CNV Calling Enhancements

The v10.2 release of VarSome Clinical offers several novel features improving CNV detection, quality control and reporting. A new dynamic CNV browser offers an overall view of the call regions in their genomic context in every co-analysed sample. For detailed information, we recommend that users refer to the User Manual, which is accessible for download via the “Support & Manual” link in VarSome Clinical.

CNV call quality control - Explore the quality of each CNV call in depth

Additional quality data are displayed for each call that allow the user to assess result reliability. Each CNV call is assigned a set of three “traffic-lights”, which are colored green or red, depending on whether the CNV call meets the quality control criteria. These are:

• Test sample coverage to ensure a minimum coverage of the test sample at the CNV call region when calling duplications. 
• Number of reference samples to satisfy a minimum number (2) of samples from the reference set with a minimum coverage in the CNV call region. 
• Camouflaged region overlap checks whether a CNV call falls within a genomic Camouflaged Region, which typically contain duplicated genomic sequences.

CNV Browser - Gain further insight with a dynamic visualization

A novel, bespoke, interactive CNV call visualization browser for every called CNV that offers:

• Zooming to the CNV call region in the desired resolution.
• Context genomic annotations including chromosomal location and exon and intron positions.
• Local coverage information for all samples.
• Easy linking to corresponding genomic regions in co-analyzed samples of the cohort.

CNV analysis QC report - Check sample quality in every analysis

Informative sample specific features that can affect CNV call quality are included in the analysis QC report:

• Correlation to reference samples.

• Reference sample listing.

• Cohort sex data (if available). Unreliable CNV calls in sex chromosomes are filtered out.

If you would like to see a demonstration of VarSome Clinical's CNV features, you can book a time with our sales team here.