name, year, and PMID
- Labels entered by curator is a new column
- gnomAD data is now available in the population tab
- Filter Pass statuses are now shown for both the ExAC and gnomAD data
- Very_strong is now a modifier choice in the PM3 criterion pulldown
- Bug fixed whereby the Evidence Summary table was not correctly rendered when phenotype only evidence (HPO terms or HPO text) was added with no disease
- Bug fixed whereby if a LOD score was counted and a proband was made from that Family, but the proband itself was not scored, then LOD score did not appear on the Evidence Summary page
- Bug fixed where HPO terms were not rendering correctly in the evidence tables
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Affiliations implemented; users associated with an Affiliation can now:
- Edit and score/evaluate same piece of evidence
- Work on same classification/interpretation
- Approve the same classification/interpretation
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Help docs migrated from PDF to Wiki format to enable edits between releases
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PubMed articles can now be added in multiple formats (e.g. nnnnnn, PMID:nnnnn, pmid: nnnnn)
- Copy buttons added to enable copying of "Demographics" and "Methods" information from Group to Family, Family to Individual, and Group to Individual
- "Preview" of Evidence Summary now available from header, allowing curator to view a summary of their evidence before saving a Classification
- Watermark added to "Preview" of Evidence Summary to distinguish it from Evidence Summary supporting a saved Classification
- Red banner added to the Evidence Summary in the demo version of the interface to visually distinguish it from production
- Added instructive text to make it clear "Unknown" is a choice for the "Sex" pulldown field
- Removed three pulldowns that were not being used from the Methods sections in Group, Family, Individual, and Case-Control
- Changed four fields in the Power Section of Case Control to make then required
- Interface now automatically calculates the frequency fields for Case and Control in the Case-Control Power section
- Updated text for Individual de novo question
- PAGE Study data added to population tab in test site (previously only added to production site)
- Fixed bug where date was displayed incorrectly for some PubMed articles
- Disease modals updated to support MONDO IDs in coordination with the Monarch Initiative and EBI's Ontology Lookup Service (OLS)
- Existing disease annotations in the production database transferred to mapped MONDO IDs (curators contacted when this resulted in different term labels and/or definitions)
- Maximum segregation score changed from "7" to "3"
- Descriptive text added to LOD section to remind curators about minimum LOD score for inclusion in segregation score
- Contextual help added to predictors tab (linkouts to sources, table of prediction codes, and 'impact threshold" column)
- PAGE Study data added to population tab in production site (released as supplement on 2017-11-17)
- Fixed issue with some indel variants returning incorrect data
- New Evidence Summary table created, which contains a summary of all the evidence evaluated by a curator
- Multiple changes to 'Experimental/Rescue' section, including two additional new pulldown options, text changes, and changes to scoring
- Text changes to 'Experimental/Functional Alteration' pulldown options
- Text changes to 'Experimental/Model Systems' pulldown options
- Additional species (fission yeast, budding yeast, and Chlamydomonas) added to non-human model organism pulldown
- Remodeled Classification Matrix to reflect changes made to the Experimental section of the SOP
- Evidence Summary free text field added to Summary page
- AWS test instances failure fixed
- Fixed the bugs generated when curators clicked on Edit in Record Curation Central, (e.g. blank pages or ability to score was blocked for certain experimental types)
- Fixed the highlighting for the error message when a non-EFO/CL ID is added into Experimental/Model Systems
- Homepage text updated for both test and production interfaces
- Updated text on landing page for unregistered users that have gone through Auth0 process
- HPO browser link added to free text part of disease modal (where HPO terms is an option)
- Added additional score options of 0.1 and 0.25 to Individual (proband) forms for "Score" and "Review"
- Require curator to select Case Information Type once they have selected Score as status
- OLS links removed from Experimental sections
- Prevent (gray out) option to "Score" when checkbox not checked in Experimental
- Evidence Summary free text box added to Summary
- Highest MAF text updated in Population tab
- ExAC Population data now sorted by descending allele frequency
- Links to ExAC coverage region now provided for variants not found in ExAC
- REVEL data now available via MyVariant.info API (instead of from PredictVar API, which is no longer accessible)
- Fixed broken link to HumanSplicingFinder
- BP6 and PP5 criteria have now been made not editable
- ClinVar Interpretations tables relabeled on Basic Info tab
- Segregation/Case tab renamed to Case/Segregation
- Fixed bug where curators unable to save Family when no variant added
- Fixed Copy disease from Associated Family button which appeared after deleting disease from proband when no Family disease
- AWS test instances failure fixed
- Ability to annotate to Orphanet, Disease Ontology (DO), OMIM, and NCIt (NCI Thesaurus) disease terms present in the Monarch Disease Ontology (MonDO), thus greatly expanding the scope of allowed disease terms (significant data model enhancement required)
- Mapping and transfer of current annotations from Orphanet terms used in production to their equivalent MonDO disease terms (Orphanet, DO, OMIM, or NCIt)
- Ability of 2 or more curators to curate evidence from the same PMID within a Gene-Disease record
- Addition of free text fields as an alternative to MonDO disease terms, in the event an appropriate term ID cannot be found. This requires the addition of a free text term name and either HPO term(s) or a definition for the term.
- Addition of free text fields as an alternative for the following ontologies when necessary: GO (Gene Ontology), Uberon, EFO (Experimental Factor Ontology), and CL (Cell Ontology)
- Links to the OLS for various vocabulary searches (MonDO, GO, Uberon, EFO, CL)
- Help document for searching MonDO
- Updated GCI Help document to support use of MonDO disease terms and free text
- Ability to annotate to Orphanet, Disease Ontology (DO), OMIM, and NCIt (NCI Thesaurus) disease terms found in the Monarch Disease Ontology (MonDO), thus greatly expanding the scope of allowed disease terms (significant data model enhancement required)
- Mapping and transfer of current annotations from Orphanet terms to their equivalent MonDO disease terms (Orphanet, DO, OMIM, or NCIt)
- Addition of free text fields as an alternative to MonDO disease terms, in the event an appropriate term ID cannot be found. This requires the addition of a free text term name and either HPO term(s) or a definition for the term.
- Addition of a table of ClinVar SCVs on the Basic Info tab
- Reverse the display order of PP3 and BP4 criteria
- Reorder the display of BA1, PM2 and BS1
- Changes to Population tab
- Change "Highest Minor Allele Frequency to "Subpopulation with the Highest Minor Allele Frequency"
- Display this Highest MAF section directly above the ExAC table when in an Interpretation
- Updated VCI Help document to support use of MonDO disease terms and free text
- A second curator currently can’t choose to count a LOD score added by another curator
- User reported issue with ExAC data for multi-allelic variants (due to changes in ExAC's file format) was fixed in collaboration with MyVariant.info
- Fix to "Score" pulldown that affected a second curator's permission to score the evidence when changed back to "No Selection"
- Update to React 15
- HPO fields: the HPO entry fields have now been increased in size to allow the display of many HPO IDs; additionally, this entry box can now be expanded even further if more room is needed (user request)
- Model Systems HPO fields: per the request of curators, the HPO fields in this experimental evidence category allow more than one HPO term to be entered
- Modify Classification pulldown: the calculated classification value (e.g. "Limited") for a Summary has been removed from the Modify classification pulldown to eliminate confusion
- Modify Classification pulldown: the term "No Reported Evidence" has been added to the Modify Classification pulldown so curators can choose this when they save a Classification that has only Experimental evidence comprising its score
- The phrase "No reported evidence," initially used to indicate a Summary had not been saved, has been removed from the header and replaced with the word "None" to eliminate confusion (user request)
- Orphanet colons: Orphanet terms can now be entered with or without a colon separating ORPHA from the id number (e.g. a user can now enter ORPHA15 or ORPHA:15) to make it easier to copy/paste terms directly from the Orphanet (user request)
- gnomAD data: although gnomAD data is not yet available for download or via API, we have included a gnomAD section with links to gnomAD data for a variant wherever possible as well as a link to the gnomAD home page (user request)
- ExAC "mis Z" (corrected missense Z) and "syn Z" (corrected synonymous Z) scores (for "All ExAC," "Non-psych," and "Non-TCGA" datasets) have been added to the gene-centric tab (user request)
- Orphanet colons: Orphanet terms can now be entered with or without a colon separating ORPHA from the id number (e.g. a user can now enter ORPHA15 or ORPHA:15) to make it easier to copy/paste terms directly from the Orphanet site (user request)
- A second curator cannot curate evidence from a PMID added to the Gene:Disease record by another curator
- A second curator currently can’t choose to count a LOD score added by another curator
- Fixed user-reported issue where adding an additional PMID to a Gene:Disease record duplicated the proband score
- Fixed user-reported issue that Interpretations were not displaying correctly in the interface
- Fixed user-reported issue that gene-centric tab stalled for a specific variant
- Update to Auth0 authentication system because Persona is shutting down
- Update of authentication/login information in Help Document
- “Demo Login” feature that allows user to explore demo/test version of interface with registering their email and password.
- PubMed modal now returns citation for user to verify before adding to either Gene-Disease record or Variant Interpretation record
- Update to mode of inheritance list to provide only “core” modes of inheritance to be used for both gene and variant curation
- Restructuring of data model to support new scoring system
- Addition of Case-Control entry form
- Allows curator to add information about a Case Cohort side-by-side with a Control Cohort
- Provides ability to capture fields needed to evaluate & score the strength of the Case-Control Study
- Updates to the Family page
- Required updates to fields to support the capture of information needed for consideration of Segregation and the capture of published LOD scores or calculation of estimated LOD scores, necessary for new scoring framework
- Addition of fields to capture zygosity, necessary for new scoring framework
- Direct link to Evidence View in the Variant Curation Interface for variants associated with the Family
- Direct link to “Curate Variant” page for variants
- Updates to fields in Demographics section
- Updates to Individual page
- Addition of fields to capture zygosity, necessary for new scoring framework
- Direct link to Evidence View in the Variant Curation Interface for variants associated with the Individual
- Direct link to “Curate Variant” page for variants
- Addition of ability to indicate whether proband will be scored, needs review, or provides evidence that contradicts the gene-disease association
- Updates to “Curate Variant” page
- Addition of ability to select gene impact of variant, required for scoring
- Direct link to Evidence View for variant in the Variant Curation Interface
- Removal of certain fields no longer needed
- Removal of assessment of Segregation and Variant according to new scoring framework
- ClinVar and ClinGen Allele Registry links on Select Variant page now open in new tab/window
- Updates to ClinGen’s Allele Registry that return GRCh37 and GRCh38 allele representations allow for the return of Population and Predictive evidence for novel variants registered using either GRCh37 or GRCh38 allele representations.
- Scores are not yet calculated for Case Level evidence as this is still somewhat in flux; Experimental evidence scoring will be updated at same time as Case Level
- Summary View is not yet available as it requires solidified scoring algorithm, which was still in flux at time of this release
- Gene Curation Interface supports entry of one or two ClinVar VariationIDs or one CinVar VariationID and a non-ClinVar variant using any reasonable representation of that allele (CA IDs strongly encouraged).
- New links at the top of all pages support quick navigation within and between interfaces
- 'New Variant Curation' links to the 'Select Variant for Variant Curation' page
- 'New Gene Curation' links to the 'Select Gene-Disease Record' page
- '?' icon links to a Variant Curation Interface Help Document
- Improved display of criteria evaluations to minimize vertical space and scrolling
- New checkbox functionality for tabs, enabling curators to indicate when they have finished their evaluation of the evidence for that tab
- New sub-tabs now divide the evidence in the Predictors tab by molecular consequence, either 'Missense', 'Loss of Function', Silent & Intron' or 'In-frame Indel'
- Added ability to evaluate each of the 28 ACMG criteria
- Added ability to adjust the strength of an evaluation of an individual criterion
- Added all specified built-in checks to avoid positive evaluation of contradictory criteria
- Included ability to distinguish between a new evaluation and updates to a previous evaluation through use of "Save" vs. "Update" buttons
- Within the Variant Interpretation Record, a Progress bar now summarizes the number and strength of benign and/or pathogenic criteria met as well as the calculated pathogenicity
- The number of criteria meeting a certain strength is updated on-the-fly each time an evaluation of criterion/criteria is saved
- The pathogenicity is automatically calculated and updated on the Progress bar each time an evaluation of criterion/criteria is saved
- Added 'ClinVar Interpretations' table, which contains the Review Status, Clinical Significance and associated Disease(s) for each RCV from ClinVar
- Added 'RefSeq Transcripts' table, which includes the full set of RefSeq representations from Entrez and their associated molecular consequences
- All transcript tables now include an 'Exon' column that shows the exonic position of the variant within the transcript, where appropriate
- 'Canonical transcript' highlighted with an asterisk within the transcript tables
- New 'ExAC Constraint Scores' table that includes the pLI, pRec and pNull scores for all, non-psych and non-TCGA populations
- New link to ClinVar which returns all variants in the same gene
- New 'Gene Resources' table containing useful links to resources about the gene
- New 'Protein Resources' table with useful links pertaining to the protein product of the gene, where appropriate
- Attributions to resources used to aggregate data from external resources (e.g. MyVariant.info, MyGene.info and Variant Effect Predictor)
- Ability to compare old and new stored evidence, enabling a notice to curators when some of the data they based an evaluation upon has changed
- Thank you to Raj Ghosh, who spotted a bug in the ExAC population table whereby zero values were incorrectly rendered. This has now been fixed.
- Currently, each curator can only create one Interpretation/variant
- Our current login authentication provider, Persona, does not work with the most recent version of Firefox (v48). We recommend using Google Chrome instead.
- Ability to enter and view any existing evidence for 1) a ClinVar variant using a ClinVar VariationID or 2) a novel allele that has been registered with Baylor's ClinGen Allele Registry http://reg.clinicalgenome.org/ using the CA ID provided by this registry
- "View Evidence" and "Interpretation" modes for each variant
- Population evidence, when it exists for the variant, from ExAC, 1000 Genomes, and ESP
- Highest MAF value calculated and returned
- Ability to set desired CI and automatically calculate lower- and upper-CI values when in Interpretation mode
- Computational and predictive evidence, when it exists for the variant, from the ClinGen meta-predictor REVEL https://sites.google.com/site/revelgenomics/about (Bustamante Group) and dbNSFP https://sites.google.com/site/jpopgen/dbNSFP
- Search ClinVar for variants in same codon (Molecular Consequence: missense)
- Links to region +/- 30 bp of variant (Molecular Consequence: In-frame indel)
- Random Forest ensemble pathogenicity predictive information for the CFTR gene (Bustamante lab)
- Ability to move from "View Evidence" to "Interpretation" mode
- Ability to evaluate criteria associated with existing evidence
- Population: BA1, PM2, BS1
- Computational & Predictive: BP4, PP3, BP7, PM5, PS1, BP1, PP2, BP3, PM4
- Ability to associate a disease (Orphanet term) with an Interpretation
- Ability to view and distinguish between disease-dependent and -independent criteria
- Collapsible section headers
- Direct links to relevant resources for variant
- Interpretation history
- Currently, each curator can create only one Interpretation/variant
- Population and Computational data is currently returned for SNPs only
- Manual refresh of a page causes page to refresh several times
- Implement variant list refresh on submitForm of Individual Edit page
- Link text in curation palettes are offset from the baseline
- Briefcase button
- The edit form of Group/Family Method does not retain pre-existing data
- Set character limit on Group, Family, Individual and Experimental Labels
- Fix overhanging labels on curation palette
- Publications should be sorted only alphabetically and not by case
- Replace deprecated react-tools and jstransform with babel
- Cloud monitoring of production site
- Added note above Segregation Assessment on edit Family page when the assessment is not editable
- Added note to Edit/Assess page to indicate that the original curator has not yet provided an assessment
- Extended help text on Family page to indicate when a proband has been added to the Family
- Updated help text on Group Information edit page to clarify the options available for curators after a Group is created
- Updated help text for variants without ClinVar VariationIDs
- Established consistent use of "VariationID" and "ClinVar Preferred Title" labels throughout the site
- Fixed instruction text to make sure it never overlays the buttons in a narrow browser window
- Fixed form error message on Experimental Data Information page which previously remained displayed after the fields had been reset
- Fixed variant text in "Associated Variants" panel of the GDM page so that it doesn't wrap to the next line
- Fixed Mutalyzer text displaying on the line below on Family page in a narrow browser window
- Fixed error that occurred when clicking on some of the Variant pages' navigation breadcrumb links
- Fixed error where curators could not update the names of some variants in the production interface
- Fixed bug where Family segregation could be assessed without any segregation data
- Upgraded user interface JavaScript framework to React 0.14
- Added ClinVar Preferred Titles for all variants that had a ClinVar VariationID
- Version compiled JavaScript and CSS for new releases to prevent caching of old versions
- Added ability to write JavaScript maps while in development mode
- Ability to return to the Gene-Disease-Mode+selected PMID from various locations
- Obtain ClinVar preferred name based on ClinVar Variation ID [curator request]
- Check for ClinVar preferred name based on ClinVar variation ID and ask curator if variant is correct
- Display ClinVar preferred name (if it is available in database) throughout site [curator request]
- Variant section (blue bars near top) on main Gene-Disease-Mode page
- Variant curation palette (area on bottom of curation palette on right side of Gene-Disease-Mode page)
- Better differentiation of selected/non-selected PMID (background/text color + box around citation + Abstract)
- Add help note to Name/Label fields [curator request]
- Change "Name" to "Label" for Group, Family and Individual [curator request]
- Change slanted less than or equal to standard less than or equal on Summary
- Add link to Mutalyzer to interface where variants are entered
- Add warning note to "Individual Name" field [curator request]
- Switching between A and B for Experimental evidence types should clear entry fields
- Add example text under "Other description" for variant [curator request]
- Add message to check if individual/family part of group [curator request]
- Add note to Summary page when contradictory assessment exists
- Placement of title on Submit pages
- Adjust schema to store ClinVar preferred name for a variant
- Fixed PMID not shown as selected (out of view in PMID list) for long lists of PMIDs
- Fixed spinning "Add Article" button after invalid PMID added
- Restored ability to add multiple variants on Experimental curation
- Fixed Assessment panel not being visible on View pages
- Fixed Assessment/page navigation disabling subsequent curation forms
- Fixed Curate Variant page (not rendering properly)
- Fixed explanation text for HPO terms (was HP_ instead of HP:)
- Fixed Family creation: Indiv name + Orphanet required only if VariationID present OR "Other description" has variant info
- Fixed inability to cancel Add PMID and Add OMIM ID modals on IE11
- Added configs for testing of Chrome on Windows virtual machines
- "Genome-wide Study?" method question updated with clarified text for Group/Family/Individual creation
- Curation central page (Gene-Disease-Mode main page) will default to show the first PMID abstract if none has been selected
- Updated delete functionality: - Report to user all related sub-items that would be deleted before deletion occurs - Make all children of the deleted item also have a status of 'deleted' - Items marked as deleted will not be returned in search results
- Generate Summary button greyed out and turned off on the Summary page
- For Group, Orphanet ID is no longer a required field if either an HPO or free text phenotype is entered - i.e. only one of the following is required for a Group: Orphanet ID, HPO term, or phenotype free text.
- Add ability to copy Orphanet ID or Phenotype (HPO) or Phenotype (free text) from parent Group or parent Family
- On Group and Family pages, updated text for Phenotype and Disease
- Text expanded for methods 'High resolution melting' and 'Sanger sequencing'
- Additional explanatory text for HPO term or Phenotype description requirements
- Fixed login on Windows 7 + IE11
- Fixed unresponsive delete button on Windows 7 and Chrome
- Multiple open window handling: Use REST call to get up-to-date version of the parent object before save
- Improved ability to track history/provenance of records
- Added lines to history items on dashboard to make them clearer
- Entire Gene-Disease-Mode block now clickable
- ClinVar Variation ID linked to ClinVar
- Link to Family from family name from Individual when User needs to edit it to change Variant
- Copy Orphanet ID for Orphanet field for Family, Individual pages when coming from a Group (Family, Individual) or Family (Individual)
- Linkouts to HPO, ClinVar, PubMed, Uberon, QuickGO for various IDs throught the site
- Show term names, when available, for IDs (e.g. disease names for Orphanet IDs)
- Enhancements to clearly show test vs. production sites
- Increase methods in "Experimental"->"Protein Interactions"->"Method by which interaction detected"
- Orphanet ID no longer required for Group/Family/non-proband Individual
- Generate New Summary button now inactive on Provisional page
- Potential error in counting when 3 curators working on a record resolved
- Upgrade to Node 5 and npm 3
- Move to eslint JavaScript style/error checking vs JSX/JShint, plus use babel package for JS
- Variant curation/assessment
- Experimental Data curation/assessment
- Assessments for Family segregation
- Summary and Provisional Classification
- Display/Usability changes throughout site
- Variant curated icon
- Proband icon
- Changed required fields for Group curation
- Individual curation proband designation moved to more prominent location
- Displaying waiting symbol on form Save buttons while Save is in progress
- Demo notice will not be shown on production site
- Only 2 Variants can be added for Family and Individuals
- Direct users to create proband for Family only through Edit Family page
- Family segregation assessment can only be made if segregation data added
- Curator can generate and save Summary and Provisional Classification
- Assessments
- Pathogenicity
- Experimetal
- Provisional Classification
- Group
- Family
- Annotation
- Article
- Individual
- Variant
- Gene-Disease-Mode parent object
- Submission of some forms using Firefox
- Owner of object changed on update by addtional curator
- Parameters passed to assessments
- PMID invalid message despite successful PMID addition
- Assessment of Experimental Data had incorrect evidence_type
- Multiple assessment objects created from View page
- Prevent multiple form submissions
- Prevent pathogenicity being shared amongst multiple users
- Remove cross Gene-Disease record assessments
Feedback and Comments? Please email us at: clingen-helpdesk@lists.stanford.edu