Summary of Key New Features for 11.14 

• Expand user-control over workflows
• Improvements in WGS CNV analysis results
• Support for SureSelect XT HS2 libraries, including the SureSelect CGP Cancer panel
• Improved clinical evidence utilization in the germline classifier

VarSome Clinical improvements 

Expand user control over workflows

The group supervisor can now grant workflow creation privileges to designated users. This is to empower the team's efficiency and collaboration by giving the group supervisor the flexibility to delegate the workflow management to other users.

The supervisor can find the workflow settings in the user preferences menu: 

CNV analysis for WGS samples

New columns in the variant table

We have introduced two new columns to the CNVs table derived from WGS samples (utilizing Delly): Zygosity and Delly precision:

These new columns aim to increase the available information regarding the discovered CNVs in the sample. This enhancement facilitates the filtration process, enabling the identification of CNVs that are likely to be genuine and relevant. To amplify this benefit, we've incorporated two additional filters that seamlessly integrate with your existing WGS CNV filters:

CNV browser for WGS samples

The new data we've incorporated, along with other pertinent information such as coverage, has been smoothly integrated into a new genomic viewer accessible from the CNV browser tab.

In this browser, you can observe all CNVs present in your sample, color-coded based on the pathogenicity, alongside the coverage in that region. You have the capability to filter the displayed CNVs by pathogenicity, type, precision, or zygosity. This feature enhances your ability to efficiently explore and analyze CNVs, empowering you to make decisions based on a comprehensive understanding of your genomic data.

SureSelect XT HS2 support,  including the SureSelect CGP Cancer panel 

We are excited to announce that we are introducing support for Agilent's SureSelect XT HS2 chemistry, including the SureSelect CGP Cancer Panel, incorporating Unique Molecular Identifiers (UMIs) to elevate the accuracy of variant calling through UMI-wise deduplication for Illumina sequencing.

This update integrates UMI-wise deduplication with the use of SureSelect XT HS2 assays, providing a singular, advanced solution for variant detection. By harnessing the power of UMIs to mark each DNA molecule uniquely before amplification, our platform can now accurately identify and eliminate duplicate sequences. This process ensures that only unique, true, sequences are considered in the variant calling process; aiming to reduce false positives and improving the reliability of detected variants.

Note: this feature is currently available only for Illumina sequencing; support for MGI sequencing will follow.

VarSome Picks improvements

We have implemented several enhancements to the VarSome Picks algorithmic filter. This includes the incorporation of mitochondrial variants and the exclusion of variants previously flagged as artifacts. The filter now retains variants found in genes listed in the ACMG secondary findings gene list (v.3.2).

CNV - Live Annotation

In line with the SNV and small indels, it is now possible to view the live annotation of CNV variants. This removes the need of loading VarSome to visualize the current annotation of your CNVs.

VarSome's Germline Classifier

We have refined the way we incorporate this information into our classifier. This is following the advice of our curation team, who have thoroughly reviewed all of the databases that we currently utilize, such as clinical evidence, in our classifier. The goal is to ensure that variants with clear and substantial evidence of pathogenicity are appropriately emphasized in our classifier, thus influencing the classifier's designation as pathogenic.

Support

As ever we hope you find these changes and improvements helpful. We would love to hear any feedback and suggestions you may have. Support is available as usual from support@varsome.com.

The VarSome Team.