1. Improvements

For the XetaBase 1.4.0 release we have been focussed on improving the testing and
reliability of the system, while enabling key customer requirements. Together these help us
move towards providing a fully certified system for clinical use.

The key improvements we have made include:

• All improvements and fixes from the following patch releases:
  • 1.2.10.1
  • 1.2.11
  • 1.2.12
• Built out the Zetta automation test suite for key components of the software
  • Key testing for CellBase
  • Key testing for the Catalog functionality of OpenCGA
• Upgraded the MongoDB version to 5.0.14, for the following components:
  • CellBase
  • OpenCGA
  • DevOps

1.1 OpenCGA version 2.6.0

The key functionality we have added includes:

Added the ability to filter by role in cancer independently of any other filters

• Implemented HRDetect analysis for mutational signatures
• Removed the hybrid selection analysis from the alignment Quality Control section
• Enabled OpenCGA to use the DataRelease functionality in CellBase to specify which
  version of the data to use
• Improvements to mutational signature analysis
  • Allowed steps to be run independently. Users may now execute; only the
  • counting step, only the fitting step, both steps
  • Allowed users to keep different signature fitting objects

1.2 CellBase version 5.2.8

The key functionality we have added includes:

• Updated CellBase to include both Genomes and Exomes data from GnomAD
• Updated the ClinVar data to 2022-11 version
• Added the ability to filter by role in cancer independently of any other filters

1.3 IVA version 2.6.0

The key functionality we have added includes:

• Enabled the ability to bulk add Genes when creating or editing Disease Panels
• Implemented the Study Admin Interface in IVA
• Enabled IVA to use the DataRelease functionality in CellBase to specify which
  version of the data to use
• Implemented a configurable ‘select all’ option for forms that contain more than one element. The select all option will only appear when the config parameter is set to true
• Improved usability of the Aggregation view of the Variant browser by changing the
  consequence type filter to a drop down list.

1.4 DevOps 1.4.0

The key functionality we have added includes:

• Added Grafana dashboard to monitor the XetaBase infrastructure
• Added additional alerting to identify expiring certificates
• Made the upload process more fault tolerant
• Delivered further automation of the release process to make it more reliable and
  scalable

2. Bug Fixes

The key bug fixes were:

• Allowed the first occurrence of a SNV and SV plot, displayed in the Mutational
  Signatures section of the report, to be configured
• Ensured the mutational signature analysis checks the Fitting ID is unique
• Provided a warning message in IVA when complex conditions need to be met
• Ensured IVA forms are cleared of data when the endpoint is changed

3. Future Improvements

Improvements scheduled for the XetaBase 1.5 release include:

• Continuing to increase the coverage of automation tests, both additional components
  and additional tests
• Improvements to filtering to enable quicker and more complete analysis of cases
• Making additional source data available to be displayed in IVA
• Continuing to improve the efficiency of the system
• Continuing to increase the stability and reliability of the system

Note: Planned improvements are for information purposes and may change subject to Zetta
Genomics internal processes.