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 |
|---|---|---|---|
| Not all genes are coloured green when they should be | 4.0.0, 4.1.0 | 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 4.2.0 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. |
| Dataset versions for some Exomiser datasets are incorrect | 4.0.0, 4.1.0 | 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 SDummary 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. |
| Missing description for UPD case warning ("Uniparental disomy detected that segregates with disease." should be visible under the header) | 4.0.0, 4.1.0 | It may be unclear what this case warning is / means. | Fix scheduled for 4.2.0 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 | 4.1.0 | In these circumstances, users are not provided with a full and complete record of the evidence used by Exomiser | None - fix scheduled for 4.2.0 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 | 4.1.0 | In these circumstances, users are not provided with a full record of the evidence used by Exomiser | None - fix scheduled for 4.2.0 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 | 4.1.0 | 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 4.2.0 |
Fixed issues
These issues are those that existed previously but are fixed in this version of the product.
| Issue | Affects version | Impact | Workaround |
|---|---|---|---|
| When the clinical indication is a long line of text, it overlaps into the penetrance field on the case summary page | 4.0.0 | Cosmetic. Minor impact as most of the text is still visible. | None – fix scheduled for 4.1 |
| Duplicated tiering results in tiering overlay | 4.0.0 | Cosmetic (minor impact) and user confusion, as you may wonder why the tiering result and metadata is repeated. N.B. This issue will only manifest when the tiering result is corresponds to a known pathogenic variant prioritised by KPVP |
None – fix scheduled for 4.1 We will provide the source of the tiering event as part of the tiering results, so you can see whether a variant was tiered via KPVP ClinVar, KPVP CVA or standard tiering rules, for transparency. |
| Not all diseases associated with an OMIM gene are displayed | 4.0.0 | User misinterpretation (and at extreme) risk of false negatives, as not all OMIM diseases associated with a gene are shown in the New IB, which may lead you to wrongly assume that a gene is not known to be disease causing when it is. N.B. This issue only affects genes that have >1 OMIM gene ID. |
Review OMIM gene-disease associations separately via the OMIM link provided, for safety. Fix scheduled for 4.1 / 4.2 |
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 |