• Manuals

Browse the manual

• Introduction
  • The concept of Biomedical Genomics Analysis
  • System requirements
  • Contact information
• QIAseq Panel Analysis
  • Data management
  • 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 (beta) ready-to-use workflow
    • Output of the Detect QIAseq MSI Status workflow
  • Targeted DNA tools detailed description
    • Calculate TMB Score
    • Detect MSI Status (beta)
    • Generate MSI Baseline (beta)
    • Remove and Annotate with Unique Molecular Index
    • Calculate Unique Molecular Index Groups
    • Create UMI 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
    • Interpretation of the Detect QIAseq RNAscan Fusions results
  • Targeted RNAscan tools detailed description
    • Detect Fusion Genes
    • Refine Fusion Genes
    • Annotate Fusions with Known Fusion Information
    • QC for RNAscan Panels
    • Import Known Fusion Information Track
• 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
  • QIAseq miRNA Differential Expression
  • QIAseq miRNA Expert Tools
    • Create UMI Reads for miRNA
    • Quantify miRNA
    • Annotate with RNAcentral Accession Numbers
    • Create Combined miRNA Report
• 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

The Upload to QCI Interpret tool

The Upload to QCI Interpret tool can be found here:

        Tools | QIAseq Panel Expert Tools | QCI Interpretation Integration | Upload to QCI Interpret

Double-click on the Upload to QCI Interpret tool to send a VCF file and possibly metadata information to QCI Interpret.

Select the variant track you want to send (as VCF) to QCI Interpret (figure 8.3), and then select the reference sequence (hg19 by default, but hg38 is also supported). You can then choose which application you would like for the QCI Interpret results (Somatic or Hereditary). Note that the somatic and germline/hereditary workflows of QCI Interpret focus on different end user needs, with somatic being primarily focussed on therapeutic, prognostic, and diagnostic actionability, while germline/hereditary primarily better suited for disease diagnosis/risk.

In case you are working with RNAscan panels analysis, select a Fusions track to upload to QCI Interpret.

Figure 8.3: The Upload to QCI Interpret dialog.

QCI Interpret configuration requires the user to fill the QCI Interpret dialog (figure 8.4) with the following information:

• Server location. QCI Interpret is hosted in multiple locations. Your QCI Interpret account is created for a specific QCI Interpret server that should be specified here.
• API key ID and API key secret. If you do not know your API credentials, contact support-license@qiagen.com.
• Username. Insert the username associated with the QCI Interpret account.

For additional information on QCI Interpret user account and the QCI Interpret uploader, please refer to the QCI Interpret documentation.

Figure 8.4: Configure the connection to the QCI Interpret server dialog.

In the case of uploading a variant file to QCI Interpret, a dialog called "Variants Filters" will appear next (figure 8.5).

Figure 8.5: The Variants Filters dialog, with the pop up window that allows users to select variants based on their chromosomal location opened as example.

Larger VCF files may need to be filtered to remove the excess variants found during second analysis. Use the next dialog to reduce the number of variants uploaded to QCI Interpret, in particular for somatic pipeline where the upload of variants is currently limited to 400.

Different types of filter are available:

• Genes and chromosomes. Select from the list that opens when clicking to the right of the relevant field all genes or chromosomes of interest. By clicking OK, the pop up window closes and reveals how many variants passed the filtered in the Preview section of the dialog.
• Coding changes. Choose between No restriction, Only gene region changes, Only amino acid changes.
• Frequency and quality. Modify the different filters to reduce the list of variants passing filters (see the Preview section of the dialog).

In the last wizard window, click on Finish to initiate the transfer of variants or fusions to QCI Interpret. The tool will open a browser window with the QCI Interpret interview page. This page must be filled in and the button Submit must be pressed to complete the upload of the files and metadata to QCI Interpret. In cases where a browser window fails to open automatically, the tool will also output a report containing the link to the QCI Interpret interview page.

---