More ORPHA-related refactoring, other improvements and fixes

[4.79]

Added

• Added tags for Sniffles and CNVpytor, two LRS SV callers
• Button on case page for displaying STR variants occurring in the dynamic HPO panel
• Display functional annotation relative to variant gene's MANE transcripts on variant summary, when available
• Links to ACMG structural variant pathogenicity classification guidelines
• Phenomodels checkboxes can now include orpha terms
• Add incidental finding to case tags

Changed

• In the diagnoses page genes associated with a disease are displayed using hgnc symbol instead of hgnc id
• Refactor view route to allow navigation directly to unique variant document id, improve permissions check
• Do not show MANE and MANE Plus Clinical transcripts annotated from VEP (saved in variants) but collect this info from the transcripts database collection
• Refactor view route to allow navigation directly to unique case id (in particular for gens)
• Institutes to share cases with on institute's settings page now displays institutes names and IDs
• View route with document id selects view template based on variant category

Fixed

• Refactored code in cases blueprints and variant_events adapter (set diseases for partial causative variants) to use "disease" instead of "omim" to encompass also ORPHA terms
• Refactored code in scout/parse/omim.py and scout/parse/disease_terms.py to use "disease" instead of "phenotype" to differentiate from HPO terms
• Be more careful about checking access to variant on API access
• Show also ACMG VUS on general report (could be missing if not e.g. pinned)

Case status labels, ORPHA disorders, MANE and ClinVar updates

[4.78]

Added

• Case status labels can be added, giving more finegrained details on a solved status (provisional, diagnostic, carrier, UPD, SMN, ...)
• New SO terms: sequence_variant and coding_transcript_variant
• More MEI specific annotation is shown on the variant page
• Parse and save MANE transcripts info when updating genes in build 38
• Mane Select and Mane Plus Clinical badges on Gene page, when available
• ClinVar submission can now be downloaded as a json file
• API endpoint to pin variant
• Display common/uncommon/rare on summary of mei variant page

Changed

• In the ClinVar form, database and id of assertion criteria citation are now separate inputs
• Customise institute settings to be able to display all cases with a certain status on cases page (admin users)
• Renamed Clinical Significance to Germline Classification on multistep ClinVar form
• Changed the "x" in cases.utils.remove_form button text to red for better visibility in dark mode
• Update GitHub actions
• Default loglevel up to INFO, making logs with default start easier to read
• Add XTR region to PAR region definition
• Diagnoses can be searched on diagnoses page without waiting for load first

Fixed

• Removed log info showing hgnc IDs used in variantS search
• Maintain Matchmaker Exchange and Beacon submission status when a case is re-uploaded
• Inheritance mode from ORPHA should not be confounded with the OMIM inheritance model
• Decipher link URL changes
• Refactored code in cases blueprints to use "disease" instead of "omim" to encompass also ORPHA terms

Updates to ClinVar submission, GnomAD constraints, ORPHA and bug fixes

[4.77]

Added

• Orpha disease terms now include information on inheritance
• Case loading via .yaml config file accepts subject_id and phenotype_groups (if previously defined as constant default or added per institute)
• Possibility to submit variants associated with Orphanet conditions to ClinVar
• Option update path to .d4 files path for individuals of an existing case using the command line
• More constraint information is displayed per gene in addition to pLi: missense and LoF OE, CI (inluding LOEUF) and Z-score.

Changed

• Introduce validation in the ClinVar multistep form to make sure users provide at least one variant-associated condition
• CLI scout update individual accepts subject_id
• Update ClinVar inheritance models to reflect changes in ClinVar submission API
• Handle variant-associated condition ID format in background when creating ClinVar submissions
• Replace the code that downloads Ensembl genes, transcripts and exons with the Schug web app
• Add more info to error log when transcript variant frequency parsing fails.
• GnomAD v4 constraint information replaces ExAC constraints (pLi).

Fixed

• Text input of associated condition in ClinVar form now aligns to the left
• Alignment of contents in the case report has been updated
• Missing number of phenotypes and genes from case diagnoses
• Associate OMIM and/or ORPHA diagnoses with partial causatives
• Visualization of partial causatives' diagnoses on case page: style and links
• Revert style of pinned variants window on the case page
• Rename Clinical significanc to Germline classification in ClinVar submissions exported files
• Rename Clinical significance citations to Classification citations in ClinVar submissions exported files
• Rename Comment on clinical significance to Comment on classification in ClinVar submissions exported files
• Show matching partial causatives on variant page
• Matching causatives shown on case page consisting only of variant matching the default panels of the case - bug introduced since scout v4.72 (Oct 18, 2023)
• Missing somatic variant read depth leading to report division by zero

d4 files, ClinVar event audit, and winter bug fixes

[4.76]

Added

• Pydantic validation of image paths provided in case load config file
• Info on the user which created a ClinVar submission, when available
• Associate .d4 files to case individuals when loading a case via config file

Changed

• In diagnoses page the load of diseases are initiated by clicking a button
• Revel score, Revel rank score and SpliceAI values are also displayed in Causatives and Validated variants tables
• Remove unused functions and tests
• Analysis type and direct link from cases list for OGM cases
• Removed unused case_obj parameter from server/blueprints/variant/controllers/observations function
• Possibility to reset ClinVar submission ID
• Allow ClinVar submissions with custom API key for users registered as ClinVar submitters or when institute doesn't have a preset list of ClinVar submitters
• Ordered event verbs alphabetically and created ClinVar-related user events
• Removed the unused "no-variants" option from the load case command line

Fixed

• All disease_terms have gene HGNC ids as integers when added to the scout database
• Disease_term identifiers are now prefixed with the name of the coding system
• Command line crashing with error when updating a user that doesn't exist
• Thaw coloredlogs - 15.0.1 restores errorhandler issue
• Thaw crypography - current base image and library version allow Docker builds
• Missing delete icons on phenomodels page
• Missing cryptography lib error while running Scout container on an ARM processor
• Round CADD values with many decimals on causatives and validated variants pages
• Dark-mode visibility of some fields on causatives and validated variants pages
• Clinvar submitters would be cleared when unprivileged users saved institute settings page
• Added a default empty string in cases search form to avoid None default value
• Page crashing when user tries to remove the same variant from a ClinVar submission in different browser tabs
• Update more GnomAD links to GnomAD v4 (v38 SNVs, MT vars, STRs)
• Empty cells for RNA fusion variants in Causatives and Verified variants page
• Submenu icons missing from collapsible actionbar
• The collapsible actionbar had some non-collapsing overly long entries
• Cancer observations for SVs not appearing in the variant details view
• Archived local observations not visible on cancer variantS page
• Empty Population Frequency column in the Cancer SV Variants view
• Capital letters in ClinVar events description shown on case page

Display gene panel membership on gene hovers, Fusion variant filters, Alamut link improvements, and more

[4.75]

Added

• Hovertip to gene panel names with associated genes in variant view, when variant covers more than one gene
• Tests for panel to genes
• Download of Orphadata en_product6 and en_product4 from CLI
• Parse and save database_found key/values for RNA fusion variants
• Added fusion_score, ffpm, split_reads, junction_reads and fusion_caller to the list of filters on RNA fusion variants page
• Renamed the function get_mei_info to set_mei_info to be consistent with the other functions
• Fixed removing None key/values from parsed variants

Changed

• Allow use of projections when retrieving gene panels
• Do not save custom images as binary data into case and variant database documents
• Retrieve and display case and variant custom images using image's saved path
• Cases are activated by viewing FSHD and SMA reports
• Split multi-gene SNV variants into single genes when submitting to Matchmaker Exchange
• Alamut links also on the gene level, using transcript and HGVS: better for indels. Keep variant link for missing HGVS
• Thaw WTForms - explicitly coerce form decimal field entries when filters fetched from db

Fixed

• Removed some extra characters from top of general report left over from FontAwsome fix
• Do not save fusion variants-specific key/values in other types of variants
• Alamut link for MT variants in build 38
• Convert RNA fusions variants tool_hits and fusion_score keys from string to numbers
• Fix genotype reference and alternative sequencing depths defaulting to -1 when values are 0
• DecimalFields were limited to two decimal places for several forms - lifting restrictions on AF, CADD etc.

Fix BioNano API FSHD report requests, missing icons and load OMIM terms not associated to genes

[4.74.1]

Changed

• Parse and save into database also OMIM terms not associated to genes

Fixed

• BioNano API FSHD report requests are GET in Access 1.8, were POST in 1.7
• Update more FontAwesome icons to avoid Pro icons
• Test if files still exist before attempting to load research variants

Loading of RNA fusion variants, missing icons fix & other

[4.74]

Added

• SNVs and Indels, MEI and str variants genes have links to Decipher
• An owner + case display name index for cases database collection
• Test and fixtures for RNA fusion case page
• Load and display fusion variants from VCF files as the other variant types
• Option to update case document with path to mei variants (clinical and research)

Changed

• Details on variant type and category for audit filters on case general report
• Enable Gens CN profile button also in somatic case view
• Fix case of analysis type check for Gens analysis button - only show for WGS

Fixed

• loqusdb table no longer has empty row below each loqusid
• MatchMaker submission details page crashing because of change in date format returned by PatientMatcher
• Variant external links buttons style does not change color when visited
• Hide compounds with compounds follow filter for region or function would fail for variants in multiple genes
• Updated FontAwesome version to fix missing icons

Fix loading of cases without display name and other improvements

[4.73]

Added

• Shortcut button for HPO panel MEI variants from case page
• Export managed variants from CLI

Changed

• STRs visualization on case panel to emphasize abnormal repeat count and associated condition
• Removed cytoband column from STRs variant view on case report
• More long integers formatted with thin spaces, and copy to clipboard buttons added

Fixed

• OMIM table is scrollable if higher than 700px on SV page
• Pinned variants validation badge is now red for false positives.
• Case display name defaulting to case ID when family_name or display_name are missing from case upload config file
• Expanded menu visible at screen sizes below 1000px now has background color
• The image in ClinVar howto-modal is now responsive
• Clicking on a case in case groups when case was already removed from group in another browser tab

GnomAD default build change

A patch release to correct links to match the new GnomAD v4 release, which changed default build to 38 in their API just in time for ASHG.

[4.72.4]

Changed

• Automatic test mongod version increased to v7

Fixed

• GnomAD now defaults to hg38 - change build 37 links accordingly

Fix cancer cases general report report

[4.72.3]

Fixed

• Somatic general case report small variant table can crash with unclassified variants