# Release notes: Latest releases

Major versions Minor versions
v1.12 v1.12.1, v1.12.2, v1.12.3
v1.11 v1.11.1, v1.11.2, v1.11.3
v1.10 v1.10.1

See older releases for earlier versions.

# Version 1.12.3

Release date: 19.02.2021

# Highlights

This release adds a few bugfixes.

# All changes

  • Fixed a bug causing loading of certain historical analyses to fail.
  • Fixes to deposit and backend.

# Version 1.12.2

Release date: 29.01.2021

# Highlights

This release adds a few bugfixes.

# All changes

  • Fixed a bug causing ELLA not to start.
  • Fixed a bug causing excessive memory use in exports of variant interpretation database.
  • Fixed an error in test configuration.

# Version 1.12.1

Release date: 19.01.2021

# Highlights

This release adds a few bugfixes.

# All changes

  • Fixed a bug that caused pre- and postprocessing to fail.
  • Fixed a bug that caused missing "Requested" date on imported analyses.
  • Fixed a bug that caused performance problems.

# Version 1.12

Release date: 13.01.2021

# Highlights

This release includes many fixes and improvements, both to the frontend and backend/development environment. The most significant changes for users include changes to classification, history and variant warnings:

# Redefined classification choices

Variant classification choices have been redefined in line with ClinVar definitions (opens new window):

  • CLASS U was renamed to NOT PROVIDED, meant for recording various information (literature/research/clinical/phenotyping) without interpreting clinical significance. It is recommended to configure this class to be immediately outdated.
  • The choice RISK FACTOR was added, meant for variants that are interpreted not to cause a disorder but to increase the risk.

The classification choices are now:

Figure: Redefined variant classification choices.

# Improvements to history

History for changes to the variant CLASSIFICATION REPORT field was added, and the HISTORY pop-up now shows a drop-down for viewing previous versions instead of listing them:

Figure: Modified variant history view with addition of Report history and drop-down for previous versions.

In addition, when opening a previously finalized analysis, ELLA will now default to displaying the state corresponding to the latest interpretation round, i.e. showing variant interpretations, classifications and annotation exactly as they were presented at the time of the last finalization. The previous default, CURRENT DATA (along with any other interpretation round), is still available using the drop-down in the top bar. To prevent confusion, a warning was added when viewing historical data.

Figure: Latest interpretation round now selected by default (with warning) for historic analyses.

# Improved warnings

To improve visibility of the different variant warnings displayed on the CLASSIFICATION page, collision warnings are now shown in a yellow banner separate from annotation and user group warnings (red), and collision warnings are no longer included in the ! tag in the sidebar:

Figure: Collision and annotation warnings are now separate.

In addition, ELLA now displays a message at the bottom of the page if a finalized variant in an ongoing analysis has been updated and finalized by another user:

Figure: Message when evaluation has been updated by another user.

Note that the message is only displayed when a user finalizes another variant or manually refreshes the view.

# Select user group on custom imports

To better support custom gene panel imports that should be available to more than one user group, the custom gene panel import dialogue now includes an option to select user groups:

Figure: Message when evaluation has been updated by another user.

# All changes

# Version 1.11.3

Release date 11.11.2020

# Highlights

This release adds a bugfix for the frequency filter.

# All changes

  • Fixed a bug that caused a timeout in the frequency filter and failed loading of the associated analysis.

# Version 1.11.2

Release date: 27.10.2020

# Highlights

This release adds bugfixes related to manually appending results to an analysis.

# All changes

  • Fixed a bug where filters using inheritance_mode failed to load when there are more than two proband samples in an analysis (e.g. on manual appending import).
  • Fixed a bug where manually appending an import to a finalized analysis fails.

# Version 1.11.1

Release date: 21.08.2020

# Highlights

This release adds a few bugfixes and improvements.

# All changes

# Version 1.11

Release date: 25.06.2020

# Highlights

This release brings an improved gene information popup with editing possibilities, and several changes and improvements to the OVERVIEW page.

# User-editable gene information

The gene information popup (click the gene name in the top bar) has been improved, with the possibility to add and edit comments about the gene. This can be used for information that is important for evaluating variants in this gene, and is available for all analyses where the gene is included.

Figure: User-editable gene information.

If a comment has been added, an INFO tag is shown next to the gene name.

# New OVERVIEW filter feature

A new filter feature was added to the ANALYSES OVERVIEW page to quickly locate subsets of analyses. You can filter by these parameters:

  • Analysis name
  • Comment text (e.g. useful with auto-comments)
  • Date requested (ranges up to current date)
  • Show only
    • HTS/Sanger
    • Priorities Normal/High/Urgent

Any combination of these filters is allowed.

Figure: User-editable gene information.

Note that the filters do not include finalized analyses.

# Optional OVERVIEW sections replaced with auto-comments

This release retires the optional classification status sections on the OVERVIEW page and replaces them with a possibility to auto-add comments (ALL CLASSIFIED/NO VARIANTS) upon deposit of new analyses to the ELLA database. In addition, the VARIANTS OVERVIEW page has been limited to manually imported, stand-alone variants or individual variants opened from search.

# Option to set GQ thresholds for de novo candidates

To remove false positive de novo predictions in the segregation filter, it is now possible to set a genotype quality (GQ) threshold. This will disregard any de novo prediction where the proband, father or mother in a trio has a GQ value below the given thresholds.

# All changes

# Version 1.10.1

Release data: 15.06.2020

# Highlights

This release fixes a few bugs bugs related to references and reference assessments.

# All changes

  • Fixed a bug where existing reference assessments would not show if no longer part of annotation
  • Fixed a bug where ClinVar references would not be recognized during import of ClinVar annotation
  • Fixed a bug where HGMD reference comments would display un-translated character sequences

# Version 1.10

Release date: 09.06.2020

# Highlights

This release brings improvements to the variant filters, a new version of IGV for Visual mode, as well as several smaller improvements and fixes.

# Improved variant filters

All criteria in the segregation filter can now be enabled/disabled separately, allowing for increased flexibility. In addition, the quality filter can now use the VCF FILTER status (PASS/...) as a parameter.

# All changes

  • Added configuration for segregation filter.
  • Renamed "Inherited mosaicism" to "Parental mosaicism"; The associated M tag can now appear together with other Segregation tags in the sidebar if multiple conditions are true.
  • Added possibility for using VCF FILTER status in quality filter.
  • Removed QUAL≤300 as a criterion for the NEEDS VERIFICATION warning and the Q tag.
  • Upgraded IGV (in Visual mode) to version 2.5.4, with several minor improvements.
  • The number shown on the WORK LOG button now includes a count of all user added messages, including from previously finalized analysis rounds.
  • Removed VARIANT REPORT button from OVERVIEW.
  • Open the previously selected overview page when returning from search.
  • Fixed a bug causing wrong open-end position for insertions.
  • Fixed a bug causing incorrect filtering for regions with 1 base.
  • Fixed a bug causing incorrect rescue of variants annotated with non-standard terms in the ClinVar database.
  • Fixed a bug causing a wide sidebar with long indication comments.
  • Fixed a bug causing missing word wrap in comment fields.
Last Updated: 2/19/2021, 1:24:07 PM