New version of Genomenal 2.2.0

Mon, 05/22/2023 - 09:00
New version of Genomenal 2.2.0

New features:

  • A new, unique interpreter collaboration system - Genomic Relationship Management.
  • A new pipeline has been introduced that allows for the prediction of polygenic traits for samples in FASTQ format.
  • The display now includes the interpretation of identical variants in other samples that have been uploaded to the account and previously interpreted.
  • A new setting, "Compound Heterozygotes", has been added to the query builder. This setting, used after applying other filters, allows for the extraction of those variants that may be in a compound heterozygous form from the filtered ones. This setting is particularly relevant for group analysis.
  • The display now includes the interpretation of identical variants in other samples uploaded to the account and previously interpreted.
  • The ability to add tracks of other samples uploaded to the account to the Integrative Genomics Viewer (IGV) has been implemented.

Improvements:

  • Databases updated to the latest versions.
  • Added support for variant phase groups (new column in VV "Phase group status", by default the column is not shown).
  • Added Enigma database annotation (new columns in VV "ENIGMA clinical significance" and "ENIGMA clinical significance comment", by default the columns are not shown).
  • Added new scorers MaxEntScan, MutationAssessor, added precalculated CADD and SpliceAI.
  • Added ability to export variants whose parameters (interpretation, anchoring, pathogenicity, etc.) have been changed.
  • Added a new "Label" column in the Variant Viewer (VV) to allow the significance of a variant to be marked or to indicate that a variant is a sequencing error (by default the column is not displayed).
  • Added the ability to filter by multiple HPO terms.
  • Added the ability to sort by multiple columns.
  • Added additional external links to open databases (UCSC, Franklin).
  • Added color coding of ClinVar pathogenicity, shortened pathogenicity names.
  • Copying variant positions from the variant table to VV is now done with a single mouse click.
  • In VV, a frequency filter (using gnomAD) with defined thresholds has been added to the basic filters. The option is enabled in the VV settings in the user profile.
  • The ability to add new samples to a previously created run has been implemented.
  • The Variant Interpretation/Comment field can now be edited in the General tab at the bottom of the VV window.
  • Variant details can be opened in a separate tab for easier comparison and analysis by right clicking on the "Show Variant Details" icon in the variant row.
  • Finding the required parameters to set filter conditions for variants in the Query Builder has been improved.