Known Issues¶
All known issues with a fix version have been resolved in the specified release.
| Issue | Fix Version |
|---|---|
| Chromosomal bands for DUX4 fusions is unavailable in cDSS for the "DUX4 region" and partner gene, whereas the HTML report displays the chromosomal band for the partner gene | 6.7.0 |
| The IGV link out for DUX4 fusion partner genes directs the user to the wrong coordinate in IGV | 6.7.0 |
| The Decipher gene link out for DUX4 fusion partner genes directs the user to the wrong coordinate on the gene track | 6.7.0 |
| A case disclaimer regarding ploidy for cases processed by Dragen v4 is missing from the cDSS | 6.7.0 |
| Very small gnomAD allele frequencies are being rounded to 0 and displayed as 'Not Found' | 6.7.0 |
| The variant coordinates will display incorrectly for DUX4 fusions added to the export preview | 6.7.0 |
| Cases processed by Dragen v4 are missing the ploidy case disclaimer in the cDSS | 6.7.0 |
| 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 |
| The table of alternative transcript IDs is being sorted page wise rather than table wise | TBC |
| Variants overlapping un-domained/un-tiered genes aren't "searchable" from the variant list page | 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 |
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.
Variant List Searching
We have identified a bug when searching the variant list. If a search is performed for a gene e.g., "TGFBR3" and selected from the search box dropdown, then the search bar is cleared and the same gene is searched for again i.e., "TGFBR3", the gene will not display in the search box dropdown a second time. The gene will still display in the variant list when entered into the search bar. Please see the video below illustrates the issue. For further information and an example, see the "Searching" section in Somatic Small, Germline Small or Somatic Structural and Copy Number variant list documentation.
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.