Identify QIAseq DNA Pro Somatic Variants with MSI (Illumina)
The Identify QIAseq DNA Pro Somatic Variants with MSI (Illumina) template workflow has been designed to identify somatic variants and detect microsattelite instability (MSI) status). It is set up to analyze data from one of the following panels:
- PHS-001Z Breast Cancer Research Panel
- PHS-002Z Colorectal Cancer Research Panel
- PHS-101Z Breast Cancer Focus Panel
- PHS-102Z Colorectal Cancer Focus Panel
- PHS-202Z Hereditary Colorectal Cancer Panel
- PHS-205Z Hereditary Pancreatic Cancer Panel
- PHS-3000Z Comprehensive Cancer Research Panel
- PHS-3100Z Comprehensive Cancer Focus Panel
- PHS-3200Z Comprehensive Hereditary Cancer Research Panel
Reference data for the panels is available in the reference data set QIAseq DNA Pro MSI Panels hg38.
To run the workflow go to:
Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq DNA Workflows (
) | Identify QIAseq DNA Pro Somatic Variants with MSI (Illumina) (
)
If you are connected to a CLC Server via the CLC 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.
A detailed description of the individual steps of the workflow is available in Running the Identify QIAseq DNA Variants workflows. Note that to detect the MSI status of a sample, the workflow requires an MSI baseline which is provided in the MSI baseline dialog. Per default, the workflow will use a demo baseline based on 20 microsattelite stable (MSS) samples. We recommend creating a new baseline with at least 30 MSS samples processed under the same lab conditions as test samples, see Generate MSI Baseline for additional details.
Launching using the QIAseq Panel Analysis Assistant
The workflow is also available in the QIAseq Panel Analysis Assistant under Targeted DNA Pro.
Subsections