Release notes: Latest releases
See older releases for earlier versions.
Release date: 02.12.2019
- Fixed bug where quality filtering did not work for multiple probands.
- Fixed bug where importing the same sample more than once caused a crash.
- Fixed bug causing several variants not to be filtered out as they should in the region filter.
Release date: 30.10.2019
- Fixed bug where users were not able to finalize analyses with reused allele assessments and auto-ignored references under "Pending evaluation".
- Fixed bug where reference data was not reloaded when including a variant from filtered variants.
Release date: 30.10.2019
Add "other" and unweighted ACMG criteria
Sometimes, criteria that don't match the ACMG guidelines are important for a variant interpretation, e.g. the ENIGMA criteria for the BRCA1/BRCA2 genes. ELLA now allows adding these to the interpretation as a generic
OTHER criterion. The type and impact on the classification should be given in this criterion's comment field once added.
In addition, users can often spend significant time evaluating an ACMG criterion for a particular interpretation, but in the end decide that the requirements are not met. ELLA now allows setting an added ACMG criterion as
NOT WEIGHTED, so that comments related to this work can be properly recorded.
Note that neither "other" or unweighted ACMG criteria are counted in the calculation of suggested classification.
Filter improvements: Gene and allele ratio
The filter settings now allows using genes as a variable in rules for filters or exceptions. This allows conditioning any rule on the presence/absence of a gene, e.g. exclude certain genes from a particular filter.
In addition, it is now also possible to use allele ratio (alternative allele reads/total reads) as a variable in the quality filter. In our experience, this gives a more powerful filter than using the
qual variable, especially for high sequencing depths. A caveat is that mosaic variants may be missed, but this can be partially be circumvented by adding particular genes where mosaics are expected to a gene exclusion rule as described above.
- Added possibility for adding non-ACMG criteria.
- Added possibility for setting ACMG criteria as unweighted.
- Added possibility to filter out or rescue variants in specific genes.
- Added possibility to use allele ratio in quality filter.
- Added possibility to configure irrelevant references to be automatically IGNORED; see Technical documentation for details.
- Made controls FULL - QUICK - VISUAL and INDICATION comment field in the sidebar sticky to reduce need for scrolling when there are many variants.
- Made collision warnings below the top bar sticky and collapsible.
- Increased number of retrieved reference search results.
- Added "Documentation" link to all pages.
- Added possibility to copy gene + transcripts from filtered results in GENE PANEL INFO.
- Fixed bug that caused non-working filtering in GENE PANEL INFO if using wrong case.
- Fixed bug resulting in empty interpretation window when no variant was selected.
- Fixed bug causing no alerts when navigating away from interpretation view with unsaved work.
- Import jobs now show time of day when job was started, and time stamp when status of job last changed.
- Improved Technical documentation.