Summary of Key New Features for VarSome Clinical 11.9

• Workflows 
• Long Reads 
• Sample and CNV Browser - New ROH track
• Live Annotation for somatic samples
• Multiple Minor Clinical UI enhancements 

Note: In order to enhance your account security,  from 19th December it will be mandatory for all users signing into VarSome Clinical to use two factor authentication. For further information on how this works please see the support page. 

New Clinical Features

Workflows

The most significant feature in this release is the ability to use Workflows to set parameters for your team’s analyses. Only your Group Supervisor is able to manage workflows. You can still continue to use VarSome Clinical without applying workflows. 

Long Reads 

Repeat Expansions

Now you can annotate VCFs with repeat expansion variant types. The analysis will run as a subanalysis of a main analysis and the results will be accessible from the dashboard or from the analysis tabs displayed in the main analysis. The variant results table will display, among other information, the variant's position, gene, the number of repeats, and the variant's pathogenicity. The variant is labeled as pathogenic if the observed number of repeats is greater than the minimum number of pathogenic repeats. 

Phasing

We can now parse the phasing information from long-read ONT VCFs. There will be a new column in the variant table that will display the phasing group number for those variants that are phased. This is also represented in the Zygosity columns that will now display different icons for heterozygous variants phased and unphased.

If your variant of interest is phased, you can click on above the variant table to filter the table and display other variants that are in the same phasing group.

The phasing information is also available in the Sample View. 

Improved filters for detecting cases of compound heterozygosity

We have improved the filtering offering for detecting cases of compound heterozygosity:

• Single samples: a new parameter named “Phased mode” has been added to the “Compound Heterozygous Candidates” filter. When selected, it will only filter those variants with phasing information to identify compound heterozygous variant pairs in the same gene and phasing group and in different zygosities (1|0 vs 0|1).

• Family Trio: we have added a new filter called “Compound Heterozygous for Trios”. This filter is aimed to support the identification of compound heterozygous variants in an affected child when the genome of the two unaffected parents is also provided (Family Trio analysis (n=3)). It also contains a parameter named “Phased mode” that works in the same way as explained in the previous filter. 

Sample View and CNV Browser - Runs of homozygosity track  

A new track displaying Runs of Homozygosity has been added to both the Sample and CNV browser. This works on a per sample basis. 

Sample View / Region Browser / SV Browser / CNV Browser  - High resolution zoom level  now shows at gene level rather than at transcript level   

For further information on the changes to the CNV browser please view our help document

Somatic - Live Annotation

In line with germline, it is now possible to view the live annotation of somatic samples. This removes the need of loading VarSome to visualize the current annotation of your variants and as such we have removed the links back to VarSome which are no longer required

Minor Clinical UI changes 

Sample definitions and workflows - The top Clinical menu has been restructured new “Manage Menu” option

Analysis results table -  new rsID column

Analysis results table now shows variant tags from VarSome Clinical system

CNV QC report - Column name change from “Mean” to “Median fragment count” to more accurately describe the column content. 

CNVs found in the same gene

Additional display in the main analysis (small variants table) to show if there are CNVs found in the same gene where the variant was found. This will help users to visually identify compound heterozygous candidates involving one small variant and one CNV.

LOVD - New search field added to the card

Analysis Table - We have added to the sub-analysis the main analysis that  it is based on. This links back to the main analysis

VarSome Picks - Improved help text to clarify the top 20 variants selected and new algorithmic filter description card. 

Support

As ever we hope you find these changes and improvements helpful. Support is available as usual from support@varsome.com.

The VarSome Team.