

Software release notes Print Bookmark Share more.. Release December 2018 Main Image Navi QCI Powerstation GeneRead Link QCI Analyze QCI Powerstation 1.6 Updates: Various QCI PowerStation components updated with security patches GeneRead Link default Workflow Extension version 1.1.3 Configuration upgrades: Configuration data (application and tests) for QIAact Myeloid DNA UMI panel has been added. BRCA UMI application and tests have been activated in the application. New features and improvements Kit information specific to the new Myeloid DNA UMI assay has been added. QCI Analyze 1.5.1 New Myeloid DNA UMI analysis workflow and report Secondary analysis for the QIAact Myeloid DNA UMI Panel on blood or bone marrow samples. Variant reporting for the 25 genes targeted by the panel, including detection of large deletions (e.g. CALR deletions). Detection of large insertions such as internal tandem duplications in the gene FLT3. Some of these duplications exceed the length of the sequencing reads. Therefore, the presence of these variants is inferred from unaligned read ends. In the QCI Analyze report, these variants are reported as type "insertion". Reporting of low frequency variants in high sensitivity regions defined for genes KIT and JAK2. These are regions where the detection of low frequency variants is of particular interest. The frequency cut-off and therefore significant coverage thresholds for these regions are tuned accordingly, and thus differ from the settings for the rest of the panel. Two additional quality control criteria for high sensitivity regions: Percentage of base positions in high-sensitivity regions of interest with more than significant coverage. Percentage of base positions in high-sensitivity regions of interest with more than minimum coverage. New features and improvements Changes in this software upgrade are specific to the new Myeloid DNA UMI analysis workflow. The results and report content for all analysis workflows previously released for QCI Analyze 1.5.0 will be unchanged. Results produced in version 1.5.1 will be identical to results obtained with QCI Analyze 1.5.0. Known issues  For genes on the positive strand, variant coding impact for duplications of intron-exon splice sites may be wrong Description:* Genomic duplications of the intron-exon splice site - an event that effectively adds bases to the exon codon region and thus changes the amino acid sequence - will be reported in QCI Analyze as an insertion. As insertions in QCI Analyze by default are left-aligned relative to the reference genome, for genes on the positive strand the duplication can, in rare cases, be attributed to the intro and consequently, the mutation will be reported incorrectly as having no amino acid impact. For genes on the negative strand, the duplication will be attributed to the exon, and the corresponding amino acid impact correctly assigned. Based on the QIAGEN Knowledgebase, we could identify the following pathogenic variants in BRCA2 associated with hereditary breast cancer: BRCA2 p.A2603Gfs*46 BRCA2 p.Asn2879Lysfs Pathogenic variants in somatic cancer, which are affected by this issue, could not be identified for the current GeneReader QIAact panels and therefore the risk that this issue will have an impact for you is very small. How to identify potentially affected variants: 1. In the variant table column 'Type', look for 'insertions'. Select the 'Filter' item to access the 'Advanced Filter' and filter for ‘Type/contains/Insertion’. 2. Look for variants with no p. variant annotation (indicating placement in non-coding area). Sort by clicking the column header. 3. In the column ‘c. variant’, look for annotations signifying placement in the 3’ end of an intron. The format will be ‘c.ex-in’, ‘ex’ and ‘in’ being digits (e.g. c.88-3). ‘ex’ indicates the first position in the downstream exon, ‘-‘ (minus) that the insertion is placed 5’ of this exon, and ‘in’ the position in the intron measured from the splice site. Use the Advanced Filter to filter for ‘c.variant/contains/-‘. If any variants remain, inspect the ‘in’ digit. Only variants for which ‘in’ is smaller than the length of the insertion will potentially be affected by this issue. 4. Check to see if the variant is located in a gene on the positive strand. Select the variant and inspect the blue gene annotation bar in the right-hand side track viewer. Zoom out to view the full gene. If located on the positive strand, the gene annotation bar will point to the right. If a variant is located in a negative strand gene it will not be affected by this issue. For variants which, based on the above, are flagged as potentially affected by this issue, check the read mapping to determine if the insertion is in fact a duplication covering the intron-exon splice site. If so, note that this variant will in fact give rise to amino acid changes and should be considered for downstream interpretation. Sub-optimal mapping of reads may impact reporting of deletions When mapping input reads to the reference, gaps in reads, which indicate deletions, are sometimes placed sub-optimally. As variant calls are based on the alignment, this in turn means that deletions may be called at sub-optimal positions or may be split in two. In effect, the amino acid impact may not be represented correctly. This issue impacts calling of deletions only. It is expected to occur rarely. It will be more prevalent for complex data where many deletions are present. Lung DNA: Two variants of interest will not be placed in Table 3.1 even when passing defined thresholds Affected variants: EGFR: NP_005219.2:p.Lys745_Glu746insValProValAlaIleLys MAP2K1: NP_002746.1:p.Gln56_Lys57delinsProGlu Some variants, such as insertions, have multiple representations e.g. an insertion of a T in a homopolymer stretch of T’s can be represented both as an insertion in the left-hand side, the right-hand side, or inside the poly-T region. In QCI Analyze, variants will always left-align variants calling them at the left-most representation. In the Lung panel, two variants of interest will, if present in samples, be called at a position placed outside the defined Region of interest. This has the following effect: Lung DNA FFPE default: Detect variants outside ROI: Yes => affected variants will be placed in table 3.2. Lung DNA plasma default: Detect variants outside ROI: No => affected variants will not be reported. Work-around: Lung DNA FFPE: Detected variants outside ROI can be manually moved from table 3.2 to 3.1. Lung DNA plasma: The workflow configuration to “Detect variants outside ROI: Yes”. Detected variants outside ROI can be manually moved from table 3.2 to 3.1. Contact QIAGEN Global contacts Technical Service Customer Care GeneReader product portfolio Back to products

Software release notes

QCI Powerstation
GeneRead Link
QCI Analyze

QCI Powerstation 1.6

Updates:

Various QCI PowerStation components updated with security patches

GeneRead Link default Workflow Extension version 1.1.3

Configuration upgrades:

Configuration data (application and tests) for QIAact Myeloid DNA UMI panel has been added.
BRCA UMI application and tests have been activated in the application.

New features and improvements

Kit information specific to the new Myeloid DNA UMI assay has been added.

QCI Analyze 1.5.1

New Myeloid DNA UMI analysis workflow and report

Secondary analysis for the QIAact Myeloid DNA UMI Panel on blood or bone marrow samples.
Variant reporting for the 25 genes targeted by the panel, including detection of large deletions (e.g. CALR deletions).
Detection of large insertions such as internal tandem duplications in the gene FLT3. Some of these duplications exceed the length of the sequencing reads. Therefore, the presence of these variants is inferred from unaligned read ends. In the QCI Analyze report, these variants are reported as type "insertion*".
Reporting of low frequency variants in high sensitivity regions defined for genes KIT and JAK2. These are regions where the detection of low frequency variants is of particular interest. The frequency cut-off and therefore significant coverage thresholds for these regions are tuned accordingly, and thus differ from the settings for the rest of the panel.
Two additional quality control criteria for high sensitivity regions:
- Percentage of base positions in high-sensitivity regions of interest with more than significant coverage.
- Percentage of base positions in high-sensitivity regions of interest with more than minimum coverage.

New features and improvements

Changes in this software upgrade are specific to the new Myeloid DNA UMI analysis workflow. The results and report content for all analysis workflows previously released for QCI Analyze 1.5.0 will be unchanged. Results produced in version 1.5.1 will be identical to results obtained with QCI Analyze 1.5.0.

Known issues

For genes on the positive strand, variant coding impact for duplications of intron-exon splice sites may be wrong

Description: Genomic duplications of the intron-exon splice site - an event that effectively adds bases to the exon codon region and thus changes the amino acid sequence - will be reported in QCI Analyze as an insertion. As insertions in QCI Analyze by default are left-aligned relative to the reference genome, for genes on the positive strand the duplication can, in rare cases, be attributed to the intro and consequently, the mutation will be reported incorrectly as having no amino acid impact. For genes on the negative strand, the duplication will be attributed to the exon, and the corresponding amino acid impact correctly assigned.

Based on the QIAGEN Knowledgebase, we could identify the following pathogenic variants in BRCA2 associated with hereditary breast cancer:
- BRCA2 p.A2603Gfs*46
- BRCA2 p.Asn2879Lysfs
Pathogenic variants in somatic cancer, which are affected by this issue, could not be identified for the current GeneReader QIAact panels and therefore the risk that this issue will have an impact for you is very small.

How to identify potentially affected variants:

1. In the variant table column 'Type', look for 'insertions'. Select the 'Filter' item to access the 'Advanced Filter' and filter for ‘Type/contains/Insertion’.
2. Look for variants with no p. variant annotation (indicating placement in non-coding area). Sort by clicking the column header.
3. In the column ‘c. variant’, look for annotations signifying placement in the 3’ end of an intron. The format will be ‘c.ex-in’, ‘ex’ and ‘in’ being digits (e.g. c.88-3). ‘ex’ indicates the first position in the downstream exon, ‘-‘ (minus) that the insertion is placed 5’ of this exon, and ‘in’ the position in the intron measured from the splice site. Use the Advanced Filter to filter for ‘c.variant/contains/-‘. If any variants remain, inspect the ‘in’ digit. Only variants for which ‘in’ is smaller than the length of the insertion will potentially be affected by this issue.
4. Check to see if the variant is located in a gene on the positive strand. Select the variant and inspect the blue gene annotation bar in the right-hand side track viewer. Zoom out to view the full gene. If located on the positive strand, the gene annotation bar will point to the right. If a variant is located in a negative strand gene it will not be affected by this issue.

For variants which, based on the above, are flagged as potentially affected by this issue, check the read mapping to determine if the insertion is in fact a duplication covering the intron-exon splice site. If so, note that this variant will in fact give rise to amino acid changes and should be considered for downstream interpretation.

Sub-optimal mapping of reads may impact reporting of deletions
When mapping input reads to the reference, gaps in reads, which indicate deletions, are sometimes placed sub-optimally.

As variant calls are based on the alignment, this in turn means that deletions may be called at sub-optimal positions or may be split in two. In effect, the amino acid impact may not be represented correctly. This issue impacts calling of deletions only. It is expected to occur rarely. It will be more prevalent for complex data where many deletions are present.

Lung DNA: Two variants of interest will not be placed in Table 3.1 even when passing defined thresholds
Affected variants:
- EGFR: NP_005219.2:p.Lys745_Glu746insValProValAlaIleLys
- MAP2K1: NP_002746.1:p.Gln56_Lys57delinsProGlu
Some variants, such as insertions, have multiple representations e.g. an insertion of a T in a homopolymer stretch of T’s can be represented both as an insertion in the left-hand side, the right-hand side, or inside the poly-T region. In QCI Analyze, variants will always left-align variants calling them at the left-most representation.

In the Lung panel, two variants of interest will, if present in samples, be called at a position placed outside the defined Region of interest. This has the following effect:
- Lung DNA FFPE default: Detect variants outside ROI: Yes => affected variants will be placed in table 3.2.
- Lung DNA plasma default: Detect variants outside ROI: No => affected variants will not be reported.
Work-around:
- Lung DNA FFPE: Detected variants outside ROI can be manually moved from table 3.2 to 3.1.
- Lung DNA plasma: The workflow configuration to “Detect variants outside ROI: Yes”. Detected variants outside ROI can be manually moved from table 3.2 to 3.1.