The Identify QIAseq DNA Pro Somatic Variants with LOH Detection (Illumina) workflow has been designed to detect LOH events on chromosomes 1p and 19q using these panels:
- PHS-004Z Brain Cancer Research Panel
- PHS-104Z Brain Cancer Focus Panel
- PHS-3000Z Comprehensive Cancer Research Panel
- PHS-3100 Comprehensive Cancer Focus Panel
Reference data for the panels is available in the reference data set QIAseq DNA Pro Panels hg38. Hence, when running the workflow, all the Targeted DNA Pro panels are available for selection, however, only the ones listed above have been designed to support detection of LOH.
To run the workflow go to:
Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | QIAseq Analysis Workflows () | Identify QIAseq DNA Pro Somatic Variants with LOH Detection (Illumina) ()
These workflows can also be launched from the Analyze QIAseq Samples guide, which is described in The Analyze QIAseq Samples guide. They are available in the drop down menus under each panel analysis listed on the Targeted DNA Pro tab.
If you are connected to a CLC Server via your Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.
To run LOH detection the workflow needs CNV control mappings or control coverage tables. Otherwise the settings for this workflow are the same as for the other DNA Pro workflows (see The Identify QIAseq DNA Variants template workflows).