Known Issues¶
Please report any bugs or issues with the New IB via the Service Desk, as per the instructions on the feedback page.
| Issue | Affects version | Impact | Workaround |
|---|---|---|---|
| Dataset versions for some Exomiser datasets are incorrect | 4.0, 4.1, 4.2 | Users may be misled about the data foundations of their analyses, or incorrect versions of software recorded by GLHs. Exomiser software version (13.2.0) and dataset release version (2209) displayed in the product are correct N.B. Exomiser dataset versions aren't propagated downstream to CIP-API or CVA, nor the Summary of Findings, so this information is not propagated anywhere further |
Fix version not yet confirmed. Please refer to the correct versions of datasets in the Rare Disease Genome Analysis User Guide here, instead of the dataset versions for Exomiser displayed in the front end on the case summary and reporting pages. |
| Bug in exon overlap annotations means Not available is displayed in place of the overlapped exons for some CNVs | 4.2 | It may not be possible to determine which exons are overlapped by the CNV for some transcripts | Fix scheduled for v4.3. This may require users to check for exon overlap using external resources such as Ensembl. |
| A dash is displayed in place of the region name in the Tier overlay | 4.2 | It is not possible to determine the region that each Tiering event is linked to when the CNV overlaps multiple regions | Fix scheduled for 4.3. For any assistance required in determining which report event each region is linked to, GEL support can be contacted |
| CNV multi-gene overlay displays only a maximum of 100 genes. This means that for CNVs spanning more than 100 genes, genes will be missing from the table | 4.2 | It will not be possible to view the summary data for some genes | Fix scheduled for 4.3. More comprehensive information for each gene is displayed on the individual gene tab for each gene, so this tab can be used instead |
| Sometimes opening the gene overlay in the SNV grid can cause an error (The We are sorry, something went wrong page will display) This error is caused by incorrect handling of phenotypes that don't have an associated OMIM MIM number |
4.2 | It isn't possible to view the gene overlay for some genes. N.B. this error occurs only very rarely | Fix scheduled for 4.3. The same information can be viewed instead by opening the SNV details page for the variant. |
| When the gene mode of inheritance for a PanelApp panel has a comma, it isn't handled correctly by the front end (it is treated as if it were two separate modes of inheritance) | 4.2 | This can make it more difficult to read, however the expected impact on users is minor | Fix scheduled for 4.3. The gene MOI can also be viewed directly in PanelApp through the provided link-outs. If any further assistance is required, GEL support can be contacted |
Fixed issues
These issues are those that existed previously but are fixed in this version of the product.
| Issue | Affects version | Impact | Workaround |
|---|---|---|---|
| Not all genes are coloured green when they should be | 4.0, 4.1 | User confusion, as you may wonder why a Tier 1 or Tier 2 gene isn't always shown as green, when it should be. N.B. This issue will manifest when the GMS panel applied to the patient is a superpanel and there is no other panel applied to the case that contains the affected gene. |
None – fix scheduled for 4.2 We will improve gene colouring logic to ensure that all green genes are coloured appropriately, regardless of presence in superpanel and/or GMS PanelApp panels, for comprehensiveness. |
| Missing description for UPD case warning ("Uniparental disomy detected" should be visible under the header) | 4.0, 4.1 | It may be unclear what this case warning is / means. | Fix scheduled for 4.2 The details of what the header means can be found here, and if it is still unclear, GEL support can be contacted. |
| The consequence used by Exomiser is not shown in the New IB in some circumstances | 4.1 | In these circumstances, users are not provided with a full and complete record of the evidence used by Exomiser | None - fix scheduled for 4.2 The variant consequence annotated by CellBase can be seen in the variant grid, which is the most important one for analysis |
| The HGVS used by Exomiser is not shown in the new IB in some circumstances where there is no p. change annotated | 4.1 | In these circumstances, users are not provided with a full record of the evidence used by Exomiser | None - fix scheduled for 4.2 The gene, transcript IDs and coding sequence and protein changes annotated by CellBase can be seen in the variant grid and details pages, which are the most important annotations for analysis. |
| Exomiser allele frequency is sometimes displayed as the Max allele frequency in the SNV Grid and SNV Details pages | 4.1 | The Exomiser allele frequency may come from a dataset that is different from those we annotate with (we annotate with gnomAD genomes and exomes, and a GEL internal dataset). It may be unclear as to the origin of that allele frequency as the Study will display as "-". | View the allele frequency values directly in the gnomAD website, which has more up to date v4.1 datasets whilst we only annotate with exomes v2.1.1 and genomes v3.1.2 data. Fix scheduled for 4.2 |
| All HPO terms are displayed as Present HPO terms regardless of whether or not they were marked present, absent or uknown in the case | 4.0, 4.1, 4.1.1 | Not possible to determine which of the HPO terms are present and which are absent in the case and it appears to users that all HPO terms listed are present when that is not necessarily the case | The IP/IB shows only HPO terms marked as present, so this can be used as the source of truth for present HPO terms |
Abbreviations
| Abbreviation | Definition |
|---|---|
| ACGS | Association for Clinical Genomic Science |
| ACMG | American College of Medical Genetics and Genomics |
| CDS | Coding DNA Sequence |
| CNV | Copy Number Variant |
| CVA | Clinical Variant Ark |
| New IB | New Interpretation Browser |
| GEL | Genomics England |
| GMS | Genomic Medicine Service |
| GLH | Genomic Laboratory Hub |
| HGVS | Human Genome Variation Society |
| HTML | Hyper Text Markup Language |
| HSCN | Health and Social Care Network (N3) |
| IGV | Integrative Genomics Viewer |
| IP | Interpretation Portal |
| NGIS | National Genomics Informatics System |
| PID | Patient Identifiable Data |
| QC | Quality Control |
| SO | Sequence Ontology |
| SNV | Single Nucleotide Variant |
| SV | Structural Variant |
| TOMS | Test Order Management Service |
| UAT | User Acceptance Testing |
| VCF | Variant Call Format File |
| WGS | Whole Genome Sequencing |