Known Issues
Known Issues¶
All known issues with a fix version have been resolved in the specified release.
| Issue ID | Issue Description | Fix Version |
|---|---|---|
| IPDSS-13882 | When searching for SVs by chromosome or genomic coordinates, the search functionality only takes into account one SV breakpoint instead of both breakpoints. This issue affects the results displayed in the tumour SV plot and the results returned in the variant grid. | 6.18.0 |
| IPDSS-13709 | Tooltip for the GG flag should refer to the gnomAD database | 6.18.0 |
| IPDSS-13853 | Clicking on an empty region of the SV chart removes all results from the corresponding variant list | 6.18.0 |
| IPDSS-13717 | Switching the SV and CNV plots from split screen to fullscreen view and returning to split screen view results in the plots becoming misaligned | 6.18.0 |
| PDSS-2335 | The total variant counts are discrepant in cDSS and HTML due to the cDSS displaying undomained and untiered variants | TBC |
| PDSS-1268 | Cancer Hotspots are not yet available for splice variants or Indels | TBC |
| IPDSS-13047 | 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 |
| IPDSS-13368 | Coverage plots may show CNV calls that disappear when zooming in | TBC |
| IPDSS-13091 | 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 |
| IPDSS-13969 | When clicking on the 1-2kb region shown in the variant grid for DUX4 rearrangements, the tumour SV plot zooms into the start of the region instead of showing the entire region | TBC |
| IPDSS-12620 | Searching the variant list using ensembl identifiers does not yield any results | TBC |
| IPDSS-11891 | Incorrect tooltip is shown for Paired reads and Supporting reads per billion in the variant details page | TBC |
| IPDSS-13609, IPDSS-13504, IPDSS-13610 | 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 |
| IPDSS-13963 | Search bar queries do not zoom into the region of interest in plots, they remain at the whole genome view | 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.