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• Introduction
  • The concept of Biomedical Genomics Analysis
  • System requirements
  • Contact information
• Data import and export
• Reference Data Management
  • The Reference Data Manager
  • QIAGEN Sets
• QIAseq Panel Analysis
  • The Analyze QIAseq Panels guide
    • Import your reads
    • Start a QIAseq panel analysis
    • Upload to QCI Interpret
  • How to create a custom panel analysis workflow
    • Import QIAGEN Primers
  • Create a custom Trim adapter list (optional)
• Targeted DNA
  • The Identify QIAseq DNA Variants ready-to-use workflows
    • Output from the Identify QIAseq DNA Variants workflow
    • Quality Control for the Identify QIAseq DNA Variants workflow
  • The Identify TMB Status ready-to-use workflows
    • Output from the Identify TMB Status workflow
  • The Detect QIAseq MSI Status ready-to-use workflow
    • Output of the Detect QIAseq MSI Status workflow
  • Detect MSI Status with Baseline Creation ready-to-use workflow
  • Targeted DNA tools detailed description
    • Calculate TMB Score
    • Detect MSI Status
    • Generate MSI Baseline
    • Remove and Annotate with Unique Molecular Index
    • Calculate Unique Molecular Index Groups
    • Create UMI Reads from Grouped Reads
    • Create UMI Reads from Reads
    • Remove Ligation Artifacts
    • Trim Primers of Mapped Reads
    • Annotate Variants with Unique Molecular Index Info
    • Prepare Guidance Variant Track
    • Import Gene-Pseudogene Table
• Targeted RNAscan
  • The Detect QIAseq RNAscan Fusions ready-to-use workflow
    • Output from the Detect QIAseq RNAscan Fusions workflow
  • The Perform QIAseq RNA Fusion XP Analysis ready-to-use workflow
    • Output from the Perform QIAseq RNA Fusion XP Analysis workflow
  • Interpretation of fusion results
  • Targeted RNAscan tools detailed description
    • Detect Fusion Genes
    • Refine Fusion Genes
    • Annotate Fusions with Known Fusion Information
    • QC for RNAscan Panels
    • Annotate RNA Variants
    • Import Known Fusion Information Track
• Targeted Multimodal
  • Perform QIAseq Multimodal Analysis (Illumina) ready-to-use workflow
    • Output from the Perform QIAseq Multimodal Analysis (Illumina)
    • Running the workflow in batch using Metadata
• Targeted RNA
  • The Quantify QIAseq RNA Expression ready-to-use workflow
    • Output from the Quantify QIAseq RNA Expression workflow
  • Targeted RNA tools detailed description
    • The Quantify QIAseq RNA tool
• UPX 3'
  • Demultiplex QIAseq UPX 3' reads
  • The Quantify QIAseq UPX 3' ready-to-use workflow
    • Output from the Quantify QIAseq UPX 3' workflow
• Targeted Methyl
  • The Detect QIAseq Methylation ready-to-use workflow
    • Output from the Detect QIAseq Methylation workflow
    • Finding differentially methylated regions
• QCI Interpret Integration
  • Configuration of the Upload to QCI Interpret tool
  • The Upload to QCI Interpret tool
• QIAseq miRNA Analysis
  • QIAseq miRNA Quantification
    • QIAseq miRNA Quantification outputs
    • Naming isomiRs
  • QIAseq miRNA Differential Expression
  • QIAseq miRNA Expert Tools
    • Create UMI Reads for miRNA
• QIAGEN GeneRead DNA Panel Analysis
  • The QIAGEN GeneRead Panel Analysis workflow
    • Output from the QIAGEN GeneRead Panel Analysis
  • Trim Primers and their Dimers of Mapped Reads
• Ready-to-use workflows descriptions and guidelines
  • General Workflow
  • Somatic Cancer
  • Hereditary Disease
• Getting started
  • Import sequencing data
  • Prepare Raw Data
• Whole genome sequencing (WGS)
  • General Workflows (WGS)
    • Annotate Variants (WGS)
    • Identify Known Variants in One Sample (WGS)
  • Somatic Cancer (WGS)
    • Filter Somatic Variants (WGS)
    • Identify Somatic Variants from Tumor Normal Pair (WGS)
    • Identify Variants (WGS)
  • Hereditary Disease (WGS)
    • Filter Causal Variants (WGS-HD)
    • Identify Causal Inherited Variants in Family of Four (WGS)
    • Identify Causal Inherited Variants in Trio (WGS)
    • Identify Rare Disease Causing Mutations in Family of Four (WGS)
    • Identify Rare Disease Causing Mutations in Trio (WGS)
    • Identify Variants (WGS-HD)
• Whole exome sequencing (WES)
  • General Workflows (WES)
    • Annotate Variants (WES)
    • Identify Known Variants in One Sample (WES)
  • Somatic Cancer (WES)
    • Filter Somatic Variants (WES)
    • Identify Somatic Variants from Tumor Normal Pair (WES)
    • Identify Variants (WES)
    • Identify and Annotate Variants (WES)
  • Hereditary Disease (WES)
    • Filter Causal Variants (WES-HD)
    • Identify Causal Inherited Variants in Family of Four (WES)
    • Identify Causal Inherited Variants in Trio (WES)
    • Identify Rare Disease Causing Mutations in Family of Four (WES)
    • Identify Rare Disease Causing Mutations in Trio (WES)
    • Identify Variants (WES-HD)
    • Identify and Annotate Variants (WES-HD)
• Targeted amplicon sequencing (TAS)
  • General Workflows (TAS)
    • Annotate Variants (TAS)
    • Identify Known Variants in One Sample (TAS)
  • Somatic Cancer (TAS)
    • Filter Somatic Variants (TAS)
    • Identify Somatic Variants from Tumor Normal Pair (TAS)
    • Identify Variants (TAS)
    • Identify and Annotate Variants (TAS)
  • Hereditary Disease (TAS)
    • Filter Causal Variants (TAS-HD)
    • Identify Causal Inherited Variants in Family of Four (TAS)
    • Identify Causal Inherited Variants in Trio (TAS)
    • Identify Rare Disease Causing Mutations in Family of Four (TAS)
    • Identify Rare Disease Causing Mutations in Trio (TAS)
    • Identify Variants (TAS-HD)
    • Identify and Annotate Variants (TAS-HD)
• Whole Transcriptome Sequencing (WTS)
  • Annotate Variants (WTS)
  • Compare Variants in DNA and RNA
  • Identify Candidate Variants and Genes from Tumor Normal Pair
  • Identify Variants and Add Expression Values
  • Identify and Annotate Differentially Expressed Genes and Pathways
• Batching workflows
• Appendices
  • Legacy tools
    • Trim Primers of Mapped Single Reads
    • Trim Primers of Mapped Paired End Reads
  • Install and uninstall plugins
    • Install
    • Uninstall
• Bibliography

Output of the Detect QIAseq MSI Status workflow

The workflow will output an annotation track containing information about the loci, as well as a report indicating whether the sample was found to be stable (MSS) as seen in figure 5.21 or unstable (MSI) as in figure 5.22. Instability is reported as low instability (MSI-L) or high instability (MSI-H). Below the summary tables, are graphs representing length distributions for each locus (shown here to the right of the summary tables).

Figure 5.21: Report from a stable sample, and graph for the locii NR21(A)21 loci.

Figure 5.22: Report from an unstable sample, and graph for the locii NR21(A)21 loci.

Additional information about the MSI report is available in the Detect MSI Status tool description (Detect MSI Status ).

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