Biomedical Genomics Analysis latest improvements

Biomedical Genomics Analysis 24.1

Released on July 2, 2024

New features and improvements

QIAseq Multimodal DNA/RNA Library Kit

Data generated with the QIAseq Multimodal DNA/RNA Library Kit, optionally followed by hybrid capture-based target enrichment, such as QIAseq Human Exome, QIAseq xHYB Human, or panels from a third party provider, is now supported.

• Six new template workflows are available:
  • For DNA data, located in QIAseq DNA Workflows
    • Identify QIAseq Multimodal DNA Lib Kit and Hybrid Capture Somatic Variants (Illumina): for data generated with UMIs, followed by target enrichment.
    • Identify QIAseq Multimodal DNA Lib Kit and Hybrid Capture Somatic Variants with TMB and MSI (Illumina) (beta): for data generated with UMIs, followed by target enrichment with sufficiently large target regions.
    • Identify QIAseq Multimodal DNA Lib Kit with UMI Somatic Variants (WGS) (Illumina): for WGS data generated with UMIs.
    • Identify QIAseq Multimodal DNA Lib Kit without UMI Somatic Variants (WGS) (Illumina): for WGS data generated without UMIs.
  • For RNA data, located in QIAseq RNA Workflows
    • Perform QIAseq Multimodal RNA Lib Kit Expression Analysis (Illumina)
    • Perform QIAseq Multimodal RNA Lib Kit Expression Analysis and Fusion Calling (Illumina)
  • All workflows can be launched from the QIAseq Panel Analysis Assistant.
  • Reference data for these workflows is available in the reference data set QIAseq Multimodal Library Kit and Hybrid Capture hg38.
• Four existing template workflows have been renamed to reflect that they can also be used for data generated with the QIAseq Multimodal DNA/RNA Library Kit without UMIs, followed by target enrichment. "xHYB" has been replaced with "Hybrid Capture DNA" in the names:
  • Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina)
  • Identify QIAseq Hybrid Capture DNA Germline Variants including Mitochondrial (Illumina)
  • Identify QIAseq Hybrid Capture DNA Somatic Variants (Illumina)
  • Identify QIAseq Hybrid Capture DNA Somatic Variants including Mitochondrial (Illumina)

Other improvements

• Remove and Annotate with Unique Molecular Index supports ambiguous bases in common sequence verification.
• The Restrict to chains option is unlocked in the Perform QIAseq Targeted TCR Analysis template workflow.

Bug fixes

• Fixed an issue that could cause Create UMI Reads from Reads to fail on large datasets when using the option "Rolling min k-mer hasher" to cluster reads. This happened when the total number of hashes exceeded 2^31.
• Fixed an issue that caused Create UMI Reads from Reads to fail on single reads and on paired end reads in combination with the option "Paired end reads (discard read 2)" when using the option "Rolling min k-mer hasher" to cluster reads.

Changes

• The two template workflows for analysis of QIAseq Multimodal Panels data have been renamed to include "Panel":
  • Perform QIAseq Multimodal Panel Analysis
  • Perform QIAseq Multimodal Panel Analysis with TMB and MSI
• The Multimodal category from the QIAseq Panel Analysis Assistant has been renamed to Multimodal Panels.
• The Filter Immune Repertoire report output by Perform Immune Repertoire Analysis and Perform QIAseq Targeted TCR Analysis template workflows has been renamed to Filter_immune_repertoire_report and is located in QC & Reports folder. Previously, it was named Immune_repertoire_report and was located at the root of the results folder.

Advance Notice

• We plan to remove Microhaplotype Caller (beta) in a future release of the software. If you are concerned about this proposed change, please contact our Support team by emailing ts-bioinformatics@qiagen.com.

Biomedical Genomics Analysis 24.0.2

Released on May 23, 2024

Bug fixes

• Fixed an issue that could cause Create UMI Reads from Reads to have significantly extended runtime on input data with very large UMI groups.
• Fixed an issue that in some situations could cause Create UMI Reads from Reads to group single-stranded consensus sequences incorrectly when creating duplex UMI consensus reads. The overall effect of this fix is expected to be small, but fewer duplex UMI groups may be created and there may be fewer reads per duplex UMI group.
• Fixed an issue that in very rare cases could cause Structural Variant Caller to fail. This could happen in situations where unaligned ends extended beyond the end of a chromosome.
• Fixed an issue causing well detection preview to show no detected wells for the four QIAseq UPXome RNA Library Kit analyses in the QIAseq Panel Analysis Assistant.

Improvements

• Create UMI Reads from Reads has a new option that allows grouping of reads that do not start at the same position. For details, see Important notification - Create UMI Reads from Reads.
• The CNV graining level option can be changed when running Perform QIAseq Multimodal Analysis (Illumina) or Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina).

Compatibility

At time of release, Biomedical Genomics Analysis 24.0.2 is available for CLC Genomics Workbench 24.0 or higher. It will be compatible with later releases in this major release line.

At time of release, Biomedical Genomics Analysis 24.0.2 is available for CLC Genomics Server 24.0 or higher. It will be compatible with later releases in this major release line.

Biomedical Genomics Analysis 24.0.1

Released on January 25, 2024

Bug fixes

• Fixed an issue causing Convert Legacy QIAseq Custom Analysis to not detect Custom Analyses configured using Analyze QIAseq Panels in earlier versions of the software.
• Fixed an issue causing incorrect detection of wells by the Demultiplex Reads analysis in the UPX 3’ RNA category of the QIAseq Panel Analysis Assistant when the option “Allow mismatches” was checked before other options were adjusted.

Biomedical Genomics Analysis 24.0

Released on January 9, 2024

New features and improvements

Custom Analysis of QIAseq data

• QIAseq Panel Analysis Assistant replaces Analyze QIAseq Samples and does not support Custom Analyses. Convert Legacy QIAseq Custom Analyses enables the creation of Custom Sets and/or custom workflow copies for Custom Analyses created using Analyze QIAseq Samples.

Immune repertoire

• The new tool Merge Immune Repertoire reduces the number of false positives by merging clonotypes.
• Compare Immune Repertoires can now reduce the number of false positives by resolving clonotypes that are similar across samples.
• The option "Set frequencies per chain" is checked by default in Immune Repertoire Analysis, Filter Immune Repertoire, Create Clonotypes from Selection, and Create Comparison from Selection.
• Clonotypes are sorted by frequency instead of count in the table view of Clonotypes data elements. This also impacts the order of clonotypes in the Side Panel of the alignments view.
• Cumulative frequencies plot, scatter plot, and Jaccard distance heat map use the clonotypes' frequencies rather than their counts.
• Standard Import of files in VDJtools format sets the clonotypes' frequencies to those from the "freq" column in the file. Export of clonotypes to VDJtools format sets the "freq" column to the clonotypes' frequencies. Previously, the frequencies were calculated from the counts, both for import and export.
• CDR3 quality scores can be visualized in the table view of Clonotypes data elements.
• Sample reports and combined reports containing summaries for immune repertoire analysis and created in earlier versions of the software should not be used as input to Combine Reports in CLC Genomics Workbench 24.0 or above.
• Perform QIAseq Targeted TCR Analysis and Perform QIAseq Immune Repertoire Analysis template workflows have been substantially revised.

Template workflows

• The template workflows in the folders QIAseq RNA Workflows and Other QIAseq Workflows produce more comprehensive sample reports.
• Identify ARTIC V3 SARS-CoV-2 Low Frequency and Shared Variants (Illumina), Identify Ion AmpliSeq SARS-CoV-2 Low Frequency and Shared Variants (Ion Torrent) and Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina) template workflows have been revised:
  • The consensus sequence coverage threshold has been changed from 30X to 10X.
  • More comprehensive summary reports are obtained by combining sample reports for each separate sample.
• Default reference data for template workflows has been updated to use the newest Reference Data Elements available.

Other improvements

• Quality control summary items for reports produced by Calculate TMB Score and Detect MSI Status are available for Create Sample Report.
• Create Methylation Level Heat Map outputs a heat map with just one row when the input contains just one CpG site or the provided target regions contains just one target. Previously, it created an empty heat map.
• The "Whole genome sequencing noise filter" option in Structural Variant Caller uses a new neural network based method to filter structural variants. The noise filter now removes fewer variants, leading to higher sensitivity.
• In the Structural Variant Caller, underlying variants filters have been adjusted, this may lead to higher sensitivity for insertions and deletions.
• Structural Variant Caller has improved sensitivity for inversions.
• Calculate Unique Molecular Index Groups and Remove Ligation Artifacts support analysis of reads where the UMI was present in the fastq file read header instead of being part of read 1 or read 2.
• Calculate HRD Score (beta) requires a centromere track. Centromere information is needed for correct calculation of HRD scores.
• The runtime of Import VCF to Genotype Track (beta) has been improved.
• Annotations can be renamed or excluded when exporting a genotype track to VCF using Export Genotype VCF (beta).
• Table Export of genotype tracks includes the option to only export columns that are shown in open table views.
• Import VCF to Genotype Track (beta) is no longer available for on-the-fly import in workflows.
• The "Show filtered" option is synchronised between track view and table views of genotype tracks.
• Visualization of filtered variants in genotype tracks in track view has been improved.
• Various minor improvements

Bug fixes

• Fixed an issue that could cause Structural Variant Caller to report too low coverage on variants. This was most likely to happen on primer based data, in regions that were amplified by only one primer.
• Fixed an issue causing Detect Regional Ploidy to fail if target regions were located inside centromeres. Targets that are in between or overlap centromeres are now ignored.
• Fixed an issue that caused Trim Primers and their Dimers from Mapping to fail if the reference contained a circular chromosome that was not the last chromosome.
• Fixed an issue causing the Compare Variants in DNA and RNA and Compare Variants in DNA and RNA (M and R) template workflows to swap the outputs containing the union and intersection of the DNA and RNA variants.
• Fixed an issue that caused Immune Repertoire Analysis to report too few fragments with identified V and J segments.
• Various minor bug fixes

Changes

• Analyze QIAseq Samples has been replaced by QIAseq Panel Analysis Assistant, which can be used directly from the CLC Genomics Workbench.
• Convert Annotation Track Coordinates uses UCSC Lift Genome Annotations instead of NCBI Genome Remapping Service which has been retired.
• Immune Repertoire Analysis no longer merges clonotypes and all clustering options have been removed. Use Merge Immune Repertoire to merge clonotypes instead.

Biomedical Genomics Analysis 23.1

Released on September 13, 2023

QIAseq Targeted TCR panel support

• The template workflow Perform QIAseq Targeted TCR Analysis is available for analysis of data generated using the QIAseq Targeted RNA-seq Panel for T-cell Receptor.
  • The workflow can be launched from Analyze QIAseq Samples using the Human Targeted TCR and Mouse Targeted TCR analysis from the Immune tab.
  • Reference data for the workflow is available in the QIAseq Immune Repertoire Analysis and QIAseq Immune Repertoire Analysis Mouse reference data sets.
• Validate QIASeq Read Structure (beta) can now be used for data generated using the QIAseq Targeted RNA-seq Panel for T-cell Receptor.

New workflow

• Identify QIAseq DNA Somatic Variants with HRD Score (Illumina) (beta) is available for analysis of data generated using custom QIAseq Targeted DNA panels designed to investigate homologous recombination deficiency (HRD).

Improvements

• QIAseq template workflows for Targeted DNA Pro, Targeted DNA Ultra, Exome and xHYB panels as well as Targeted DNA workflows with TMB have been configured with the GenomeReferenceConsortium_masking_hg38_no_alt_analysis_set masking track. Masking the annotated regions during read mapping is recommended for removing false reference duplications, including one affecting the gene U2AF1. Masking is not used by default, but can be chosen when executing the workflows from the toolbox and from Analyze QIAseq Samples.
• Immune Repertoire Analysis has a new option "Restrict to chains" for removing false positives when only specific chains have been sequenced.
• Immune Repertoire Analysis and Filter Immune Repertoire have a new option "Set frequencies per chain" to calculate clonotype frequencies such that they add up to 100% for each individual chain.
• Filter Immune Repertoire can now use Clonotype Sample Comparison elements as input and "Clonotypes to retain".
• Compare Immune Repertoires can also use Clonotype Sample Comparison elements as input.
• Clonotype Sample Comparison elements have a new table view enabling easier comparison of the clonotype count and frequency across the different samples.
• When creating a Clonotypes or Clonotype Sample Comparison element by using the "Create Clonotypes from Selection" or "Create Comparison from Selection" buttons in the table views, respectively, the following options are available:
  • "Recalculate frequencies" for recalculating frequencies to add up to 100% for the selected clonotypes.
  • "Set frequencies per chain" for recalculating frequencies to add up to 100% for each individual chain for the selected clonotypes.
• Sankey plots for clonotypes show clonotypes with out of frame CDR3 using a "None" box for the CDR3 amino acid sequence.
• Upload to QCI Interpret and Prepare QCI Interpret Upload can upload reports as PDF to QCI Interpret.
• The template workflow Identify QIAseq DNA Pro Germline Variants (Ion Torrent) can be launched from Analyze QIAseq Samples.
• Various minor improvements

Bug fixes

• Fixed an issue causing the analysis of Human Pan Cancer (UHS-5000Z) data using Analyze QIAseq Samples to fail to start.
• Fixed an issue causing the scatter plot of Clonotype Sample Comparison data elements to swap the samples on the axes and in the legend.
• Fixed an issue causing Annotate RNA Variants to fail when annotating insertions located between two exons that were not separated by an intron.
• Various minor bug fixes

Compatibility

At time of release, Biomedical Genomics Analysis 23.1 is available for CLC Genomics Workbench 23.0.1 or higher. It will be compatible with later releases in this major release line.

At time of release, Biomedical Genomics Analysis 23.1 is available for CLC Genomics Server 23.0.1 or higher. It will be compatible with later releases in this major release line.

Biomedical Genomics Analysis 23.0.2

Released on July 05, 2023

Improvements

• The Perform QIAseq Multimodal Analysis (Illumina) and Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) template workflows have been configured with the GenomeReferenceConsortium_masking_hg38_no_alt_analysis_set masking track. Masking the annotated regions during read mapping is recommended for removing false reference duplications, including one affecting the gene U2AF1. Masking is not used by default, but can be chosen when executing the workflows from the toolbox and from Analyze QIAseq Samples.
• Various minor improvements

Bug fixes

• Fixed an issue that could cause Create UMI Reads from Reads to fail when the input reads contained several very large UMI groups with highly similar UMI barcodes.
• Fixed an issue where a few DNA primers and target regions were missing in the QIAseq Multimodal Pan Cancer hg38 reference data set. The issue has been fixed in reference data set version 1.5, which is also used by the template workflow Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina).
• Fixed an issue affecting the template workflow Identify QIAseq DNA Ultra Somatic Variants (Illumina) where the input read mapping to Annotate Variants with Unique Molecular Index Info was defined as consisting of raw reads instead of UMI reads. Variant annotations that should only be calculated from raw reads were therefore incorrectly added to the variant table.
• Fixed an issue causing Annotate Variants with Unique Molecular Index Info to ignore the option “Minimum consensus % of a Consistent Unique Molecular Index” when provided an input read mapping consisting of raw reads. Instead of using the user-defined value, all UMI reads where at least one raw read contained a given variant, were included in Count (UMI) and Count (big UMIs).
• Fixed an issue causing Import QIAGEN Primers to fail when importing custom primer files containing non-human targets. The non-human targets are now ignored and skipped upon import.
• Various minor bug fixes

Biomedical Genomics Analysis 23.0.1

Released on March 23, 2023

Improvements

• Create UMI Reads from Reads discards very large UMI groups and their corresponding reads. Previously, the analysis of these groups caused significantly extended runtime.

Bug fixes

• Fixed an issue causing Immune Repertoire Analysis to sometimes fail if some reads had multiple assigned segments.
• Fixed an issue causing Calculate HRD Score (beta) to include LOH events identified on chromosomes where all regions were affected by LOH in the HRD score. This could lead to a too high HRD score.
• Fixed an issue in Analyze QIAseq Samples where the QIAseq Ultra panel YHS-005 was written as PHS-005. The underlying target regions and primers were correct.
• Various minor bug fixes

Biomedical Genomics Analysis 23.0

Released on January 17, 2023

New functionality and improvements

Immune repertoire improvements

• The situations where ambiguous J or D segments are reported by Immune Repertoire Analysis have been reduced. The segment with the lowest error rate among segments with equally good alignments is now chosen. If multiple segments lead to equally good alignments and the same error rate, they are still reported as ambiguous.
• Clonotypes data elements have new and updated views:
  • A new alignment view, containing alignments between the reads and the reference V, D, J and C segments.
  • New plots are available for individual chains:
    • Sankey plot summarizing the composition of clonotypes.
    • Rarefaction plot
    • CDR3 length distribution
    • Segment usage histogram
    • Cumulative frequencies curve
  • Table view:
    • Includes a "Clonotype #" column.
    • Has a "Create Clonotypes from Selection" button for creating new Clonotypes data elements from selected rows.
• Filter Immune Repertoire can produce a report summarizing the filtered clonotypes.
• Compare Immune Repertoires:
  • Can produce a new Clonotype Sample Comparison data element containing the following views:
    • Table view showing the clonotypes across samples.
    • Jaccard distance heat map view.
    • Plots are available for individual chains:
      • Sankey plot summarizing and comparing across samples the composition and frequencies of clonotypes.
      • Scatter plot
      • Rarefaction plot
      • CDR3 length distribution
      • Segment usage histogram
  • Can no longer produce stand-alone heat maps or similarity tables. These can be obtained from the Jaccard distance heat map view of the Clonotype Sample Comparison data element.
  • Displays the CDR3 length distribution as a histogram instead of a box plot in the report.

New workflow

• Identify QIAseq DNA Pro Germline Variants (Ion Torrent) is available for analysis of data generated using QIAseq Targeted DNA Pro panels and Ion Torrent sequencing platforms. Reference data for the workflow is available in the reference data set QIAseq DNA Pro Panels hg38.

Workflow improvements

• The four UPXome and FastSelect with fusion calling template workflows no longer detect fusions with exon skippings or novel exon boundaries.
• Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) uses Copy Number Variant Detection (CNVs) instead of CNV and LOH Detection (legacy). This does not affect results.
• In Perform QIAseq Multimodal Analysis (Illumina) template workflow the minimum fold change for deletion has been lowered to 1.3 from 1.4 in Copy Number Variant Detection (CNVs). This can potentially lead to fewer detected deletions.
• To improve the precision of variant detection, a gene-pseudogene track has been added as input to Trim Primers of Mapped Reads in the following workflows:
  • Identify QIAseq DNA Pro Somatic Variants (Illumina)
  • Identify QIAseq DNA Pro Somatic Variants with LOH Detection (Illumina)
  • Identify QIAseq DNA Pro Somatic Variants (Ion Torrent)
• In the QIAseq DNA Pro template workflows for analysis of Ion Torrent data, read alignment scores in Map Reads to Reference have been adjusted. The changes may slightly improve the precision of variant detection.
  • The Mismatch cost has been changed from 4 to 6.
  • Both the Insertion and Deletion open costs have been changed from 6 to 8.
  • Both the Insertion and Deletion extend costs have been changed from 1 to 2.

Haplotype calling functionality

• The Genotype Track - A track type representing variants in a format similar to VCF. The track can represent phasing information and include PASS/FILTER annotations.
• Microhaplotype Caller (beta) - Supports haplotype-aware variant detection and outputs variants to Genotype tracks.
• Convert to Genotype Track (beta) - Converts variant tracks to Genotype tracks.
• Import VCF to Genotype Track (beta) - Imports VCF files to Genotype tracks.
• Export Genotype VCF (beta) - Exports Genotype tracks to VCF.
• Export Genotype CSV (beta) - Exports Genotype tracks to CSV.
• Export Marker Genotypes (beta) - Supports export of genotypes at specified marker positions from Genotype tracks to text based formats. This allows export to formats that are compatible with third party analysis software.
• The template workflow Detect QIAseq Human Identity SNPs and Microhaplotypes (beta) - Calls SNPs and microhaplotypes in data from QIAseq Human Identity panels.

The above were previously distributed in the Haplotype Calling (beta) plugin.

Other improvements

• Upload to QCI Interpret and Prepare QCI Interpret Upload support upload of variants in annotation tracks such as the long InDels track from the Structural Variant Caller, and variants that have been imported to annotation tracks using VCF import.
• Structural Variant Caller has more options to allow individual filtering of structural variants supported by single breakpoints and structural variants supported by paired breakpoints. Before, it was not possible to set specific filters for structural variants only supported by single breakpoints.
• Minor improvements to Structural Variant Caller which might cause very small changes to results.
• Create Methylation Level Heat Map:
  • Supports analysis of Whole Genome Bisulfite Sequencing Data (WGBS) data. Clustering is only performed when there are < 5,000 regions.
  • Can create heat maps based on individual CpG sites when not provided with a target regions track.
• Various minor improvements.

Bug fixes

• Fixed an issue in Create Sample Report where several options were duplicated in the wizard when Biomedical Genomics Analysis 22.2 was installed.
• Fixed an issue causing Identify Mispriming Events to prefer small insertions over mismatches when aligning reads representing potential mispriming events to target regions, giving a too high alignment score. Fewer mispriming events are now identified, and the alignment in the mispriming events reads track has been improved. When using the mispriming events track as input to Trim Primers of Mapped Reads, no or very few changes to the trimmed read mapping are expected.
• Fixed an issue in the Identify QIAseq DNA Somatic Variants with TMB (Ion Torrent) template workflow where the mapping graph used to identify regions with sufficient coverage for TMB calculation was based on paired reads. The mapping graph is now created from uniquely mapped reads. Before, no regions were identified and the TMB score was not calculated.
• Fixed an issue in the Identify QIAseq DNA Somatic Variants with TMB (Ion Torrent) and Create QIAseq DNA CNV Control Mapping (Ion Torrent) template workflows, where the mismatch score in Map Reads to Reference was set to 4. The mismatch score has now been set to 2, to align with the other QIAseq Ion Torrent workflows. The variant calls and the TMB score produced by the TMB workflow may change slightly. The coverage profiles only change very little, and this fix is unlikely to affect the results of copy number variant detection.
• Fixed an issue that caused display of the Genotype Track to fail if it contained empty columns.
• Fixed an issue that could cause Structural Variant Caller to call too many overlapping variants. This could happen when small structural variants were completely contained within longer variants.
• Fixed an issue causing CNV gain and loss columns with only zeros to be included in the Structural Variant Caller report. The columns have now been removed.
• Fixed an issue where Immune Repertoire Analysis incorrectly assigned just one segment if its sequence was duplicated in the reference data. Segments duplicated in the reference data are now reported as ambiguous segments.
• Various minor bug fixes.

Changes

• The following tools are now available directly in the CLC Genomics Workbench:
  • Target Region Coverage Analysis
  • Create Consensus Sequences from Variants
  • Detect and Refine Fusion Genes
• Tools previously located under the QIAseq Panel Expert Tools folder in the Toolbox are now under the Biomedical Genomics Analysis folder. Manual sections have been reorganized accordingly.
• QIAseq miRNA Differential Expression and QIAseq miRNA Quantification template workflows have been moved to the QIAseq RNA workflow folder.

Retirements

The following have been retired:

• Tools:
  • CNV and LOH Detection (legacy). Copy number variants (CNVs) can be detected using Copy Number Variant Detection (CNVs), LOH events can be detected using Detect Regional Ploidy.
• Template workflows:
  • Identify Causal Inherited Variants in Family of Four (WGS) (legacy)
  • Identify Causal Inherited Variants in Trio (WGS) (legacy)
  • Identify Rare Disease Causing Mutations in Family of Four (WGS) (legacy)
  • Identify Rare Disease Causing Mutations in Trio (WGS) (legacy)
  • Identify Causal Inherited Variants in Family of Four (WES) (legacy)
  • Identify Causal Inherited Variants in Trio (WES) (legacy)
  • Identify Rare Disease Causing Mutations in Family of Four (WES) (legacy)
  • Identify Rare Disease Causing Mutations in Trio (WES) (legacy)
  • Identify Causal Inherited Variants in Family of Four (TAS) (legacy)
  • Identify Causal Inherited Variants in Trio (TAS) (legacy)
  • Identify Rare Disease Causing Mutations in Family of Four (TAS) (legacy)
  • Identify Rare Disease Causing Mutations in Trio (TAS) (legacy)

Biomedical Genomics Analysis 22.2.1

Released on February 2, 2023

Improvements

• Create UMI Reads from Reads discards very large UMI groups and their corresponding reads. Previously, the analysis of these groups caused significantly extended runtime.
• Create Methylation Level Heat Map supports analysis of Whole Genome Bisulfite Sequencing Data (WGBS) data. Clustering is only performed when there are < 5,000 regions.
• Various minor improvements

Bug fixes

• Fixed an issue in Create Sample Report where several options were duplicated in the wizard when Biomedical Genomics Analysis 22.2 was installed.
• Various minor bug fixes

Biomedical Genomics Analysis 22.2

Released on October 19, 2022

Immune repertoire improvements

• Import Immune Reference Segments has been updated to:
  • import the D segments
  • output the C segments in the sequence list instead of a trim adapter list
• The table view of the immune reference segments has been updated to show the Chain and Segment type of each sequence as separate columns.
• Immune Repertoire Analysis has been updated with the following:
  • provide subsections for all identified chain types in the report
  • renamed the "V/J-segment length/similarity fraction" options to "V/J length/similarity fraction"
  • updated the "V length fraction" option to refer to the length fraction of the reference segment, instead of the read
  • report D and C segments, both in the report and the output clonotypes
• Filter Immune Repertoire has been updated to also filter using the identified segment types.
• Compare Immune Repertoires has been updated to also report D and C segments.
• Both import and export of VDJtools clonotypes format has been updated to include the D segment. The VDJtools clonotypes format does not support the C segment.
• New versions (v1.1) for both human and mouse of the TCR reference segments containing reference segments for D and C segment types are available in the reference data sets "QIAseq Immune Repertoire Analysis" and "QIAseq Immune Repertoire Analysis Mouse". The Reference data sets no longer contain the TCR constant trimming adapter list.
• Perform QIAseq Immune Repertoire workflow has been updated with the following:
  • Merge Overlapping Pairs was added to the workflow and uses the UMI reads as input. This collapses paired reads that overlap, leading to a better identification of clonotypes
  • Reads are no longer trimmed to remove the constant gene. Trimming is kept for removing bases that are ambiguous and have low quality at the ends of the reads.
  • The default reference data has been updated to human v1.1

QIAseq FastSelect RNA kit and QIAseq UPXome RNA kit support

• Six new workflows provide support for QIAseq UPXome RNA kit and QIAseq FastSelect RNA kit and two capture protocols:
  • Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primers)
  • Perform QIAseq UPXome RNA Gene Expression (ODT-RT primers)
  • Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT + ODT-RT primers)
  • Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT + ODT-RT primers)
  • Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT primers)
  • Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT primers)
• The workflows are located in QIAseq RNA workflows.
• All workflows can be launched from the Analyze QIAseq Samples guide using the FastSelect RNA and UPXome RNA tabs, respectively.
• Reference data for the workflows is available in the reference data set QIAseq FastSelect and UPXome hg38.

New QIAseq Tool

• A new tool, Validate QIAseq Read Structure (beta), is now available in the QIAseq Expert toolbox. The tool takes a graphical report from QC for Sequencing Reads as input and validates whether the structure is compatible with a given QIAseq protocol and hence matches the template workflows.

New workflows

• Identify QIAseq xHYB Somatic Variants and Identify QIAseq xHYB Somatic Variants including Mitochondrial are available for analysis of data generated using the QIAseq xHYB Panels without or with a mitochondrial spike-in probe set, respectively. Reference data for the workflows is available in the reference data set QIAseq xHYB Human hg38. The workflows can be run from the xHYB Human tab in Analyze QIAseq Samples.
• Create QIAseq DNA Ultra CNV Control Mapping (Illumina) can be used to generate control read mappings or coverage tables for copy number variant detection using QIAseq DNA Ultra data. The workflow can be run from the Targeted DNA Ultra tab in Analyze QIAseq Samples.

Improvements

• Template workflows for QIAseq panels have been moved into three subfolders: QIAseq DNA Workflows, QIAseq RNA Workflows and Other QIAseq Workflows.
• CNV detection has been added to the template workflow Identify QIAseq DNA Ultra Somatic Variants (Illumina). To generate control mappings or control coverage tables for CNV detection, use the new workflow Identify QIAseq DNA Ultra CNV Control Mapping (Illumina).
• Create QIAseq Exome CNV Control Mapping can now also be used to create control mappings for xHYB panels.
• The template workflow Identify QIAseq DNA Pro Germline Variants (Illumina) can be run from the Targeted DNA Pro tab in Analyze QIAseq Samples.
• The following QIAseq Targeted DNA Pro panels have been added to the reference data set QIAseq DNA Pro Panels hg38. The panels are also available in Analyze QIAseq Samples under the Targeted DNA Pro:
  • Hereditary Breast and Ovarian Cancer Panel (PHS-201Z)
  • Hereditary Colorectal Cancer Panel (PHS-202Z)
  • Hematologic Malignancy Panel (PHS-203Z)
  • Hereditary Prostate Cancer Panel (PHS-204Z)
  • Hereditary Pancreatic Cancer Panel (PHS-205Z)

Bug fixes

• Upload to QCI Interpret and Upload Prepared QCI Interpret Report now supports upload using a proxy server.
• Fixed an issue in QIAGEN Sets Ensemble reference data elements (v103 and v106) where gene annotation for pseudogenes was missing leading to false fusion calls. The new version is Ensembl v106.1.

Changes

• Export VDJtools Clonotypes is now available from the Biomedical Genomics Analysis plugin.

Advanced notice

• CNV and LOH Detection (legacy) will be removed in a future release of the software.

Biomedical Genomics Analysis 22.1.1

Released on August 22, 2022

Improvements

SARS-CoV-2 workflow improvements

• The Refine Read Mapping option to remove reads with more than 6 SNPs in a 100bp window has been disabled in all three SARS-CoV-2 workflows. This change supports identification of all Omicron mutations that tend to cluster closer together compared to other current strains.
• The three SARS-CoV-2 workflows now output the InDels track from the Structural Variant Caller. Some InDels that are not fully covered by reads will be misannotated by design, but can be assessed in full from this track.
• Trimming of a common sequence has been removed from the SARS-CoV-2 ARTIC and QIAseq workflows. No common sequence should be present. This may marginally change results in rare cases where the common sequence is similar to the biological read. It is not expected to have an impact on the overall analysis.
• A QIAseq DIRECT with Booster A SARS-CoV-2 reference data set that can be used with the QIAseq SARS-CoV-2 workflow has been added to QIAGEN Sets and is available from the Reference Data Manager.

Reference data improvements

• A new Trim Adapter List for trimming of QIAseq RNA Panel (hg38 and Mouse) reads is available in the corresponding QIAGEN Sets located in the Reference Data Manager.
• New reference data sets for Mouse and Rat, where MT is marked as circular in the genome, are now available from the QIAGEN Sets in the Reference Data Manager.

General improvements

• Import QIAGEN Primers can now also import amplicon.bed files. The imported amplicons are split into forward and reverse primers. An example file in this format is: https://www.qiagen.com/us/resources/resourcedetail?id=7d64f00d-748e-4203-b8e6-bd0f40b16c33&lang=en
• Detect and Refine Fusion Genes can now be used with the Combine Reports tool. Only Fusion reports generated with Biomedical Genomics Analysis 22.1.1 and later can be used by the tool.

Bug fixes

• Fixed an issue where many non-QIAseq Biomedical Template Workflows were pointing to an incomplete version of ClinVar. This ClinVar database has been removed from the QIAGEN Sets (see Changes and ClinVar Important Notification).
• Fixed an issue in Detect and Refine Fusion Genes where the "Found in-frame CDS" column was missing from the results.
• Fixed an issue causing Detect Regional Ploidy to fail when all somatic variants provided to the tool had frequencies below 50%.

Changes

• The ClinVar 20220528 reference data element from version 3 of the Reference Data Sets hg38 (Ensembl) and hg19 (Ensembl) was incomplete and has been removed. If downloaded, we strongly advise deleting the local version of the element. If annotations from ClinVar 20220528 are used in downstream analyses, we recommend rerunning samples. See ClinVar Important Notification for further details.
• In the Reference Data Manager, dbSNP is no longer available under QIAGEN Sets, it is still possible to download the database using Download Genomes.

Biomedical Genomics Analysis 22.1

Released on June 28, 2022

New workflows and reference data

• Identify QIAseq xHYB Germline Variants and Identify QIAseq xHYB Germline Variants including Mitochondrial are available for analysis of data generated using the QIAseq xHYB Panels without or with a mitochondrial spike-in probe set, respectively. Reference data for the workflows is available in the new reference data set QIAseq xHYB Human hg38. The workflow can be run from the xHYB Human tab in Analyze QIAseq Samples.
• Identify QIAseq DNA Pro Germline Variants (Illumina) is available for analysis of Illumina data generated with QIAseq Targeted DNA Pro Panels. Reference data for the workflow is available in the reference data set QIAseq DNA Pro Panels hg38.
• Identify QIAseq DNA Pro Somatic Variants with LOH Detection (Illumina) is intended for analysis of the brain and comprehensive cancer QIAseq Targeted DNA Pro panels, which targets chromosomes 1p and 19q deletions. The workflow expands the existing Identify QIAseq DNA Pro Somatic Variants (Illumina) workflow with LOH detection. Reference data for the QIAseq Targeted DNA Pro panels is available in the reference data set QIAseq DNA Pro Panels hg38. The workflow can be launched from relevant panels under the Targeted DNA Pro tab in Analyze QIAseq Samples.
• A new reference data set, QIAseq DNA Ultra Panels hg38, is available for use with the Identify QIAseq DNA Ultra Somatic Variants (Illumina) workflow.
• Reference elements in the reference data sets, hg19 (Ensembl) and hg38 (Ensembl), have been updated.

Bisulfite Sequencing

• A new tool Create Methylation Database simplifies the creation of databases for Predict Methylation Profile when the aim is to discriminate between 2 or 3 "pure" types.
• The quality of the Predict Methylation Profile tool has been tested more thoroughly and the beta label has been removed. No changes were required.
• Improved selection of "Known methylation level column" to be more automated in Predict Methylation Profile.
• Made it more clear that Predict Methylation Profile takes input created by Call Methylation Levels in the wizard.
• A new tutorial, Creating a Methylation Database for Three Cell Types, has been added to the CLC tutorial portfolio. The tutorial uses data generated with the QIAseq T Cell Infiltration Panel (MHS-202Z) for building a database and testing of performance.

Immune Repertoire Expert Tools

• A new importer, Import Immune Reference Segments, is now available for import of immune reference data to be used for processing reads and when running the Immune Repertoire Analysis tool.
• A new tool Filter Immune Repertoire has been added, which allows clonotypes to be filtered based on a series of criteria.
• The following tools now support the analysis of BCR-Seq data:
  • Immune Repertoire Analysis
  • Import VDJtools Clonotypes
  • Compare Immune Repertoire
• Immune Repertoire Analysis can now identify clonotypes in data from a wide variety of TCR-Seq and BCR-Seq kits.
• Clonotypes produced by Immune Repertoire Analysis are now, by default, sorted by count in decreasing order.
• A new "Frequency (%)" column has been added to the clonotypes table view.
• The report produced by Immune Repertoire Analysis has been updated to include the number of fragments for each identified V/J segment.
• The scatter plots in the report produced by Compare Immune Repertoire now show the frequencies of all clonotypes instead of just the common clonotypes. R^2 has been removed from the plots.

Changes

• Calculate LOH and HRD (beta) has been split into two tools: Detect Regional Ploidy and Calculate HRD Score (beta). The underlying algorithms have not been changed, hence Detect Regional Ploidy can be used to estimate regional ploidy states including loss-of-heterozygosity (LOH) and Calculate HRD Score (beta) can be used to calculate an HRD score from the Target-level ploidy track produced by Detect Regional Ploidy.

Improvements

• The following improvements have been made to the outputs from Detect Regional Ploidy:
  • The target-level ploidy track contains a column which annotates ploidy states with LOH Yes/No.
  • A new region-level ploidy track provides region-level ploidy states.
  • The report contains new genome and chromosome level plots showing log fold changes, variant allele frequencies and estimated ploidy states.
• Renamed the workflow Perform QIAseq cfDNA Analysis to Identify QIAseq DNA Ultra Somatic Variants (Illumina) to match the corresponding QIAseq panel names. Reference data for the workflow is available in the new reference data set QIAseq DNA Ultra Panels hg38. In addition, the workflow can now be launched from the Targeted DNA Ultra tab in Analyze QIAseq Samples.
• Reference data for the QIAseq Targeted DNA panel DHS-110Z (Human HRR Panel) has been added to the reference data element QIAseq DNA Panels hg19.
• Reference data for the hereditary QIAseq Targeted DNA Pro panels PHS-201Z (Hereditary Breast and Ovarian Cancer Panel), PHS-202Z (Hereditary Colorectal Cancer Panel), PHS-203Z (Hematologic Malignancy Panel), PHS-204Z (Hereditary Prostate Cancer Panel), PHS-205Z (Hereditary Pancreatic Cancer Panel) have been added to the reference data set QIAseq DNA Pro Panels hg38.
• Reference data for the somatic QIAseq Targeted DNA Pro panels PHS-101Z (Breast Cancer Focus Panel), PHS-102Z (Colorectal Cancer Focus Panel), PHS-103Z (Myeloid Neoplasms Focus Panel), PHS-104Z (Brain Cancer Focus Panel), PHS-105Z (Lung Cancer Focus Panel), and PHS-3100Z (Comprehensive Cancer Focus Panel) have been added to the reference data set QIAseq DNA Pro Panels hg38.

Bug fixes

• Fixed an issue where Upload to QCI Interpret and Upload Prepared QCI Interpret Report failed with the error "Access is denied" even though upload succeeded. The issue would only occur for some QCI Interpret Translational accounts.
• Fixed an issue causing Create UMI Reads from Grouped Reads to fail in the rare situation where the read not carrying the UMI was generated by two individual primers, the reads from the individual primers did not overlap and one of the reads started with an insertion.
• Fixed an issue affecting Convert Annotation Track Coordinates which failed when trying to convert insertions between hg19 to hg38.
• Fixed a rare integer overflow in the Immune Repertoire Analysis tool when redistributing reads among clonotypes during merging. The issue would lead to incorrect (typically too low) counts for the merged clonotypes and sometimes an error. In order to be affected, clonotypes must have at least ~10^4 counts.

Advanced Notice

• The tool CNV and LOH Detection will be removed in a future release of the software. The tool has been moved to the legacy toolbox and is now called CNV and LOH Detection (legacy). Copy number variants can be called using Copy Number Variant Detection (CNVs) and the new tool Detect Regional Ploidy can be used to identify LOH events.

Retirements

• Calculate LOH and HRD (beta). Note that no functionality has been retired, LOH can be called using Detect Regional Ploidy and and HRD scores can be calculated using Calculate HRD Score (beta).

Biomedical Genomics Analysis 22.0.4

Released on May 09, 2022

Improvements

• Convert Annotation Track Coordinates now reports which genome assemblies were used for conversion.

Bug fixes

• Fixed an issue that caused Convert Annotation Track Coordinates to fail. The issue was caused by a change in the underlying service at NCBI.

Biomedical Genomics Analysis 22.0.3

Released on April 27, 2022

Bug fixes

• Fixed an issue where Annotate RNA Variants would fail when annotating one or more variants within 30nt of a splice junction. The issue arose when the variant(s) had the effect of inserting >60nt compared to the reference genome.
• Fixed an issue in the QIAseq Multimodal PanCancer hg38 reference data located among the QIAGEN Sets where the DNA primer file has been updated. The previous version was missing some of the primers.

Biomedical Genomics Analysis 22.0.2

Released on March 03, 2022

New tools

• Calculate LOH and HRD (beta) provides loss of heterozygosity (LOH) results and a homologous recombination deficiency (HRD) score. The HRD score is estimated from LOH, telomeric-allelic imbalance (TAI) and large-scale state transition (LST) events. The LOH algorithm is identical to the algorithm in CNV and LOH Detection.

Improvements

• When running Demultiplex Reads (UPX 3' RNA) or Detect Wells (UPXome) from Analyze QIAseq Samples or QIAseq UPXome workflows the plate well names for 96 and 384 well plates have been updated to match standard nomenclature using padding to two or three digits. The output will be named accordingly.
• Various minor improvements

Bug fixes

• Fixed an issue affecting the following workflows when submitted to CLC Genomics Cloud Engine 22.0.0, where the workflows would fail with an error about invalid arguments due to missing parameters:
  • Detect QIAseq RNAscan Fusions
  • Perform QIAseq Multimodal Analysis (Illumina)
  • Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina)

Biomedical Genomics Analysis 22.0.1

Released on February 10, 2022

Improvements

• The definition of "Large" and "Small" UMI groups has been changed in Create UMI Reads for miRNA. Reads that have an ambiguous nucleotide (e.g. N) in either the UMI or biological sequence are now always classed as "Small" groups. This means that an attempt is always made to merge them with "Large" groups that do not have any ambiguity.
• The report produced by Immune Repertoire Analysis has been updated to
  • Report the number of input fragments. This is relevant for paired reads where one pair is counted as one.
  • Report detailed information (such as diversity indexes, rarefaction, etc) only for those chains that have been found in the data.
• The report produced by Compare Immune Repertoires has been updated to
  • Report reads as fragments. This is relevant for paired reads where one pair is counted as one.
  • Report detailed information (such as diversity indexes, rarefaction, etc) only for those chains that have been found in at least two input samples.
• When running Quantify QIAseq UPXome from the Analyze QIAseq Samples guide it now uses QIAseq UPXome hg38 reference data (Ensembl v103).

Bug fixes

• Fixed an issue in CNV and LOH Detection, where region- and gene-level CNVs were sometimes not correctly calculated. This could happen on chromosomes where a subset of target regions had low coverage in control samples. For further details, see Region and gene-level CNV detection problems when low coverage control targets present.
• Fixed an issue in Upload to QCI Interpret and Prepare QCI Interpret Upload that hindered selection of reference sequence and therefore upload to QCI Interpret. The issue affected both tools when run as stand-alone from the toolbox as well as Upload to QCI Interpret when started from Analyze QIAseq Samples.
• Fixed an issue in Identify QIAseq Exome Causal Inherited Variant in Trio where the coverage reports from QC for Targeted Sequencing were interchanged between proband, affected and unaffected parent.

Biomedical Genomics Analysis 22.0

Released on January 11, 2022

Updated to be compatible with with CLC Genomics Workbench 22 and CLC Genomics Server 22.

New features and improvements

New workflows

• Identify QIAseq DNA Pro Somatic Variants (Ion Torrent) and Create QIAseq DNA Pro CNV Control Mapping (Ion Torrent) are available for analysis of Ion Torrent data generated with QIAseq Targeted DNA Pro panels.
• Perform QIAseq cfDNA Analysis supports analysis of data generated with QIAseq cfDNA Panels.
• Quantify QIAseq UPXome for analyzing QIAseq RNA UPXome data is now available.
  • Barcodes for demultiplexing are available as part of QIAseq UPXome hg38 reference data set.
  • The experimental set up as well as the workflow can be evaluated and run from Analyze QIAseq Samples under the UPXome tab.

Unique Molecular Index handling

• Calculate Unique Molecular Index Groups can group reads with more than one mismatch in the UMI.
• Calculate Unique Molecular Index Groups can group reads that share a UMI but map to different positions within a specified a window. Increasing window size will likely result in fewer UMI groups.
• Create UMI Reads from Grouped Reads has a new method for calculation of consensus quality scores for UMI reads that can be useful when detecting very low frequency variants.

Performance improvements

• The runtime of Remove and Annotate with Unique Molecular Index and Structural Variant Caller has been improved through optimisation of underlying code.
• Create UMI Reads for miRNA is more memory efficient.
• In QIAseq workflows, Structural Variant Caller has been configured with target regions to improve speed. The following workflows have been updated:
  • Identify QIAseq DNA Germline Variants (Illumina)
  • Identify QIAseq DNA Germline Variants (Ion Torrent)
  • Identify QIAseq DNA Somatic Variants (Illumina)
  • Identify QIAseq DNA Somatic Variants (Ion Torrent)
  • Identify QIAseq DNA Somatic Variants with TMB Score (Illumina)
  • Identify QIAseq DNA Somatic Variants with TMB Score (Ion Torrent)
  • Identify QIAseq DNA Somatic Variants and Germline Variants from Tumor Normal Pair (Illumina)
  • Identify QIAseq Exome Causal Inherited Variants in Trio
  • Identify QIAseq Exome Germline Variants
  • Perform QIAseq Multimodal Analysis (Illumina)
  • Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina)

Other improvements

• Detect and Refine Fusion Genes can now detect partial exon skippings, partial intron inclusions, intron insertions and full+partial exon skippings.
• In Create Sample Report the percentage of target region positions that meet a set coverage threshold can be used as a QC metric.
• Control coverage tables that can be used as input to Copy Number Variant Detection (CNVs) and CNV and LOH Detection are now output from the following workflows:
  • Create QIAseq DNA CNV Control Mapping (Ion Torrent)
  • Create QIAseq DNA CNV Control Mapping (Illumina)
  • Create QIAseq DNA Pro CNV Control Mapping (Illumina)
  • Create QIAseq Exome CNV Control Mapping
• QIAseq DNA Pro Illumina workflows use Trim Reads instead of Remove and Annotate with Unique Molecular Index to trim adapter sequence on read 2 in paired reads.
• Various minor improvements

Bug fixes

• Fixed an issue in Trim Primers of Mapped Reads that in some cases could cause the tool to fail when running QIAseq TMB workflows on Windows machines.
• Fixed an issue that caused Create Sample Report and Combine Reports to fail on reports from QC for RNAscan Panels.
• Fixed an issue causing some quality metrics to not be included in the Quality Control table in the report produced by Create Sample Report. The following metrics were affected: "Number of UMI Reads" from the Create UMI Reads from Reads and Create UMI Reads from Grouped Reads reports as well as "Average number of reads per UMI" and "Median number of reads per UMI" from the Calculate Unique Molecular Index Groups report.
• Fixed an issue that caused Structural Variant Caller to fail on RNA-seq read mappings where read 1 and read 2 of a paired read were mapped to very distant positions.
• Fixed an issue that caused Upload to QCI Interpret to fail when run as part of a workflow on CLC Genomics Cloud Engine. The functionality has not changed, but existing workflows containing the tool must be manually updated during migration.
• Fixed an issue with selecting a fixed number of features in Create Methylation Level Heat Map that now uses coefficient of variance for selecting informative features.
• Various minor bugfixes

Changes

• The Biomedical workflows can now be found in the Template Workflows folder in the toolbox.
• The Analyse QIAseq Panels guide was renamed to Analyze QIAseq Samples.

Retirements

• Detect Fusion Genes (Legacy)
• Refine Fusion Genes (Legacy)
• The Illumina Custom importer. Functionality of this importer is available in the Illumina importer provided by the QIAGEN CLC Genomics Workbench 22.0 and higher.

Advanced Notice

• The following workflows have been moved to the Legacy Workflows folder and will be removed from the product in a future release:
  • 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 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 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)

Biomedical Genomics Analysis 21.2.4

Released on 09.05.2022

This plugin and server plugin is compatible with QIAGEN CLC Genomics Workbench and Server version 21.0.6, please visit myCLC for downloads.

Improvements

• Convert Annotation Track Coordinates now reports which genome assemblies were used for conversion.

Bug fixes

• Fixed an issue that caused Convert Annotation Track Coordinates to fail. The issue was caused by a change in the underlying service at NCBI.

Biomedical Genomics Analysis 21.2.3

Released on 27.04.2022

This plugin and server plugin is compatible with QIAGEN CLC Genomics Workbench and Server version 21.0.6, please visit myCLC for downloads.

Improvements

• The QIAseq UPXome functionality released in Biomedical Genomics Analysis plugin and Server plugin 22.0 is now available in this older version of the software as well.

Bug fixes

• Fixed an issue where Annotate RNA Variants would fail when annotating one or more variants within 30nt of a splice junction. The issue arose when the variant(s) had the effect of inserting >60nt compared to the reference genome.

Biomedical Genomics Analysis 21.2.2

Released on 03.03.2022

New Tools

• Calculate LOH and HRD (beta) provides loss of heterozygosity (LOH) results and a homologous recombination deficiency (HRD) score. The HRD score is estimated from LOH, telomeric-allelic imbalance (TAI) and large-scale state transition (LST) events. The LOH algorithm is similar to the algorithm in CNV and LOH Detection, but LOH results may vary between the two tools as the LOH algorithm in CNV and LOH Detection also uses some information that is internally provided by the CNV algorithm.

Biomedical Genomics Analysis 21.2.1

Released on 10.02.2022

Bug fixes

• Fixed an issue in CNV and LOH Detection, where region- and gene-level CNVs were sometimes not correctly calculated. This could happen on chromosomes where a subset of target regions had low coverage in control samples. For further details, see Region and gene-level CNV detection problems when low coverage control targets present.
• Fixed an issue in Identify QIAseq Exome Causal Inherited Variant in Trio where the coverage reports from QC for Targeted Sequencing were interchanged between proband, affected and unaffected parent.

Biomedical Genomics Analysis 21.2

Released on 15.10.2021

New tools

• Predict Methylation Profile (beta) 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.
• Calculate LOH (beta) provides loss of heterozygosity (LOH) results. The LOH algorithm is similar to the algorithm in CNV and LOH Detection, but LOH results may vary between the two tools as the LOH algorithm in CNV and LOH Detection also uses some information that is internally provided by the CNV algorithm.

New workflows

• A new workflow Detect QIAseq Methylation with T Cell Infiltration is available for analysing the T Cell Infiltration Methylation Panel (MHS-202Z). Other than reporting the Methylation levels, the workflow also provides prediction of cell composition. The QIAseq Methylation Panels hg19 reference data set has been extended to include the database that is used for the prediction.
• A new workflow Identify QIAseq DNA Pro Somatic Variants (Illumina) supports analysis of libraries generated with QIAseq Targeted DNA Pro Panels. Reference data is available from the new QIAseq DNA Pro Panels hg38 reference data element.
• A new workflow Create QIAseq DNA Pro CNV Control Mapping (Illumina) has been created to allow easy generation of read mappings that can be used as CNV Control Mappings for QIAseq Targeted DNA Pro Panels.
• The new Methylation and DNA Pro workflows are available from Analyze QIAseq Samples.

Analyze QIAseq Samples

• Changed the name from Analyze QIAseq Panels to Analyze QIAseq Samples.
• A new tab called miRNA has been added to the Analyze QIAseq Samples guide. It is possible to run QIAseq miRNA Quantification and perform QIAseq miRNA Differential Expression on two groups.
• The workflow Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina) is now available to run from Analyze QIAseq Samples. It can be run with both the QIASEQ DIRECT SARS-CoV-2 kit and the QIAseq SARS-CoV-2 Primer Panel.
• A new option to analyse the T-Cell Infiltration Methylation Panel (MHS-202Z) with methylation prediction has been added to the Targeted Methylation tab of the Analyze QIAseq Samples guide.

General improvements

• Immune Repertoire Analysis has been updated to better handle situations where the J segment cannot be uniquely identified for a clonotype. This change is not expected to impact the results significantly but may lead to slight changes in read counts as well as identification of clonotypes with low read counts.
• The SARS-CoV-2 workflows now outputs the consensus sequence list in addition to the consensus sequence track.
• Two parameters for LOH detection have been added in CNV and LOH Detection and Calculate LOH (beta) tools: Transition factor controls how often the copy number state is expected to switch and the HMM decoding method can be set to either Viterbi or posterior decoding.
• QC for RNAscan Panels has been updated to report DNA contamination as a ratio instead of a percentage.
• ClinVar has been updated and added to the hg38 and hg19 reference data set under the QIAGEN sets tab.
• The V/J usage plots in the report from Compare Immune Repertoires are now organised in subsections for the alpha, beta, gamma and delta chains.
• Identify Mispriming Events no longer includes filtered reads in the read mapping visualising off-target reads mapping back to the primer design location.
• Identify Mispriming Events no longer accepts BLAST databases and reference sequences if the two do not match.
• The tools Trim Primers of Mapped Reads and Create UMI Reads from Reads have been improved to accept empty inputs. This allows workflows to finish when empty inputs are provided to tools and can facilitate easier troubleshooting as all reports will be available.
• The RNA primer track for the QIAseq Multimodal Pan Cancer Panel has been updated to improve representation of the primer sequences.
• Various minor improvements

Bug fixes

• Fixed an issue in Analyze QIAseq Samples where the parameter Minimum frequency was exposed when running Create QIAseq DNA CNV Control Mapping. Minimum frequency is not relevant for generation of control mappings.
• Fixed an issue in Analyze QIAseq Samples where changes to applied to thresholds in previous analysis runs replaced default settings in subsequent runs.
• Fixed an issue where, in a few cases, the report from QC for RNAscan Panels was missing entries in "Target genes" and "Number of target genes".
• Fixed an issue where Trim Primers of Mapped Reads would fail if a primer was located near a chromosome end.
• Fixed an issue where Calculate Unique Molecular Index Groups would not group single and paired-end reads when the UMI was on read 1. In most UMI protocols, including QIAseq Targeted DNA, the UMI is on read 2, but for QIAseq Targeted DNA Pro Panels, data should be analysed with Biomedical Genomics Analysis plugin version 21.2 or newer.
• Various minor bugfixes

Advance Notice

• The following workflows will be removed in a future release of the software:
  • 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 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 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)

Biomedical Genomics Analysis 21.1.1

Released on 25.08.2021

Improvements

• Structural Variant Caller now discards reads that are longer than 5000 bp. Long reads could previously cause the tool to fail and are of minimal value for structural variant detection based on unaligned ends.

Bug fixes

• Fixed an issue in Structural Variant Caller that prevented workflows from being automatically migrated when installing a new version of the Biomedical Genomics Analysis plugin. Workflows containing a Structural Variant Caller element will need to be updated.
• Fixed an issue that caused Structural Variant Caller to fail when breakpoints were positioned close to the junction of a circular chromosome.
• Fixed an issue in the reference dataset QIAseq Exome hg38 where two target regions have been shortened by one base pair each to avoid overlapping regions. Overlapping regions cause Copy Number Variant Detection (CNVs) to fail when Merge overlapping targets is not checked. The two Create QIAseq Exome CNV Control Mapping, Identify QIAseq Exome Causal Inherited Variants in Trio and Identify QIAseq Exome Germline Variants have been updated to use the new target regions by default.
• Fixed an issue affecting Calculate Unique Molecular Index Groups that caused increased runtime.
• Fixed an issue causing CNV and LOH Detection to fail if the order of the chromosomes in the gene and target region annotation tracks differed.
• Various minor bug fixes

Biomedical Genomics Analysis 21.1

Released on 24.06.2021

New features and improvements

Upload to QCI Interpret and QCI Interpret Translational

• Upload to QCI Interpret now also supports upload to QCI Interpret Translational.
• Easy authentication is available through a browser log in.
• It is possible to upload a wider range of variants including CNVs, fusions, inversions, TMB and MSI.
• New tools designed for workflows support bundling of files and upload in separate steps. Prepare QCI Interpret Upload bundles CLC elements into a report and Upload Prepared QCI Interpret Report uploads the resulting report.
• All tools are server- and workflow enabled to allow easy automation of upload.

New tools

• Create Consensus Sequences from Variants produces a consensus sequence from a variant track and the matching reference. Low coverage regions can be masked.

New importers/exporters

• A new BGI/MGI Sequencing Import tool has been added.
• A new Custom Reads Illumina Sequencing Importer with extended options for fastq file import has been added to support 10X data, it is e.g. now possible to import three fastq files with R1, R2, and I1 as paired reads where I1 is added in front of R1.
• Import/export of clonotypes has been introduced for use with VDJtools.

Structural Variant Caller

• The runtime of Structural Variant Caller has been improved through optimisation of calculation methods and underlying code. Runtime improvements primarily affect WGS analysis and/or analysis of samples with many broken pair reads.
• The calculation of the consensus sequence for breakpoints has been refined, this is particularly relevant for samples where multiple breakpoints are located close to each other.
• RNA-seq reads are accepted as input. Reads spanning two exons are considered two individual reads.
• It is possible to ignore broken reads. Choosing this option can improve speed but may reduce sensitivity.
• When running in targeted mode, variants where breakpoints are located in different target regions are detected.

RNA-seq read type improvements (QIAseq RNA Fusion XP)

• Import QIAGEN Primers now accepts a new QIAseq RNA Fusion XP primer format for specific annotation of primers as Fusion, GEX (Expression count) or Variant Calling.
• Extract Reads Matching Primers now has an option to annotate reads with primer information for Fusion, Variant calling and GEX (Expression count) when the information is available in a primer track.
• In Create UMI Reads from Reads, primer specific read annotations are transferred to the created UMI reads.
• Detect and Refine Fusion Genes has been updated with an option to only use specific "Fusion" annotated reads for detection and refinement of fusions.
• The Perform QIAseq RNA Fusion XP Analysis (Illumina) workflow has been updated with functionality to classify reads as Fusion reads, GEX reads or Variant Calling.
• A new workflow called Perform QIAseq RNA Fusion XP Analysis (Ion Torrent) similar to the existing Perform QIAseq RNA Fusion XP Analysis (Illumina) workflow, for Ion Torrent data has been added. The workflow can be executed from the Analyze QIAseq Panels guide.

SARS-CoV-2 workflow and reference data

• A new Ready-to-use workflow called Identify ARTIC V3 SARS-CoV-2 Low Frequency and Shared Variants (Illumina) has been added to the SARS-CoV-2 workflows toolbox. The workflow is capable of analysing Illumina reads sequenced with the ARTIC v3 primer set.
• The Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina) workflow has been updated to use Low Frequency Variant Detection. Variants are post-filtered to ensure quality. The low frequency variant detection threshold has been opened in the Identify low frequency variants filter and the Discard short reads changed to length 60 from previously 50, to reduce the chance of identifying false positive variants in the new Default QIAseq DIRECT panel. In addition, the new tool Create Consensus Sequence from Variants replaces the Extract Consensus Sequence tool.
• The Identify Ion AmpliSeq SARS-CoV-2 Low Frequency and Shared Variants (Ion Torrent) workflow has been updated to use Low Frequency Variant Detection. Variants are post-filtered to ensure quality. The low frequency variant detection threshold has been opened in the Identify low frequency variants filter. In addition, the new tool Create Consensus Sequence from Variants replaces the Extract Consensus Sequence tool.
• A new reference data set called ARTIC SARS-CoV-2 is available in the Reference Data Manager.

Workflow improvements

In the following QIAseq workflows Structural Variant Caller has been configured with target regions to improve speed:

• Identify QIAseq DNA Germline Variants (Illumina)
• Identify QIAseq DNA Germline Variants (Ion Torrent)
• Identify QIAseq DNA Somatic Variants (Illumina)
• Identify QIAseq DNA Somatic Variants (Ion Torrent)
• Identify QIAseq DNA Somatic Variants with TMB Score (Illumina)
• Identify QIAseq DNA Somatic Variants with TMB Score (Ion Torrent)
• Identify QIAseq DNA Somatic Variants and Germline Variants from Tumor Normal Pair (Illumina)
• Identify QIAseq Exome Causal Inherited Variants in Trio
• Identify QIAseq Exome Germline Variants
• Perform QIAseq Multimodal Analysis (Illumina)
• Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina)

In the following WGS workflows the new setting Ignore broken pairs in Structural Variant Caller has been enabled to improve speed:

• Identify Somatic Variants from Tumor Normal Pair (WGS)
• Identify Variants (WGS)
• 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)

Other improvements

• CNV and LOH Detection can use coverage tables generated by QC for Targeted Sequencing as control mappings. Read mappings can still be used as control mappings.
• Boundaries for normalising coverage based on allele frequency information can be adjusted in CNV and LOH Detection, making it better suited for samples where a large percentage of targets are affected by CNV events.
• Trim Primers of Mapped Reads can trim primers on read 2 for paired-end reads.
• Grouping of paired-end UMI reads using Calculate Unique Molecular Index Groups has been improved for the case where the UMI is located on read 1.
• The reports from Create UMI Reads from Reads, Calculate Unique Molecular Index Groups and Create UMI Reads for miRNA have been aligned so that they contain comparable UMI group size statistics and histograms of UMI group sizes.
• The report from Create UMI Reads from Grouped Reads shows the distribution of quality-scores before and after UMI grouping as a box-plot.
• A new version of the Human TCR reference data is now available.
• The runtime for Detect and Refine Fusion Genes has been reduced, especially for reads with many unaligned ends.
• The fusion gene track has been added to the genome browser (WT) view output from Perform QIAseq RNA Fusion XP Analysis and Perform QIAseq Multimodal Analysis workflows.
• The rarefaction section of the Compare Immune Repertoires report now contains a legend linking color to sample for the case where the number of samples exceeds 10 and we do not show a legend directly on the plot.
• Ready-to-use workflows using Create UMI Reads from Reads are now using the default parameters for the tool.
• The report from Create UMI Reads for miRNA now details how many reads were discarded as either too long or too short.
• Various minor improvements

Bug fixes

• Fixed an issue in Extract Reads Matching Primers so that detection of primers now work when primers are situated at the end of a read.
• Fixed sample names in summary report output from the SARS-CoV-2 workflows.
• Fixed an issue where the fusion plot column was missing from the fusion tracks generated by Detect and Refine Fusion Genes.
• Fixed an issue in Create UMI Reads from Reads where if "Enable advanced settings" was enabled and one or more of the advanced settings was altered, and "Enable advanced settings" was then disabled again, the altered settings would still apply. The tool has been updated, so that if "Enable advanced settings" is disabled, default settings will now be used for all advanced settings.
• Fixed an issue causing Structural Variant Caller to fail when reads near the ends of chromosomes had unaligned ends.
• Fixed an issue affecting Structural Variant Caller that caused an error when unaligned ends spanned the junction of a circular reference sequence.
• Fixed an issue in variant tracks created by the Structural Variant Caller that caused heterozygous variants to be annotated as homozygous in exported VCF files.
• Fixed an issue in CNV and LOH Detection, where setting "Minimal purity" to a value higher than 0.7 and enabling "Normalize coverage using allele frequencies" would cause the tool to fail.
• Fixed an issue in CNV and LOH Detection, where features in the same position could have different predicted ploidy states.
• Fixed an issue affecting Target Region Coverage Analysis where an error occurred if inputs had different chromosome names but compatible genomes.
• Fixed an issue in the Create UMI Reads from Grouped Reads report where one of two identical plots showing "Quality scores of all UMI read nucleotides" has now been removed.
• Fixed an issue that caused Create UMI Reads from Reads to fail if highly dissimilar reads were grouped. The bug was rarely seen but could occur with lenient settings for grouping reads, with the present default settings for Create UMI Reads from Reads the bug has not been observed.
• Replaced Create Sample Report with Combine Reports in the workflow Identify QIAseq Exome Causal Inherited Variants in Trio to fix an issue causing some summary statistics to be missing.
• Various minor bug fixes.

Biomedical Genomics Analysis Plugin 21.0.1

Released on February 3, 2021

Improvements

• Import QIAGEN Primers now supports paired primers that will work with Trim Primers and their Dimers from Mapping.
• The Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina) workflow now uses an updated set of primers.
• The workflows Perform QIAseq Multimodal Analysis (Illumina) and Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) now saves indels, long indels, and inversion in individual tracks in the output.
• Various minor improvements

Bug fixes

• Fixed an issue in all ’Identify Variants’ workflows where the Target regions workflow input was locked to a workflow role not part of the main reference data sets (e.g. hg38 (refseq), hg19 (ensembl), etc.). Affected workflows:
  • Identify Variants (TAS)
  • Identify Variants (TAS-HD)
  • Identify Variants (WES)
  • Identify Variants (WES-HD)
  • Identify and Annotate Variants (TAS)
  • Identify and Annotate Variants (TAS-HD)
  • Identify and Annotate Variants (WES)
  • Identify and Annotate Variants (WES-HD)

• Fixed an issue that caused Trim Primers and their Dimers from Mapping to fail when reads were completely trimmed away with no mapped bases left in the read
• Fixed an issue in the QIAseq miRNA Differential Expression workflow so that it now handles inputs as Small RNAs instead of as Whole transcriptome RNA-Seq.
• Fixed an issue in Perform TSO500 DNA Analysis (Illumina) workflow where the UMI read-through now trims UMI sequences before mapping.
• Fixed an issue in Analyze QIAseq Panels where the history for the reports from Remove and Annotate with Molecular Index and Create UMI Reads from Reads would incorrectly say the read-structure "is paired end" when running the Ion Torrent RNAscan workflow from Analyze QIAseq Panels.
• Fixed an issue where RNAscan panels could not be run from the Analyze QIAseq Panels guide with Ion Torrent reads.
• Fixed an issue in Structural Variant Caller sometimes causing a null pointer exception when constructing de novo assemblies.
• Fixed a minor issue in Perform TSO500 DNA Analysis (Illumina) where one of the workflow outputs was placed in the wrong folder.

Biomedical Genomics Analysis 21.0

Released on January 12, 2021

New features

Detect and Refine Fusion Genes

Detect and Refine Fusion Genes potential fusions in RNA data and then accumulates and evaluates the evidence for each potential fusion.

This tool replaces the Detect Fusion Genes and the Refine Fusion Genes tools, which have been moved to the Legacy section of the Toolbox. We recommend that workflows containing the legacy tools are updated to include Detect and Refine Fusion Genes instead.

The following ready-to-use workflows have been updated to use Detect and Refine Fusion Genes in place of the the two legacy tools, which they used previously:

• Perform QIAseq RNA fusion XP Analysis
• Detect QIAseq RNAscan Fusions
• Perform QIAseq Multimodel Analysis (Illumina)
• Perform QIAseq Multimodel Analysis with TMB and MSI (Illumina)

Identify Mispriming Events

Identify Mispriming Events produces a track of potential mispriming events, i.e. events where reads were amplified from a region of the genome other than the intended target region. Using this track as input to Trim Primers of Mapped Reads, reads originating from mispriming events can be removed from mappings, decreasing the potential for false positive variants to be called in downstream analysis steps. This track can also be used to evaluate the quality of a set of primers.

Improvements

Performance improvements

• Create UMI reads for miRNA is now faster.
• Structural Variant Caller uses less memory, allowing it to be run on machines with lower numbers of cores.

Improvements to workflows

• The mismatch cost in the Map Reads to Reference element in ready-to-use workflows provided with this plugin has been increased from 2 to 4 to better reflect current sequencing quality.
• The post-filtering of variants with "high UMI evidence" in the QIAseq ready-to-use workflows has been relaxed: fewer variants are considered as having "high UMI evidence", and the Average Quality cut-off for these has been reduced to 38.
• The Indels and SV tool has been replaced by the Structural Variant Caller in all ready-to-use workflows. In addition to being used for guiding the local realignment, the indel track produced by the Structural Variant Caller is output as part of the results of the workflows. The QIAseq targeted DNA workflows further produce an inversion and a long indel track among the results; these are also generated by the Structural Variant Caller.
• Indel tracks generated by Structural Variant Caller elements in ready-to-use workflows have been updated to include gene information.
• The Identify QIAseq DNA Somatic Variants ready-to-use workflows include detection of internal tandem duplications, including FLT3.
• All ready-to-use workflows now uses the name "Genome Browser View" for the Track Lists generated.
• QC for RNAscan Panels can make use of primer tracks imported from BED format files.

Other improvements

• Convert Annotation Track Coordinates includes remapped positions from second pass alignments.
• Reports generated by the following tools can be used when defining QC metrics in the new Create Sample Report tool of the QIAGEN CLC Genomics Workbench:
  • Remove and Annotate with Unique Molecular Index
  • Calculate Unique Molecular Index Groups
  • Create UMI Reads from Grouped Reads
  • Create UMI Reads from Reads
  • QC for RNAscan Panels
• The plots in the Loss-of-heterozygosity section of the CNV and LOH Detection report use consistent colors, and include lines that indicate the expected allele frequencies and coverage ratios for each state. The colors in the LOH-track match the colors used in the LOH plot.
• Various minor improvements

Bug fixes

• Create UMI reads for miRNA accepts only sequence lists as input. Previously a single sequence could be input, but the tool would then fail with an error.
• Fixed an issue affecting Create UMI Reads from Reads, where if the "Read structure" option was set to "Paired end reads (discard read 2)" and the read list generated had an odd number of reads, a downstream Trim Reads job would fail with an error.
• Fixed an issue in the Structural Variant Caller that caused some inversion calls to be incorrectly classified as tandem duplications.
• Fixed an issue in the Refine Fusion Genes (legacy) tool where the number of wild type supporting reads were under-counted if the genes involved had other fusion partners.
• Various minor bug fixes

Changes

The following tools have been moved to the QIAGEN CLC Genomics Workbench 21.0:

• Extract IsomiR Counts
• Annotate with Repeat and Homopolymer Information
• Merge Variant Tracks

Retirements

• Trim Primers of Mapped Single Reads (legacy)
• Trim Primers of Mapped Paired Reads (legacy)
• The VCF (Biomedical) exporter. Functionality of this exporter is available in the VCF exporter provided by the QIAGEN CLC Genomics Workbench 21.0 and higher.
• Identify QIAseq DNA Somatic Variants with FLT3 Identification (Illumina) FLT3 detection is included in the Identify QIAseq DNA Somatic Variants workflows.

Advance Notice

• Detect Fusion Genes (legacy) and Refine Fusion Genes (legacy) have been moved to the legacy folder in the Toolbox. We recommend using the new Detect and Refine Fusions Genes tool.

Biomedical Genomics Analysis Plugin 20.2.1

Released on February 3, 2021

Improvements

• The Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina) workflow now uses an updated set of primers.

Bug fixes

• Fixed an issue in the QIAseq miRNA Differential Expression workflow so it handles inputs as Small RNAs instead of as Whole transcriptome RNA-Seq.
• Fixed an issue in Perform TSO500 DNA Analysis (Illumina) workflow where the UMI read-through now trims UMI sequences before mapping.
• Fixed an issue in Analyze QIAseq Panels where the history for the reports from Remove and Annotate with Molecular Index and Create UMI Reads from Reads would incorrectly say the read-structure "is paired end" when running the Ion Torrent RNAscan workflow from Analyze QIAseq Panels.
• Fixed in a bug in QC for RNAscan Panels where the reported "Mean read coverage per reference gene control primer" was 100-fold too high and "Target gene vs reference gene coverage (%)" was 100-fold too low.
• Fixed an issue that caused Trim Primers and their Dimers from Mapping to terminate when reads were completely trimmed away with no mapped bases left in the read
• Fixed an issue in Structural Variant Caller sometimes causing a null pointer exception when constructing de novo assemblies.

Biomedical Genomics Analysis Plugin 20.2

Released on November 26, 2020

New Features

New ready-to-use workflows

New workflows are available under the Ready-to-Use Workflows area of the Toolbox:

• SARS-CoV-2 Workflows Under this folder are two workflows:
  • Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina)
  • Identify Ion AmpliSeq SARS-CoV-2 Low Frequency and Shared Variants (Ion Torrent)
    These workflows generate a consensus sequence for each SARS-CoV-2 sample and support the identification of variants in each sample as well as supporting cross-sample comparisons.
• TSO500 Panel Analysis Under this folder are two workflows for analysis of the TruSight Oncology 500 Illumina bundle, one for DNA analysis and one for RNA analysis.
  • Perform TSO500 DNA Analysis (Illumina) This workflow includes somatic variant calling, CNV detection and reporting of a TMB score. (MSI detection is not yet supported.)
  • Perform TSO500 RNA Analysis (Illumina) This workflow does gene expression analysis and reports detected fusions.
• QIASeq Panel Analysis | QIASeq Analysis Workflows. Two new workflows have been added:
  • Identify QIAseq DNA Somatic and Germline Variants from Tumor Normal Pair (Illumina) This workflow analyses matched tumor normal samples and reports somatic and germline variants in addition to low frequency somatic variants that are also present in the normal sample. It is useful for analysis of driver mutations and we recommend using it in combination with QIAGEN Clinical Insight (QCI) Interpret.
  • Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) This workflow is for analysis of the multimodal Pan Cancer panel (UHS-5000Z). It reports filtered variants, TMB score, microsatellite instability status, fusion genes and when control samples are provided, CNVs are also reported. The Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) can also be launched using the Analyze QIAseq Panels guide where it is located under the tab labeled Multimodal TMB/MSI.

New tools

• Structural Variant Caller Detects indels, tandem duplications and inversions in somatic and germline WGS and targeted applications. This tool improves upon the detection of tandem duplications and inversions offered by existing tools in the CLC Genomics Workbench, while the InDels track produced can be used as a guidance track in the Local Realignment tool and is expected to provide similar results to outputs of the InDels and Structural Variants tool used for that purpose. If you have been using the Advanced Structural Variant Detection (beta) tool, provided in a separate plugin, we recommend instead using this tool, which has been designed to replace it.
• Compare Immune Repertoires Compares T-cell receptor repertoires identified by Immune Repertoire Analysis and generates a report containing comparisons of read composition, diversity indices, rarefaction, CDR3 length and V/J usage. A heat-map can also be produced based on the Jaccard Similarity between the samples and a similarity table.
• Extract Reads Matching Primers Extracts reads that match a primer and discards reads that do not match a primer, especially useful for cleaning up RNA sequence data to decrease false positives when detecting fusion genes and before generating targeted gene expression matrices.
• Refine Read Mapping Removes potentially problematic mapped reads. Options are provided for removing reads based on the number of SNPs in a certain window and/or remove reads with unaligned ends of a certain length.
• 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. Based on adjustable thresholds, targets with low coverage are flagged in the output track.
• CNV and LOH Detection Detects copy number variations (CNVs) and loss-of-heterozygosity (LOH) from targeted resequencing experiments. This tool expands upon the existing Copy Number Variant (CNV) Detection tool.

Improvements

• Two new tabs have been added to the Analyze QIAseq Panels guide:
  • RNA Fusion XP Analysis of seven catalog RNA FUSION XP panels can be launched from this tab. Primer information for the catalog panels are available in the QIAseq RNA Fusion XP Panels hg38 QIAGEN set in the Reference Data Manager.
  • Immune The Perform QIAseq Immune Repertoire Analysis workflow for Human and for Mouse, can be launched from this tab.
• Perform QIAseq RNA Fusion XP Analysis filters have been adjusted and are now able to detect variants at a lower coverage which improves the sensitivity.
• Perform QIAseq RNA Fusion XP Analysis and Perform QIAseq Multimodal Analysis workflows now include Extract Reads Matching Primers, which reduces false positive fusion calls as well as improving the targeted expression matrix produced.
• Improved handling of inversions by the VCF (biomedical) exporter.
  
• Trim Primers and their Dimers of Mapped Reads now includes an option to trim the primers of amplicon fragments.
• TMB score thresholds are no longer set by default in the Identify TMB Status workflow. It is now possible to set thresholds manually.
• Short read removal in Trim Primers of Mapped Reads now removes short reads based on alignment length and not just read length.
• The QC for RNAscan Panels report now accounts for missing validation genes. The symbol "-" is used to denote undefined fraction values (those where the denominator is 0). Previously, these values were reported as 0.
• The QC for RNAscan Panels report can now be used as input to the Combine Reports tool.
• The Detect QIAseq RNAscan Fusions workflow and the Perform QIAseq RNA Fusion XP Analysis workflows now include the QC for RNAscan Panels report in the combined report they generate. The Perform QIAseq Multimodal Analysis (Illumina) workflow no longer outputs the QC for RNAscan Panels report and is thus not included in the combined report generated.
• The length of a microsatellite locus read in Generate MSI Baseline and Detect MSI Status now depends not only on identification of flanking region markers, but is also assessed by comparing nucleotide composition in the read against the true locus nucleotide composition. Only reads that match the same composition as the microsatellite are kept. The two reference data baseline elements that are part of the QIAseq TMB Panels hg38 reference data set have been updated with this change.
• The manual information for the Identify QIAseq DNA Somatic Variants with FLT3 Identification workflow has been updated to clarify that that it has been optimized to detect FLT3 internal tandem duplications, and this optimization may impact the ability to detect other variants.
• Various minor improvements

Reference data bundles

New datasets supporting the new workflows are available under the QIAGEN Sets tab of the Reference Data Manager:

• AmpliSeq SARS-CoV-2 Uses MN908974.3 as reference genome
• QIAseq SARS-CoV-2 Uses MN908974.3 as reference genome
• TSO500 hg38 Uses hg38_no_alt_analysis_set and RefSeq annotations. Bundle includes all reference data types needed for the analysis of both TSO500 RNA and DNA part
• QIAseq Multimodal Pan Cancer hg38 Uses hg38_no_alt_analysis_set and RefSeq annotations. Dataset have been custom made to fit analysis of the Pan Cancer panel UHS-5000Z
• QIAseq DNA Panel hg19 Updated with mispriming events tracks
• QIAseq DNA Panel hg19 (RefSeq) Supports analysis of the QIAseq DNA Panels using RefSeq annotations

Bug fixes

• Fixed an issue in Remove and Annotate with Unique Molecular Index where the number of reads reported in the report header was incorrect.
• Fixed an issue that caused an error to be thrown by the Trim Primer of Mapped Reads tool when unaligning primers in RNA reads spanning an intron.
• The VCF (biomedical) exporter now supports exports of tracks based of compatible genomes even if the chromosome names differ. Previously, an empty VCF file was generated if the chromosome names differed, even if the tracks used as input were compatible.
• Fixed an issue introduced in Biomedical Genomics Analysis 20.0 where under particular circumstances, when the Remove and Annotate with Unique Molecular Index tool was run on a CLC Genomics Server and other tools were being run on the same execution node or single server at the same time, an empty annotated sequence list could be generated.
• Various minor bugfixes

Biomedical Genomics Analysis Plugin 20.1.1

Released on August 13, 2020

Improvements

• Empty fusion tracks can now be handled by the VCF (Biomedical) exporter.
• The average quality value in the "Low average quality variants" filter has been lowered from 44 to 41.5 in the workflows listed below. This change only affects the filtering of variants with high UMI evidence, and is intended to decrease the chance of filtering out true positive variants from the results.
  • Identify QIAseq DNA Somatic Variants (Illumina)
  • Identify QIAseq DNA Somatic Variants with FLT3 IDT Identification (Illumina)
  • Perform QIAseq Multimodal Analysis (Illumina)

Bug fixes

• Fixed a bug in Detect Fusion Genes that caused no fusion genes to be reported if reference data was used where the link between annotations on mRNA and gene tracks could not be established. This affects reference data imported from GTF format, but not reference data imported from GFF3 format files. When using the CLC Genomics Workbench Reference Data Manager to download reference, this affected results using reference data from Ensembl, but not reference data downloaded from RefSeq.
• Fixed a bug affecting the Perform QIAseq Multimodal Analysis (Illumina) and Perform QIAseq RNA Fusion XP Analysis ready-to-use workflows, where all non-reference alleles of frequencies below 3% were wrongly filtered away.

Biomedical Genomics Analysis Plugin 20.1

Released on June 29, 2020

New Features

New QIAseq ready-to-use workflows

After plugin installation, these new workflows can be found in the CLC Genomics Workbench Toolbox under Ready-to-Use Workflows | QIASeq Panel Analysis | QIASeq Analysis Workflows. They can also be launched using the Analyze QIAseq Panels guide.

• QIAseq Exome analysis workflows A new group of workflows for analyzing QIAseq exome samples is available:
  • Identify QIAseq Exome Germline Variants
  • Identify QIAseq Exome Causal Inherited Variants in Trio
  • Create QIAseq Exome CNV Control Mapping

These workflows offer some benefits over the workflows provided in the Whole Exome Sequencing folder for trio and germline variant detection, including incorporating read trimming as an initial step in the workflow, and retaining QUAL scores in the variant track produced. In addition, the Identify QIAseq Exome Germline Variants workflow provides the option to detect CNVs. The Create QIAseq Exome CNV Control Mapping can be used to generate control mappings suitable for use when running CNV detection on exome panel data.

These workflows can be launched from under the new Exome tab of the Analyze QIAseq Panels guide.

• Perform QIAseq Immune Repertoire Analysis This workflow is aimed at analysis of data generated using the QIAseq Immune Repertoire Panel. The reference data for the analysis of human and mouse TCR samples from the IMHS-001Z and IMMM-001Z panels is not yet available, but work is ongoing to release it. If you would like to register your interest in using this analysis area, please contact our support team by emailing ts-bioinformatics@qiagen.com.

• Identify QIAseq DNA Somatic Variants with FLT3 Identification (Illumina) Identify somatic variants and structural variants in FLT3 in QIAseq targeted DNA panel data. This workflow can be launched from under the Targeted DNA tab of the Analyze QIAseq Panel guide, when choosing to analyze data from the Myeloid Neoplasms Panel (DHS-003Z) or Comprehensive Cancer Panel (DHS-3501Z).
• Create QIASeq DNA CNV Control Mapping (Illumin/Ion Torrent) These workflows can be used to generate control mappings suitable for use when running CNV detection when analyzing QIAseq targeted DNA panel data. They include the QC for Targeted Sequencing tool, for easy evaluation of sample coverage and quality. The workflows can be launched from under the Targeted DNA tab of the Analyze QIAseq Panel guide, using options available in the drop-down menu for each supported panel type.

Other ready-to-use workflows

• Annotate Variants with Effect Scores (WES) This workflow adds annotations with effect scores to SNVs in variant tracks. Effect scores indicate the impact of a mutation on the gene or transcript. This workflow can be found in the Toolbox under Ready-to-Use Workflows | Whole Exome Sequencing (WES).

New tools

• Create Methylation Level Heat Map Hierarchically clusters samples and features, generating a two dimensional heat map of methylation levels, using methylation levels tracks as input.
• Merge Variant Tracks Merges multiple variant tracks into a single variant track.
  
• Annotate with Repeat and Homopolymer Information Annotates variants with repeat and homopolymer information, based on the variant itself and the genome sequence flanking it.
• Annotate with Effect Scores Annotates SNV variants with precomputed effect scores, which indicate the level of impact a mutation has on the gene or transcript.
• Extract IsomiR Counts Extracts IsomiR composition and count information from each underlying miRNA alignment of the "grouped on mature" expression table output by the Quantify miRNA tool, and produces a table containing that information.
• 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.
• Immune Repertoire Analysis Analyzes RNA data to characterize the T cell receptor repertoire.

Improvements

Extended support for paired reads, including reads generated by duplex TruSight Oncology, Illumina (TSO) UMI protocol

• The following tools are affected by this improvement:
  • Remove and Annotate Unique Molecular Index, where the read structure can be specified as single end, paired end or duplex, and where for paired end, the read the index is on can be specified.
  • Create UMI Reads from Reads, where the read structure can be specified as single end, paired end or duplex, and for paired end reads, there is now an option for not discarding read 2.
• All QIAseq ready-to-use workflows have been updated to support duplex reads.
• Single reads must now be designated as such when launching these tools and updated workflows.

Other QIAseq Panel Analysis workflow improvements

• Two new options are available under the UPX 3' RNA tab of the Analyze QIAseq Panels guide to support simple case vs. control analysis of differentially expressed genes: "Human Detect Differentially Expressed Genes Between Two Groups" and "Mouse Detect Differentially Expressed Genes Between Two Groups". These options launch the "Human Identify and Annotate Differentially Expressed Genes and Pathways" and "Mouse Identify and Annotate Differentially Expressed Genes and Pathways" workflows, respectively.
• When configuring Demultiplex Reads, launched from the UPX 3' RNA tab of the Analyze QIAseq Panels guide, the selection of the most probable wells in the well selection preview is now based on information taken from across all the input sequence lists, instead of just the first. Demultiplex Reads was formerly named "Demultiplex".
• Options specifying the input data as Illumina (Index on Read 2) or Ion Torrent are now present for each panel listed under the Targeted RNAScan tab of the Analyse QIAseq Panels guide.
• The Quantify QIAseq RNA Expression workflow produces a combined summary report per sample. These reports can be used by Combine Reports to make a summary report for many samples.
• The Detect Fusion Genes tool option "Minimum fusion read count" has been changed from 2 to 4 in the following workflows:
  • Perform QIAseq Multimodal Analysis (Illumina)
  • Detect QIAseq RNAscan Fusions
  • Perform QIAseq RNA Fusion XP Analysis
• The Perform QIAseq Multimodal Analysis (Illumina) and Perform QIAseq RNA Fusion XP Analysis ready-to-use workflows now include the new Annotate with Repeat and Homopolymer Information tool. Low frequency (<3%) repeat and homopolymer variants are now actively removed from the variants passing filters track.

Reference data

Updated data sets are available under the QIAGEN Sets tab of the Reference Data Manager:

• Updated hg19 and hg38 (no alt analysis set) reference bundles, both RefSeq and Ensembl.
• Updated versions of dbSNP for both hg19 and hg38, under the Reference Data Elements area.
• A new reference data set, QIAseq Exome Panels hg38, intended for use with the new QIAseq Exome workflows.
• SIFT effect annotations have been added, and are intended for use with the new Add Effect Score to Variants (WES) workflow.
• The hg19 reference set used by default in Biomedical Ready-to-Use workflows is now based on Ensembl version 99.

Export and upload

• VCF exporter (biomedical) can now export multiple variant tracks.
• Upload to QCI Interpret can now handle multiple variant tracks.

Reports

• The report generated by Calculate Unique Molecular Index Groups now includes "Reads by read group", where the most common UMI group sizes the inputs belong to are listed.
• The report generated by Detect MSI Status no longer contains a "Sample length" column in the second table in section "1 Summary".
• A plot has been added to the report generated by Remove and Annotate Unique Molecular Index showing the distribution of the UMI barcode nucleotides.

Quantify QIAseq RNA

• Running time has been reduced. This tool is used in the Quantify QIAseq RNA Expression workflow, thus also affecting its running time.
• A report can now be generated. These reports can be compared across samples using Combine Reports.

Fusion gene detection

• The runtime of Detect Fusion Genes has been substantially improved for paired-end, whole transcriptome RNA-seq data.
• The Fusion Report generated by Refine Fusion Genes has been updated to include the sample name, and the chromosome and exon number of fusion genes detected.
• Evidence for backsplicing in exon skipping fusions, which was sometimes reported, has been removed, as it was not consistently reported.

Calculate TMB Score has been updated to only use exon regions for calculating the TMB score. For this, it requires a track containing the exon regions (typically, an mRNA track).

Bug fixes

• Fixed an issue that caused the Quantify QIASeq UPX 3' workflow to fail if it was provided with multiple inputs.
• Fixed an issue that arose if workflows were launched in batch mode from the Analyze QIAseq Panels guide, where one Workflow Result Metadata table was created per batch unit, when a single Workflow Result Metadata table, listing results from all batch units, was expected.
• Fixed an issue where Detect Fusion Genes could fail with an error of the form "Empty region for geneA chrA positionA - geneB chrB positionB". The error was most likely to be encountered when the "Detect fusions with novel exon boundaries" option was enabled, and "Maximum distance to known exon boundary" was set to a high value.

Notifications

Tutorials for the Biomedical Genomics Analysis plugin are provided online. They will no longer be available from the Help | Plugin Tutorials menu of the CLC Genomics Workbench. The online tutorials can be reached using the Help | Online Tutorials menu option.

Biomedical Genomics Analysis Plugin 20.0.1

Released on March 10, 2020

Bugfixes

• Fixed an issue where reference alleles were being filtered out from variant tracks produced by Trio Analysis and Family of Four Ready-to-Use Workflows, which then led to incorrect coverage values in VCF files exported using these variant tracks. This issue was introduced in Biomedical Genomics Analysis 20.0.
• Fixed an issue in Refine Fusion Genes. where a given read could be counted as supporting more than one fusion if those fusions had breakpoints lying very close together. Each read can now only support one fusion model.
• Fixed an issue affecting the Identify Variants (WGS-HD, WES-HD and TAS-HD) Ready-to-Use Workflows where all reference alleles were being filtered away. This was addressed by removing the Remove Reference Variant (Legacy) tool from these workflows.
• Fixed an issue affecting the Identify Somatic Variants in Tumor Normal pairs (WGS, WES and TAS) Ready-to-Use Workflows where all reference alleles were being filtered away. In these workflows the Remove Homozygous Reference Variants tool has replaced the Remove Reference Variant (Legacy) tool, so only orphan reference alleles are removed.
• Fixed a bug where fusions could be incorrectly annotated as known or incorrectly annotated as unknown by Annotate Fusions with Known Fusion Information and Refine Fusion Genes in cases where multiple sets of breakpoints were detected for a given pair of genes. Where only one pair of breakpoints between two genes was identified, fusion annotation was not affected.

Improvements

Fusion gene pipeline improvements

• Detect Fusion Genes includes a new parameter "Detect fusions with novel exon boundaries". When this option is enabled, the analysis includes looking for fusions where at least one breakpoint is not at an exon boundary. Using Biomedical Genomics Analysis 20.0, fusion detection always included looking for such events.
• The Fusion track generated by Detect Fusion Genes now contains an annotation indicating whether a fusion has breakpoints at novel exon boundaries.
• Detect Fusion Genes no longer detects fusions with novel exon boundaries if the novel exon boundary is in a region with low sequence complexity.
• In the QIAseq Analysis Workflows, Detect QIAseq RNAscan Fusions, Perform QIAseq RNA Fusion XP Analysis and Perform QIAseq Multimodal Analysis (Illumina), the value of the "Max no of hits for a read" setting for the first of the RNA-Seq Analysis steps has been increased from 2 to 10. This new values aligns better with the definition of hits per read as distinct places on the reference that a read maps best to, introduced in QIAGEN CLC Genomics Workbench 20.0.

Various other minor improvements

Biomedical Genomics Analysis Plugin 20.0

Released on December 11, 2019

New Features

QIAseq Panel Analysis

New workflows

• Perform QIAseq Multimodal Analysis for analysing QIAseq DNA and RNA Multimodal Panel data. This workflow performs somatic variant calling on DNA down to a frequency of 0.5% and uses RNA for detecting fusion genes, exon skipping, and gene expressions. A reference data set called QIAseq Multimodal Panels hg38 is available for analysis with reference sequence, hg38 no alt analysis set. The catalog panels UHS-005Z, UHS-006Z and UHS-009Z can be run from the Multimodal tab in Analyse QIAseq Panel guide. Custom panels can similarly be configured for quick execution as long as DNA primers and target regions have been lifted to the hg38 genome before import. When running the stand-alone workflow it is possible to call CNVs if controls mapping are supplied
• Perform QIAseq RNA Fusion XP Analysis for analyzing QIAseq Fusion XP Panel data. This workflow supports variant calling, fusion detection and expression analysis.
• Detect QIAseq MSI Status with Baseline Creation for a combined analysis of MSI status and baseline creation. This workflow can be used for assessing QIAseq MSI from custom or catalog panels boosted with MSI primers or the booster MSI panel as standalone. It can be configured with the QIAseq TMB panel hg38, or a custom reference dataset for hg19 can be constructed from single reference elements, including newly added MSI loci Track for hg19. The manual includes a description on how to quickly map the samples for the baseline.

VCF Export

An additional VCF exporter, VCF (Biomedical), is now available. This new exporter extends the functionality of the standard VCF exporter by supporting the export of Copy Number Variants (CNV) Tracks (Target, Region and Gene) and Refined Fusion Genes (WT) Tracks, in addition to the export of other variant tracks. VCF files from both exporters are compatible with upload to QCI Interpret.

Fusion gene detection

Detect Fusion Genes

• Detect Fusion Genes now reports fusions with breakpoints that are not close to exon boundaries, such as fusions into exons or introns. This change leads to a wider variety of fusions being detected with a corresponding cost to fusion specificity. The parameter “Maximum distance to exon boundary” now has a slightly different meaning: reads with breakpoints further away than this distance are considered as candidates for fusions into exons or introns.
• The number of fusion partners for a gene now only counts fusions to the same partner once even if there are multiple fusion breakpoints. If the promiscuity threshold is exceeded the top fusions for the gene are selected instead of discarding all fusions that include the gene in question.

Refine Fusion Genes

• A report is now generated by Refine Fusion Genes. The report includes ‘QIMERA’ fusion plots and summary tables for each fusion passing all filters.
• Publication-ready quality plots can be opened for export by double-clicking on the plot in the report or by clicking on links in the fusion gene tracks produced by the tool.
• Reads that map ambiguously and cross a fusion breakpoint are no longer included when counting fusion crossing reads. This reduces the number of false positives from pseudogenes.

New tools

• Detect Differentially Methylated Regions Launch this tool using the new option under the Targeted Methyl tab of the Analyze QIAseq Panels guide. This runs the Call Methylation Levels tool of the CLC Genomics Workbench with parameters optimized for QIAseq Targeted Methyl data.
• Create UMI Reads from Reads Available under the QIAseq DNA Panel Expert Tools folder, this tool identifies and merges reads with similar UMIs (up to one mismatch) that likely originate from the same DNA/RNA molecule without the need to first map the reads to a reference genome. It is particularly useful for spliced reads, such as observed when working with RNA-Seq data, and is preconfigured with default values relevant for working with such data. The tool has an advanced settings dialog where hashing, grouping and merging parameters can be defined. It can be used on both single-end and paired-end reads, but will only include R1 in the output reads list in the case of paired reads. The tool is capable of processing tens of millions of reads quickly when using only 8 GB of RAM.
• Annotate RNA Variants Available under the QIAseq DNA Panel Expert Tools folder, this tool adds annotations to variants that appear to represent RNA changes rather than DNA changes. These annotations can be used when analyzing variants called from RNA data, or to remove low-frequency variants from DNA that has been sequenced together with an RNA sample such that index hopping may have occurred.

Combine Reports

Reports generated by the following tools provided by Biomedical Genomics Analysis 20.0.0 can be used with the new Combine Reports tool of the CLC Genomics Workbench:

• 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
• Detect Fusion Genes
• Calculate TMB score
• Detect MSI status

Improvements and bugfixes

UPX 3′ Analysis

The Demultiplex tool for UPX 3′ (Demultiplex 3′) reads in the panel guide has been improved:

• The wells used in an experimental setup can be selected as an initial step when launching the tool.
• On launch, the tool will determine the likely plate size, platform and which wells were populated. This information can then be adjusted manually if necessary before the analysis is run.

The Quantify QIAseq UPX 3′ workflow has been updated. The workflow now:

• Runs more quickly per sample due to use of the Create UMI Reads from Reads tool
• Produces a Combined Report summarizing key QC values
• Allows for spike-in controls to be used
• Counts ambiguously mapped reads towards total expression
• The new RNA-Seq Analysis option, “Library type setting” is set to “3′ sequencing”, providing better estimates of TPM for this application.

QIAseq Panel Analysis

• The MSI tools Detect MSI Status and Generate MSI Baseline as well the Ready-to-Use workflow Detect QIAseq MSI Status no longer have beta status.
• The tool Create UMI Reads has been renamed to Create UMI Reads from Grouped Reads due to the introduction of the new tool Create UMI Reads from Reads.
• In the Detect QIAseq Methylation workflow, the new option “Report unmethylated cytosines” of the Call Methylation Levels tool is enabled by default. When enabled, methylation levels are reported for all sites with read coverage, rather than only for sites with methylated cytosines. This results in methylation levels being reported for all sites with read coverage, rather than only for sites with methylated cytosines.
• A folder containing output tracks that can be exported using the new VCF (Biomedical) exporter is now created as an output of the Detect QIAseq RNAscan Fusions, Perform QIAseq RNA Fusion XP Analysis, and Perform QIAseq Multimodal Analysis (Illumina) workflows.
• The TMB report from Calculate TMB Score now includes the sample name in the summary table.
• Import QIAGEN Primers has been extended to preserve the spliced coordinates of primers that span splice junctions. Previously such primers were imported as a single contiguous region.
• Fixed a bug in QC for RNAscan Panels where overlapping paired-end reads were counted twice when computing primer coverage.

Detect QIAseq RNAscan Fusions

The Detect QIAseq RNAscan Fusions workflow has been optimized to maintain specificity after improvements to the fusion detection tools. The main changes are:

• An additional homopolymer trimming step has been added.
• The Detect Fusion Genes parameter “Promiscuity” has been reduced from 20 to 8.
• The Refine Fusion Genes parameter “Breakpoint distance” has been increased from 10 to 25.
• The output folder structure has been improved.

Trim Primers of Mapped Reads

• Trim Primers of Mapped Reads is now multi-threaded, supporting much faster execution.
• The handling of broken pair reads has been changed. Broken pairs are kept in the output to help visualize genomic rearrangements, but the primer sequence is unaligned from reads detected to be R1.
• Primers can now be trimmed from the the start of single-end reads, as well as from the ends.
• Spliced primers can now be trimmed from reads.

Ready-to-Use Workflows

• The new Combine Reports tool of the CLC Genomics Workbench has been added to QIAseq Panel Analysis ready-to-use workflows, resulting in the generation of a combined QC report containing QC information from supported reports generated by other tools in the workflows.
• Outputs from Biomedical Ready-to-Use workflows now have the name of the first input element added as a suffix and spaces in output names have been replaced with underscores.
• All QIAseq DNA Variants (Illumina) workflows have been updated with a new definition of medium and high coverage variants (medium = 20-200 / high > 200) and these variants are now only tested for Read Direction Test probability. Filtering on Read Position Test Probability is no longer performed for these workflows.
• Filters have been updated in the ready-to-use workflows for identifying Rare Disease Causing Mutations and Causal Inherited Variants in trios as well as Family of Four (WGS, WES and TAS), to minimize the number of false positives.
• QIAseq DNA workflows now use the CLC Genomic Workbench tools Annotate with Overlap Information and Remove Homozygous Reference Variants in place of the retired Add Information from Overlapping Genes tool.
• Various minor improvements

miRNA tools

• The tools Quantify miRNA, Annotate with RNAcentral Accession Numbers, and Create Combined miRNA Report are now provided by CLC Genomics Workbench 20.0 rather than the Biomedical Genomics Analysis plugin. The QIAseq specific tool Create UMI Reads for miRNA continues to be provided by this plugin.

Biomedical Genomics Analysis Plugin 1.2.1

Released on August 15, 2019

Bugfixes

• Fixed an issue that caused the ready-to-use workflow Identify and Annotate Variants (WES) to fail with the error “A single input object is required, encountered 2 inputs”.
• Fixed a rare issue in the Trim Primers of Mapped Reads tool that could arise when the “Mispriming events” option was enabled and at least one read in the read mapping used as input was aligned in a relatively unusual way.
• Various minor improvements

Biomedical Genomics Analysis Plugin 1.2

Released on June 27, 2019

New Features

QIAseq Panel Analysis

• The QIAseq Panel Analysis guide includes QIAseq 3′ UPX RNA analysis. The 3’UPX RNA solution supports demultiplexing of the reads by cell ID, as well as downstream analysis of the resulting samples with the Quantify QIAseq UPX 3′ workflow. At the same time as this plugin release, new reference data sets are being released, and is available via the CLC Genomics Workbench Reference Data Manager: QIAseq UPX 3′ Panels hg19 and QIAseq UPX 3′ Panels hg38.

• The QIAseq Panel Analysis guide supports four QIAseq Targeted Methylation Panels with the Detect QIAseq Methylation workflow.  At the same time as this plugin release, new reference data sets are being released, and is available via the CLC Genomics Workbench Reference Data Manager: QIAseq Methyl Panels hg38. To implement the Targeted Methylation application, the following changes were made:
  • Import QIAGEN Primers was updated to accept ambiguity codes in primer sequences. In addition, the option “Additional bases to trim” has been renamed to “Additional bases to unalign”, and while it was previously available only for trimming single reads, it is now also applied to paired end reads if enabled.
  • The outputs of the tools Calculate Unique Molecular Index Groups, Create UMI Reads, and Trim Primers of Mapped Reads can now be used for methylation analyses.

QIAseq miRNA Analysis

• Quantify miRNA now allows the use of custom small RNA reference databases to map against. The tool will optionally output a sample grouped by the references in the custom database. The sample can be used with downstream analysis tools, e.g. Differential Expression, PCA for RNA-Seq and Create Heat-Map for RNA-Seq.
• A  sequence list containing unmapped reads can now be output by the Quantify miRNA tool.
• Fixed a bug where the report generated by Create UMI Reads for miRNA would report maximum and minimum UMI group sizes as -1 if there were no UMI groups.

General changes, bugfixes and improvements

QIAseq TMB/MSI

• The workflows Identify QIAseq DNA Somatic Variants with TMB Score (Illumina) and (Ion Torrent)  now produce TMB scores calculated on the basis of target regions with coverage greater than 100x.
• The workflows Identify QIAseq DNA Somatic Variants with TMB Score now outputs the read mapping for MSI status detection before the Trim Primers of Mapped Reads step is executed. This improves the quality in the calling performed by Detect MSI Status (beta).
• TMB status is not automatically included in the TMB report any more, but can be added by enabling an option in the Calculate TMB Score tool. Once enabled, thresholds to use when determining TMB status can be adjusted.
• Detect MSI Status (beta) now outputs an annotation track containing information about loci.
• In Detect MSI Status (beta), the minimum read coverage required for a given locus to be considered testable can now be set using the “Minimum read count per locus” option. As a result, default parameters for the noise reduction threshold were adjusted from 10 to 5.
• Fixed a bug in the Interquartile range test of the Detect MSI Status (beta) tool, where previously all loci were identified as unstable. This then would result in all samples being identified as unstable.

QIAseq Targeted DNA 

• Fixed an issue in Create UMI Reads  that led to the incorrect removal of some UMI reads from the dataset, which could then lead to false negatives in downstream variant calling. This issue affected UMI reads that met all of the three following conditions: they were made from 3 or more pair-end reads, the primer was on the reverse strand, and some reads, but less than 50% of them, contained adapter read-through.
• The “Minimum frequency” option presented when launching Ready-to-Use QIAseq DNA workflows, either directly or via the Analyze QIASeq Panels guide, now shows a minimum frequency of 0.50% instead of 0.25%. This does not affect the behavior of the workflows, as downstream variant calling was already configured to detect variants down to 0.5% frequency.
• The tool Remove and Annotate with Unique Molecular Index has been optimized to take less time to run. The benefits are most apparent on paired-end data when the “Trim read-through common sequence and UMI” option is used.
• Reads in read mappings now retain their names after being processed by tools in the QIAseq DNA Panel Expert Tools folder.
• Trim Primers of Mapped Reads is slightly faster when working on IonTorrent data.
• Fixed an issue where batch units that included more than one sequence list could not be set up when using the Analyze QIAseq Panel Previously, when the Batch option was enabled, and a folder was selected as the batch unit, each sequence list within that folder was analyzed independently.
• Various minor improvements

Biomedical Genomics Analysis Plugin 1.1

Released on April 3, 2019

New Features

• An analysis pipeline for analyzing Tumor Mutational Burden (TMB). This includes  a tool called Calculate TMB Score and associated workflows for both Illumina and Ion Torrent that take advantage of a new reference data set: QIAseq TMB Panels hg38.
• Beta tools and an associated workflow for analyzing Microsatellite Instability (MSI), with two MSI baseline tracks available from the Workbench's Reference Data Manager.
• A QIAseq miRNA analysis pipeline that includes four new tools, two workflows that access new reference data: QIAseq Small RNA. The new tools are compatible with the existing RNA-Seq Analysis visualization tools.

At the same time as this plugin release, a new reference data set is being released, and is available via the CLC Genomics Workbench Reference Data Manager: hg38 no alternative reference set. This data set includes scaffolds and a virus decoy sequence for improved performance.

General changes, bugfixes and improvements

QIAseq Panel Analysis

• The Import QIAGEN Primers tool can now also import RNAscan primers.
• The Ion Torrent reads importer accessed via the Analyze QIAseq Panel Analysis tool now annotates imported reads with sequencing platform information.
• The performance of the Create UMI Reads tool has been improved, with this being particularly relevant to systems with slow I/O.
• The performance of the Calculate Unique Molecular Index Groups has been improved, and the organization of the options in the wizard improved.
• In the Identify QIAseq DNA Variants workflows there is now an option to configure the genetic code to use. This is handled automatically when workflows are launched via the the QIAseq Panel Analysis guide.
• Fixed a bug in Quantify QIAseq RNA Expression where the log would report an incorrect percentage of "reads rejected" and "reads accepted". The error only occurred when the total number of reads exceeded 20M.

Trim Primers of Mapped Reads

• The tool was updated to include options for removing mispriming events and artifacts due to pseudogenes.
• The option "Additional bases to trim" has been renamed to "Additional bases to unalign", and while it was previously available only for trimming single reads, it is now also applied to paired end reads if enabled.
• Fixed a bug in the Trim Primers of Mapped Reads tool that affected the Identify QIAseq DNA Variants Ready-to-Use workflow, where the tool would fail on panel DHS-105Z data with paired reads that spanned the origin of the MT chromosome. The tool now ignores (does not trim) such reads.
• Fixed a bug where the parameter "Maximum additional nucleotides" would be off by one nucleotide. This bug affected single forward reads with reverse primers.
• Minor improvements have been made to some tooltips.

Ready-to-Use Workflows

• The workflows Identify and Annotate Variants (WES), Identify Variants (WES) and Identify Variants (WGS) have had their filtering and variant calling parameters adjusted, and a second Indel and Structural Variant step has been added. These workflows now generate two additional variant tracks, including one with large indels.
• The Identify and Annotate Variants (WES) workflow now annotates unfiltered variants with gene information.
• The Annotate Variants WGS, WES, TAS and WTS workflows have been harmonized to consistently use dbSNP Common instead of the more comprehensive but lower quality dbSNP. The change reduces the execution time of these workflows.
• The Identify and Annotate Variants WES, WES-HD, TAS, TAS-HD workflows show dbSNP Common instead of the full dbSNP in the output track list to increase responsiveness of the view.

Prepare Guidance Variant Track

• All Ready-To-Use workflows that have a Local Realignment step have been improved through the inclusion of the Prepare Guidance Variant Track tool to capture information about structural variants in the guidance track and ensure left-alignment of insertions and deletions.
• The guidance track generated now includes "Evidence", "Repeat", "Variant ratio", "Sequence complexity" and "# Reads" annotations for variants that originate from the structural variants input.
• The tool no longer includes SNVs in the guidance track output.
• The tool is now found in the Resequencing Analysis folder of the Toolbox.

The Download Example Data functionality in the Help menu of the Biomedical Genomics Analysis plugin has been fixed.

Biomedical Genomics Analysis Plugin 1.0

First release, November 28, 2018
A CLC Genomics Workbench with the Biomedical Genomics Analysis plugin installed delivers the functionality previously provided by the Biomedical Genomics Workbench, the QIAseq Targeted Panel Analysis plugin and the QIAGEN GeneRead Panel Analysis Plugin.

Similarly, a CLC Genomics Server with the Biomedical Genomics Analysis Server Plugin installed delivers functionality previously provided using a CLC Genomics Server with a Biomedical Genomics Server Extension license, the QIAseq Targeted Panel Analysis Server Plugin and the QIAGEN GeneRead Panel Analysis Server Plugin.

The listing below is of changes to tools and workflows delivered with the Biomedical Genomics Analysis and Biomedical Genomics Analysis Server Plugin relative to the corresponding earlier functionality. Further changes relevant to Workbench- and Server-specific functionality can be found on the Latest Improvements pages for CLC Genomics Workbench 12.0 and CLC Genomics Server 11.0.

The information on those pages reflects the introduction into those products of some tools previously only available in the Biomedical Genomics Workbench and Biomedical-enabled CLC Genomics Servers. Thus some tools listed as new will not be new to users of the earlier Biomedical products.

Searching for with the name of a Biomedical Genomics Workbench 5.x tool in the Launch tool of the CLC Genomics Workbench 12.0 will return the corresponding tool(s) of interest in the new Workbench. Workflow elements within Ready-to-Use Workflows have the same names as used in the equivalent worfklows in Biomedical Genomics Workbench 5.0.1 wherever this was possible.

Changes relative to the functionality of Biomedical Genomics Workbench 5.0.1, QIAGEN GeneRead Panel Analysis 1.12 and QIAseq Targeted Panel Analysis 1.2

General changes and improvements

• An extended Reference Data Manager is available via the CLC Genomics Workbench, and is launched by clicking on the toolbar button labeled "References". The functionality of the Biomedical Genomics Workbench reference data management tool is presented under the tabs labeled "QIAGEN Sets" and "Custom Sets".
• When launching a workflow to analyze panel data, the wizard now offers the opportunity to select and, when needed, download the appropriate data set to the relevant reference data location.
• The precision of detection of insertions at positions directly after primers in the Trim Primers of Mapped Reads tool has been improved. This change may somewhat negatively affect the sensitivity of detection of insertions at positions right after primers, but does not affect the sensitivity of detection for other variant types.
• The Differential Expression for RNA-Seq tool, located in the RNA-Seq Analysis folder of the Workbench Toolbox, now includes the functionality formerly delivered by the Differential Expression for Targeted RNA-Seq tool QIAseq Targeted Panel Analysis plugin.
• The extension used when naming outputs of the Remove and Annotate with Unique Molecular Index tool has been changed to "RAUMI". Previously it was "RAMB".

Changes to Ready-to-Use Workflows

• Each Map Reads to Reference step present in Ready-to-Use workflows under the Whole Exome Sequencing folder is now followed by a Remove Duplicate Mapped Reads step.
• Workflows in the Whole Transcriptome Sequencing folder under Toolbox | Ready-To-Use Workflows designed for analyzing mouse or rat data are now under a single subfolder called Mouse and Rat. The relevant reference data can be selected when launching each workflow.
• The Differential Expression for Targeted RNA-Seq tool, previously distributed with the QIAseq Targeted Panel Analysis plugin, is no longer available. This functionality is now made available through the Differential Expression for RNA-Seq tool, located within the RNA-Seq folder of the CLC Genomics Workbench 12 Toolbox.
• The QIAGEN GeneRead Panel Analysis workflow has been updated to ensure the coverage report considers the full length of the amplicon, while maintaining appropriate trimming of reads. For this, the "Additional bases to trim" option of the Trim Primers and their Dimers from Mapped Reads tool was decreased from 2 to 0 and the Trim Reads tool was added, which includes automatic read-through adapter trimming.
• In the QIAGEN GeneRead Panel Analysis workflow the dbsnp annotation has been replaced with dbsnp common annotation.

Bug fixes

• Fixed an issue with the Reference Data Manager where custom reference sets could not be made with a customized Gene Ontology element.

Retirements

• The Prepare Overlapping Raw Data workflow is no longer available.

Advanced Notice

Trim Primers of Mapped Single Reads (legacy) and Trim Primers of Mapped Paired End Reads (legacy) will be retired in a future release.