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Biomedical Genomics Analysis

The Biomedical Genomics Analysis plugin to QIAGEN CLC Genomics Workbench offers workflows and tools for all steps from the initial data processing and quality control through to data analyses, annotation and reporting.

Applications and workflows

  • QIAseq panel analysis, including targeted DNA, targeted DNA Pro, tumor mutational burden (TMB), microsatellite instability (MSI), FLT3 complex variant detection, CNV control sample mapping, UPX 3′ Targeted RNA Panel, UPX 3′ Transcriptome Kit, QIAseq RNA UPXome, QIAseq miRNA Library Kit, Multimodal and RNA Fusion XP Panels, Targeted Methylation Panels, QIAseq Immune Repertoire RNA Library Kits, QIAseq xHYB and QIAseq Whole Exome Panels. See the complete list of supported QIAseq panels here.
  • SARS-CoV-2 panel analysis (ARTIC-v3, QIAseq and Ion AmpliSeq)
  • TruSight Oncology 500 (Illumina) panel workflow
  • GeneRead DNAseq gene panel analysis
  • Whole genome sequencing (WGS)
  • Whole exome sequencing (WES)
  • Targeted amplicon sequencing (TAS)
  • Whole transcriptome sequencing (WTS)
  • Small RNA sequencing (miRNA)

When the plugin is installed, additional workflows will be accessible from the Toolbox under ‘Template Workflows’.

Figure 1. The available template workflows in the Toolbox upon installing the Biomedical Genomics Analysis plugin.

QIAseq Panels analysis workflows

QIAseq Panels analysis workflows for Targeted DNA, Targeted RNAscan and Targeted RNA catalogue and custom panel data can be launched from a dedicated guide interface. The guide provides direct upload of both Illumina and Ion Torrent reads, and the preconfigured workflows can be run using both Illumina and Ion Torrent data. Just click through the tabs to identify the relevant panel and run the workflows directly from the guide. A list of supported QIAseq panels can be found here.

Figure 2. The QIAseq Panel Analysis guide interface. The various panel types have their own tabs, and the well picker for demultiplexing UPX 3’ is shown.

QIAseq Panel Expert Tools

A collection of QIAseq Panel Expert Tools is installed in the Tools section of the Toolbox. These tools handle Unique Molecular Indices (UMIs) panel data generated by Single Primer Extension (SPE) protocols.

Figure 3. The QIAseq Panel Expert Tools in the Toolbox.

Immune Repertoire Expert tools

A collection of tools for analyzing Immune Repertoire TCR and BCR data from various kits are provided. It is possible to import IMGT reference segments for TCR and BCR and perform downstream filtering and comparison of the clonotype repertoires. Clonotypes can be exported in the VDJ tools format.

General tools

A number of additional tools not directly related to the QIAseq panels are provided, as well. The following tools are available from the plugin:

  • Structural Variant Caller Detects indels, tandem duplications and inversions in somatic and germline WGS and targeted applications.
  • Create Consensus Sequences from Variants Creates consensus sequences from variants and a Reference sequence. Optionally low coverage regions can be masked out.
  • Extract Reads Matching Primers Extracts reads that match a primer and discards reads that do not match a primer.
  • Refine Read Mapping Removes potentially problematic mapped reads.
  • Target Region Coverage Analysis Combines per-region statistics tracks produced by QC for Targeted Sequencing across samples and assesses quality based on different coverage metrics.
  • Detect Regional Ploidy Estimates ploidy states including loss-of-heterozygosity (LOH) from targeted resequencing experiments.
  • Create Methylation Level Heat Map Hierarchically clusters samples and features, generating a two-dimensional heat map of methylation levels, using methylation level tracks as input.
  • Convert Annotation Track Coordinates Converts annotation coordinates, either from hg19 coordinates to hg38 coordinates, or vice versa, making use of the NCBI Remapping Service.
  • Annotate Structural Variants Estimates count, coverage and frequency information for indels detected by the InDels and Structural Variants tool and generates a variant track containing the original variants with these annotations added.
  • Predict Methylation Profile Estimates the cell type composition of a sample based on differentially methylated cytosines or regions. It is designed for use with the QIAseq Methyl T-Cell Infiltration Panel (MHS-202Z) that distinguishes epithelial, fibroblasts and immune cells, but can also be applied to other analyses.
  • Create Methylation Database Creates a methylation database track of two or three pure conditions. The methylation database can be used as an input to Predict Methylation Profile.

Functionality for seamless upload of analysis results to QCI Interpret

The QIAseq Panel Expert Toolbox contains tools for uploading a wide range of variants to QCI Interpret and QCI Interpret Translational interpretation software, including SNVs, InDels, CNVs, fusions and inversions, as well as TMB and MSI status. In order to use this functionality please contact sales to purchase a license for QCI Interpret.

QIAGEN GeneRead Panels

QIAGEN GeneRead Panels can be analyzed using a template workflow that can identify and annotate variants in Targeted Amplicon Sequencing data generated with catalogue and custom GeneRead DNAseq Gene Panels.

Figure 4. Application workflow available for analyzing GeneRead sequencing data.

Comprehensive collection of template workflows

The application workflows are specific to the type of data used as input: Whole genome sequencing (WGS), whole exome sequencing, targeted amplicon sequencing and whole transcriptome sequencing. For each of the first three categories, WGS, WES, and TAS, General Analysis workflows can be used for identification and annotation of variants irrespective of disease. Somatic Cancer workflows have been designed specifically for cancer research, including single sample and Tumor-Normal pairs. Hereditary Disease workflows can be used to study variants that cause rare diseases or hereditary diseases (HD).

 

Figure 5. Application workflows available for analyzing whole genome sequencing data.

In addition, application workflows for whole transcriptome sequencing are provided.

Figure 6. Workflows for whole transcriptome sequencing.

Reference data provided through the Reference Data manager

For all template workflows we provide matching reference datasets. The latest improvement is providing the “Hg38 no alternative reference” dataset for analyzing TMB and WGS and WES workflows. The additional scaffolds and virus decoy sequence in this reference dataset improve the variant calling sensitivity and precision.

 

Figure 7. Hg38 no alternative reference sequence dataset in the reference data manager.

We frequently release updates and improvements such as bug fixes or new features. To get a complete overview, please visit the latest improvements page.

Downloads

Plugin Manual
Online manual Download manual
Plugin Download
Download plugin
Download Biomedical Genomics Analysis

Version

Platform support

Download

22.2.0

QIAGEN CLC Genomics Workbench


 [22.0.2]

22.0.4

QIAGEN CLC Genomics Workbench


 [22.0.1, 22.0]

21.2.4

QIAGEN CLC Genomics Workbench


 [21.0.6]

21.2.2

QIAGEN CLC Genomics Workbench


 [21.0.5]

21.1.0

QIAGEN CLC Genomics Workbench


 [21.0.4, 21.0.3]

21.0.0

QIAGEN CLC Genomics Workbench


 [21.0.2, 21.0.1, 21.0]

20.2.1

QIAGEN CLC Genomics Workbench


 [20.0.5]

20.2.0

QIAGEN CLC Genomics Workbench


 [20.0.4]

20.0.1

QIAGEN CLC Genomics Workbench


 [20.0.3, 20.0.2]

20.0.0

QIAGEN CLC Genomics Workbench


 [20.0.1, 20.0]

1.2.1

QIAGEN CLC Genomics Workbench


 [12.0.4, 12.0.3]

1.2.0

QIAGEN CLC Genomics Workbench


 [12.0.2, 12.0.1]

1.1.0

QIAGEN CLC Genomics Workbench


 [12.0]
Server Plugin Download
Download plugin
Download Biomedical Genomics Analysis Server Plugin

Version

Platform support

Download

22.2.0

QIAGEN CLC Genomics Server


 [22.0.2]

22.0.4

QIAGEN CLC Genomics Server


 [22.0.1, 22.0]

21.2.4

QIAGEN CLC Genomics Server


 [21.0.6]

21.2.2

QIAGEN CLC Genomics Server


 [21.0.5]

21.1.0

QIAGEN CLC Genomics Server


 [21.0.4, 21.0.3]

21.0.0

QIAGEN CLC Genomics Server


 [21.0.2, 21.0.1, 21.0]

20.2.1

QIAGEN CLC Genomics Server


 [20.0.5]

20.2.0

QIAGEN CLC Genomics Server


 [20.0.4]

20.0.1

QIAGEN CLC Genomics Server


 [20.0.3, 20.0.2]