Known Issues¶
All known issues with a fix version have been resolved in the specified release.
| Issue | Fix Version |
|---|---|
| After logging into the DSS by clicking on the "Cancer DSS" button in IP for a specific referral, the DSS shows the case list instead of the referral of interest | 6.13.0 |
| Following NGIS Petra release H3C3, RXRA, SOS1, and YAP1 genes will not be labelled in the DSS with a mode of action or be flagged as being present in CGC when compared with the HTML report. | 6.13.0 |
| Following NGIS Quasar release RASA1, RICTOR, RAD51, and ROCK1 genes will not be labelled in the DSS with a mode of action or be flagged as being present in CGC when compared with the HTML report. Additionally, SET will remain labelled as an oncogene in the DSS. In the HTML report, SET mode of action will be N/A. | 6.13.0 |
| Minor allele count in the tumour absolute allele count plot doesn't match with the plot legend | 6.13.0 |
| Total allele count in the germline absolute allele count plot doesn't match with the plot legend | 6.13.0 |
| The legend of the germline absolute allele count plot shows information only available for the tumour absolute allele count plot: calculated overall ploidy and minor allele count | 6.13.0 |
| Analysis comments (added to variants or plots) when edited on the GTAB summary become GTAB comments and vice versa. | 6.13.0 |
| An error would appear when adding a comment to a germline small variant from the variant details page | 6.13.0 |
| If a gene is entered twice in the search bar of any variant list after clearing, the gene only appears in the suggestions list the first time | 6.13.0 |
| There are minor discrepancies in the whole genome coverage values in cDSS and HTML | TBC |
| The total variant counts are discrepant in cDSS and HTML | TBC |
| Cancer Hotspots are not yet available for splice variants or Indels | TBC |
| Tooltip for QC flag column name and values in the germline small variant list is not visible | TBC |
| Clicking on an empty region of the SV chart removes all results from the corresponding variant list | TBC |
| The value for paired or split reads shows as 'Not applicable' for SVs with no SR/PR support | TBC |
| Population frequencies from the GnomAD genome studies are displayed on the variant list and variant details page, while the cancer HTML report uses the GnomAD Exome studies | TBC |
| Gene mode of action is missing in the gene track tooltip on the interactive plots available in somatic SV and CNV variant list page | TBC |
| Origin field not applicable for CNVs because the current pipeline uses Dragen's somatic CNV detection model, which does not strictly perform germline substraction of CNVs | TBC |
| Incorrect tooltip is shown for Paired reads and Supporting reads per billion in the variant details page | TBC |
| High resolution BAF plots fail to load when the duplicate tab feature of some browsers is used | TBC |
| Publication date of the NGTD file used is missing in the variant lists and detail pages of some cases (please see the latest version of the Cancer Genome Analysis guide for further details). | TBC |
| Legends of the coverage and high resolution BAF plots show information that applies only to the visualisation of older versions of the coverage and BAF plots | TBC |
| The legend of the germline BAF plot shows information that applies only to the tumour BAF plot | TBC |
| Redundant calls from different variant callers will be present in the DSS. For example, detection of ITD variants at the FLT3 locus and UBTF locus is performed using PINDEL to ensure sensitivity of variant detection. Occasionally, Manta can call FLT3 and UBTF ITD variants as duplications or insertions. If the genomic location of Manta FLT3 or UBTF ITD calls coincides with the ones called by PINDEL, the DSS will show Manta and PINDEL calls. In the HTML report, Manta calls will not be reported. | TBC |
| Impacted transcript region for genes affected by copy neutral LOH is not shown correctly in the DSS | TBC |
| Coverage plots initially display in low resolution and may show CNV calls that disappear when zooming in | TBC |
| Calculated tumour content shouldn't be displayed in the DSS when the tumour sample has a high percentage of somatic variants (>40%) with a low VAF (<6%) | TBC |
Gene mode of action annotation between NGIS Petra release, NGIS Quasar release, and DSS v6.13.0 release
Following NGIS Petra release and NGIS Quasar release, H3C3, RXRA, SOS1, YAP1, RASA1, RICTOR, RAD51, and ROCK1 genes were not be labelled in the DSS with a mode of action or flagged as being present in CGC when compared with the HTML report due to a version difference. Additionally, following NGIS Quasar release, SET remained labelled as an oncogene in the DSS. Whereas, SET mode of action is N/A in the HTML report. These gene mode of action discrepancies between the DSS and the HTML report have been fixed as of the 6.13.0 release (22/10/2025) and any cases arriving to the DSS from this point onwards will be unaffected. Please check the mode of action of these genes in the HTML report if the case arrived to the DSS between NGIS Petra release (11/06/2025) or NGIS Quasar release (27/08/2025) and DSS 6.13.0 release (22/10/2025).
Dragen Cases
All cases processed by Dragen v4 (NGIS release Orion) should have the following case disclaimer in the cDSS, however it is currently not shown. This will be fixed in a future release. "The overall ploidy for this sample is estimated to be
Tumour First Cases
Variant filtering for reported variants in tumour first cases in the cDSS may differ from that in HTMLs: in these cases, we apply both somatic and germline prioritisation algorithms to all variants with GEL internal population germline allele frequency under 2%, so all such variants will appear on the cDSS. In the HTMLs and CSV tables, all variants with either GEL internal or gnomAD population germline allele frequency over 1% and no potential effect on cancer predisposition genes (nothing in the "Interpretation as germline" field) are filtered out. We are currently working on fully harmonising the variant lists between cDSS and HTML, and this discrepancy should disappear soon.
Copy Number Variant Coverage Plots
We have identified a bug in our plot generation, where genomic sex is being used rather than reported sex. If a cases genomic sex differs from the reported sex, the "expected coverage" line across chrX would display incorrectly. For further information and an example, see the "Tumour Copy Number Variant Plots" section in Visualisations.
Cancer loci files
At the time of the ‘Nembus’ release on the 9th October, 6 new loci were added used to annotate additional upstream/downstream variant data for cancer cases. These new loci were not included in cancer DSS. These variants are still visible and reported in the correct domain in cDSS, but they are not specifically annotated as being associated with the 6 new loci, which can still be visualised in IGV or the HTML report. The bug has been fixed as of the 6.4.1 release (13/11/2024) and any cases arriving to the cDSS from this point onwards will be unaffected. If you are interested in these loci and the case arrived to the cDSS between 9/10/2024 and 13/11/2024, please check the HTML report and IGV.
| Loci | chr | start | end |
|---|---|---|---|
| TAL1_upstream | 1 | 47232226 | 47242255 |
| TLX3_upstream | 5 | 171205524 | 171265681 |
| TLX3_downstream | 5 | 171312140 | 171349100 |
| ABL1_upstream | 9 | 130708042 | 130713015 |
| CRLF2_upstream | X | 1212650 | 1217650 |
| BCL11B_enhancer | 14 | 97382000 | 98876000 |
Please report any bugs or issues with the DSS via the Genomics England Service Desk.