Targeted/Untargeted Calling on VarSome Clinical

VarSome Clinical can process whole-genome sequencing data (WGS) or targeted sequencing data (e.g. whole-exome sequencing (WES), gene panels, etc). When launching an analysis from FASTQ, the reads provided are aligned against the reference genome version (hg19 or hg38) and the variant calling algorithm identifies variants in the aligned reads. Depending on the type of data provided, the variant calling is performed in targeted or untargeted mode. 

  • Untargeted variant calling.

The untargeted mode is used for either WGS or WES data. When launching a FASTQ analysis from WGS/WES data, VarSome Clinical will find variants in untargeted mode. This means that all variants will be reported no matter their position in the reference genome. 

When analyzing WES data, it is possible to find variants that do not fall within the exons (e.g. intronic variants). Please bear in mind that, even the best capture exome assay might produce reads aligning against non-exonic areas, and therefore, finding intronic variants when working with WES data is an expected outcome. You can use the dynamic filters feature to filter out any variants that are not of interest.

  • Targeted variant calling

VarSome Clinical performs variant calling in targeted mode when the reads obtained come from an assay that is neither a whole-exome nor a whole-genome. When launching the analysis, you will need to select the assay containing the information about the targeted regions. If your assay is not included in the assay list from the drop-down menu, please visit Adding an assay to VarSome Clinical

Targeted calling is used for gene panels instead of the untargeted mode because:

  • Gene panels usually cover a minor fraction of the genome. Searching for variants in the whole-genome would unnecessarily slow-down the variant calling process.
  • The targeted mode prevents incidental findings in other regions of the genome that might not be of  interest.

We therefore use the targeted calling approach to limit the results to the assay’s target regions. In order to achieve this, the variant caller will discard any reads in the alignment BAM file that do not overlap with the assay’s regions. If at least one base of a read overlaps with one of the targeted regions, then the read is kept and included in the analysis. If there is no overlap with any of the targeted regions, the read is discarded and not taken into account when calling variants. To ensure that no variants are missed because they fall at the very edges of the target regions, we also include 10bp up and downstream of each region.  

The end result of this approach is a faster and more specific analysis.