5.4.1 Release Notes
These release notes include new features, product limitations, and known issues for Connected Insights 5.4.1.
New Features
None
Defect Repairs
13046: Fixed an issue where CNV deletions with a copy number of 2 were incorrectly tagged as CNV Neutral. This caused affected variants to lose biological classification and actionability annotations, potentially excluding reportable deletions from filtered views.
12980: Resolved a performance issue that caused case ingestion to fail or severely degrade for cases with a high number of structural variant events.
13060: Improved case list page load times.
13320: Fixed an issue where the Results page failed to load when the key gene list contained a gene with no transcripts.
Known Issues
1298: Read order in the BAM track may change after zooming in the IGV viewer.
3723: The software will display two duplicating variants if they were called by two different pipelines, for example, a small variant caller and a structural variant caller.
3777: Users will not be able to upload NR transcripts into My Knowledge Base. CKB assertions will not be displayed for NR transcript variants.
3934: Reopening an approved report does not trigger notification of assertion update even if there are updated assertions for the case.
3943: For DRAGEN RNA pipeline, RNA BAM track in IGV Web is not enabled by default for small variants and needs to be turned on manually.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
5491: Coverage graph may not display findings if they use a different transcript rather than the one used to create the graph.
5494: In IGV Web, the SV variant track may show only one SV when multiple SVs are present in the same locus.
6199: Data upload of analysis results generated by the DRAGEN WGS Somatic v4.2 pipeline fails when the pipeline was run on ICA starting with BAM files. A workaround is to download data locally first. Alternatively, users can manually create a sample sheet and upload it into the analysis output folder in ICA before the analysis is completed. When the analysis is complete, the output will be automatically uploaded into Connected Insights.
6200: Variant filtering based on SpliceAI score and gene name may return incorrect results due to use of different transcripts.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
7336: When assertions from multiple knowledge sources are present on different transcripts of a variant, the default transcript may not be the transcript with the highest oncogenic classification.
8403: Annotations including CGC, ClinGen, OMIM, 1000 genomes, and custom annotations are not displayed or filterable for SV deletions and CNVs over 10 Mb in size. It can cause these events to be omitted when filtering by annotations. Review of genome view and Circos plots are recommended to identify these larger events (seen as a large deletion arc in the SV track or abnormal coverage in the coverage and CNV track) and also by filtering for SVs and CNVs with length over 10 Mb.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
12024: Some benign variants are not automatically marked as reviewed.
12017: Some co-occurring assertions for oncogenic variants may display for copy number gains when they are not applicable.
12015: NCT06904066 (phase I) is not ingested as since clinical trials are not yet supported for HLA genotypes.
11927: Report automation may report clinical trials for Australia when EU is specified.
11905: Report automation does not report FDA resistance assertions when FDA is specified.
11904: Once a gene threshold has been specified, and the disease is changed for a case ingested in <5.3, only new disease-specific genes will have the specified threshold applied.
11900: When report automation is re-run on cases ingested in <5.3, assertions reported may be out-of-sync with assertions displayed.
11151: In the transcript modal for RNA fusions, some transcript pairs may be annotated as inframe when at least one of the other transcripts pairs are inframe.
10828: When merging a TN DNA case with an RNA case, the DNA BAM may not display in biomarker details.
10809: Some non-PASS CNVs are not plotted in the correct color in the whole genome and biomarker details visualization.
12244: The tooltip is not showing up if the final classification is null after the conversion.
12580: Unable to download large MyKB contents from the My Knowledge Base UI (API download works correctly).
12729: Gene expression biomarker creation is not allowed without specifying a source.
12735: HRD column appears empty in the KB table on the variant detail page for BRCA1 and BRCA2.
12742: Users should not be allowed to update the selected transcript in a Completed case.
12745: Multibiomarker selection from the Variants page is not working as expected.
12759: Missing CKB assertions for TMB biomarker.
12930: "Manually added variant" tag is removed for a Virtual Variant after Disease update.
12933: Case meta data is not consistenly ordered in the Case details view.
12874: Users are blocked from navigating away from the Case details page when the case enters a processing state due to assertion updates or virtual variant processing.
12961: Biomarker ingestion fails when multiple biomarker sources target the same gene.
12929: Custom annotation check box is not working as expected for create or edit test definition form in CFG.
12994: Users are unable to clear an existing Karyotype value, and the Case screen may freeze when attempting to overwrite it with an empty value.
12976: Variant grid columns selection is reset when a Gene search is applied.
12852: Variant details visualization BAM track shows base counts different from IGV.
12818: User is logged out of application with saving a biological assertions with Pending Approval status.
12810: Oncogenic Biological classification is not considered while matching assertion for a large variants.
Revision History
00
Initial Release
Last updated
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