Changelog

v 1.8.4 (24.06.2024)
General changes:
  • Moved PFAM protein domains to population and in-silico tab on variant display page. They also have their own tag in downloaded vcfs now.
Bugfixes:
  • Fixed a bug where refseq consequences could not be shown
v 1.8.3 (24.06.2024)
General changes:
  • Improved automatic selection of cancerhotspots related criteria (OS3, OM3, OP3). They are now based on the amino acid residue as proposed by the VICC classification guidelines.
  • Added submitter id and selected state to classifications in downloaded vcf files
v 1.8.2 (22.04.2024)
General changes:
  • Added download routs for full versioned data download
  • Own user classifications can now be deleted
v 1.8.1 (11.04.2024)
General changes:
  • Downloading a VCF from a variant list now requires the user to first generate the VCF and then download it. This prevents timeout issues when the VCF is large.
Bugfixes:
  • Fixed a bug where the complete transcript information was inserted into the VCF. It was reverted back to the transcript name.
  • Fixed an error when inserting variants from tsv file.
v 1.8 (05.04.2024)
General changes:
  • Removed ARUP BRCA classifications since they are contained in ClinVar and the original database is no longer maintained
  • Added gnomAD popmax allele count annotation
  • Added all external ids to vcf output
  • Added BayesDEL annotation for all variants and removed TP53 DB BayesDEL annotation
  • Enhanced security with CSP
  • Updated documentation
  • Added link to genome nexus
  • The state is now automatically selected when copying evidence from users to consensus classifications
  • Added mutually exclusive criteria in VICC scheme:
    • OS3 (source) -> OM3, OP3 (target)
    • OM3 (source) -> OS3, OP3 (target)
    • OP3 (source) -> OS3, OM3 (target)
Bugfixes:
  • Fixed a bug when variants had multiple CIViC ids
  • Fixed some visual bugs
  • Resolved a bug that caused the final oncogenicity to be calculated wrong
  • Fixed a bug that caused criteria buttons to be unchecked when mutually exclusive criteria were unselected
  • Fixed a bug where some mutually exclusive criteria were not disabled properly
v 1.7.2 (28.03.2024)
Bugfixes:
  • Fixed a bug where the cancerhotspot annotations would be erroneous: If variants map to the same position in grch38 or are equal when left normalized their cancerhotspots annotations are now summed up
v 1.7.1 (25.03.2024)
General changes:
  • The OP4 criterium is now selected automatically when the variant is unknown to gnomAD
  • Improved the addition of variants to a user defined variant list. It is now possible to add a very large number without receiving a timeout.
Bugfixes:
  • Fixed a bug when searching for multiple variant strings the searched variant list would be empty in some cases
  • The transcripts could not be loaded in IGV
  • Fixed a bug when accessing the classification history page
  • The OP4 criterium was never selected automatically by the automatic classification algorithm
  • Some error flash messages when using incompatible search parameters were previously missing color
  • Fixed a bug where the SpliceAI annotation was causing an error if it didn't existed
v 1.7.0 (20.03.2024)
General changes:
  • OM4 criterion is now automatically selected
  • Improved automatic selection of OS1 criterion
  • Updated transcripts to ensembl 110
  • Added more administrator utility tooling like aborting of variant annotations and more fine grained reannotation of variant groups
  • Added more search options:
    • Variant string search
    • Changed external id search to general id search. It now allows to search for variant ids from this platform. Also added search for ClinVar ids
    • CDNA range search
    • Multiple user variant lists simultaneously
    • Mean user classification
  • Added a column to select variants from the variant list to add variants to a list in a more fine grained manner
Bugfixes:
  • Fixed a bug that caused SpliceAI to compute its scores even though they were already contained in the precomputed file
  • Removed smartmatch warning from VEP
  • When variants had multiple CIViC IDs only one was added. This also caused the annotation procedure to break
v 1.6.0 (22.02.2024)
General changes:
  • Added classification criteria state: not-selected
  • Imported variants & classifications from NGSD
  • Changed refseq transcripts to ensembl transcripts in IGV
Bugfixes:
  • In rare cases the submission condition in ClinVar submissions is na with a description. This case is now handled properly and does not produce erroneous links.
v 1.6.0 (20.11.2023)
General changes:
  • Added MaxEntScan SWA approach for non splice variants
  • REVEL annotations are now transcript specific
  • Added missing mutually exclusive criteria the full list is now:
    • OVS1 (selected) -> OM2 (disabled)
    • OS1 (selected) -> OM1 (disabled)
    • OS1 (selected) -> OM4 (disabled)
    • OS3 (selected) -> OM1 (disabled)
    • OS3 (selected) -> OM4 (disabled)
    • OM1 (selected) -> OM4 (disabled)
    • OM1 (selected) -> OM3 (disabled)
    • OM4 (selected) -> OM3 (disabled)
  • All columns in the variant overview table are now clickable and lead to the variant details page
  • Added Alpha Missense annotations
  • It is now possible to insert classifications without any criteria
  • Added UTR regions to transcripts in IGV browser
  • Fixed automatic classification using chasm and vest4
Bugfixes:
  • Improved popovers
  • Fixed a bug where certain ClinVar submissions were not shown
  • Fixed a bug which was not showing unselectable criteria correctly
v 1.5.3 (24.10.2023)
General changes:
  • Added more database statistics to the landing page
Bugfixes:
  • Fixed a bug where the user was unable to insert all variants to a user list from the browse variants table
v 1.5.2 (19.07.2023)
Bugfixes:
  • Fixed a bug where the user classification class was not shown correctly
v 1.5.1 (17.07.2023)
General changes:
  • TSV input can now also be space separated
Bugfixes:
  • Fixed a bug that prevented certain variants to be inserted
  • Fixed some wording
v 1.5 (10.07.2023)
General changes:
  • Added CIViC assertions and evidences annotations. They are also shown on the classify page for criteria OS1, OM4, OS2, OP2 and SBS2. However, they are not included in the automatic classification algorithm (yet).
  • Update landing page
  • Added possibility to hide variants
  • Added page size, sort by and include hidden options in variant search table
Bugfixes:
  • Fixed a bug where the user got a 500 error when inserting variants from tsv when not using the correct format
  • Fixed a bug where the user was not able to access their user defined variant lists in some cases
  • Fixed a bug that prevented some variants to be annotated because the disease field in oncoKB annotations was too long
v 1.4 (27.06.2023)
General changes:
  • The admin dashboard now shows some statistics about the number of variant annotation errors, warnings and number of variants in general.
  • The admin dashboard now allows to reannotate all variants that had an error during variant annotation.
  • Multiple COSMIC ids can now be shown when the variant has multiple COSMIC entries for the same transcript.
  • The literature table is now paginated, because they are sometimes very large and otherwise result in a performance issue.
Bugfixes:
  • Fixed a bug where the user classification table was not shown correctly in the classify page
  • Fixed a bug that prevented the user selected literature to be shown in the "Add from user" button on the consensus classify page
v 1.3 (26.06.2023)
General changes:
  • Status of automatic criteria selection on classify page is now shown
  • Updated columns in classification history page
  • Improved consensus classification reports
  • Activated option to add a comment to classifications
  • Improved admin dashboard
  • Improved variant table layout & added rsid and mean user class columns
  • Added an external id search
  • Improved table formatting
Bugfixes:
  • Fixed COSMIC annotations
  • Fixed a bug where the annotation pipeline was unable to update oncokb automatically
  • Fixed COSMIC links. They are now added to the header instead of the consequence table
  • Transcript specific annotations are now saved with transcript name and value in vcf
  • Fixed a bug where the criteria were not sorted correctly when displaying them in the variant details page
  • Fixed a bug that did not allow to access the variant classify page if the variant did not have any consequences
  • Fixed a bug that prevented criteria to be shown upon submitting an erroreneous classification
  • Fixed a bug that showed multiple "Nothing to show" rows in certain browsers
  • Popovers on classification criteria are now automatically closed when the user clicks outside of the popover itself
v 1.2 (11.05.2023)
General changes:
  • Improved account creation
  • Added profile page which allows changeing of name, mail and affiliation
  • Improved readability of annotations
  • External links now open in new tab on left click
  • GSvar variant import now supports "-" as reference or alternative base in case of insertion or deletion, respectively. This automatically fills the missing base from the reference genome.
  • Added cancer hotspots link to OM4 criterium on classify page
Bugfixes:
  • Fixed a bug in which the automatic classification did not correctly select some criteria
  • Fixed hover color over criteria buttons
  • Fixed a bug where the user was able to insert multi allelic variants
  • Fixed a bug in which the HGVS c. search did not show the correct error message
Known issues:
  • Links to COSMIC don't work sometimes
  • COSMIC annotations can be erroreneous when the gene is on the reverse strand
v 1.1 (05.05.2023)
General changes:
  • Added about page
  • Added documentation
  • Added impressum/disclaimer
  • Added favicon
Bugfixes:
  • Fixed variant history page unable to load in certain cases
  • Fixed access to profile page
  • Fixed a bug where the automatic classification algorithm would select wrong criteria
v 1.0
Initial release