> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/connected-insights/resources-and-references/rar-release-notes/5.5-release-notes/5.5.1-release-notes.md).

# 5.5.1 Release Notes

These release notes detail the defect repairs and known issues in Connected Insights 5.5.1. Changes are described relative to Connected Insights 5.5.

## New Features

* None

## Defect Repairs

* Fixed an issue where a newly created workgroup did not appear in Connected Insights. Only domains whose URL does not match the domain name were affected. (15117)

## Known Issues

The following issues are known in this release. Where a workaround is available, it is noted with the issue.

### Variant Review and Interpretation

* A large copy-number variant spanning many genes can match gene-level "Oncogenic Variant" therapeutic assertions for genes in the affected region, even when the case has no oncogenic biological assertion for those genes. This can surface therapies whose evidence is for gain of function (mutation or amplification) on a case that has a copy-number loss. Review therapeutic assertions matched to large copy-number variants before reporting. (12810)
* The Transcript Position shown in the variant grid may not match the value selected on the transcript selection page. (14384)
* Marking a structural-variant (non-translocation) variant as an artifact does not also mark other variants in the case that overlap it by 95% or more (reciprocal overlap). (14894)
* For cases ingested before 5.3, co-occurring assertions that include more than one signature (genome-wide) biomarker are not returned in association search. (14884)
* CNV calls from a single tumor-normal VCF can carry inconsistent origin labels (some "predicted germline", others "suspected somatic") for WGS Solid Tumor-Normal analyses. (10639)
* For a structural-variant deletion, the variant grid and the exported variant TSV can show a simplified position/reference/alternate allele (for example, an `<DEL>` alternate allele) instead of the explicit sequence from the source VCF. The Variant Details page is not affected and always shows the correct values. (14448)

### Visualization

* The base counts shown in the variant details read-alignment view can differ from those shown in IGV at a variant position. (12852)

### Knowledge Base and Assertions

* Clinical trials from countries outside those selected in report automation configuration may still appear on the report (for example, Australia when only European countries are selected). (11927)
* MSI multi-biomarker clinical trials from CKB may not be fully available in Connected Insights. (12015)
* Some CKB therapeutic assertions for the TMB biomarker are not available in Connected Insights. (12759)
* On a signature biomarker's Variant Details page, changing the status filter to a status different from the biomarker's own (for example, HRD-positive) can hide matching CKB clinical trials, including trials with an Unknown recruitment status and trials whose indications come from the CKB Clinical Trials Database. (14155, 14156)

### Configuration

* Workflow/pipeline configuration YAML validation does not catch every invalid value (for example, an unsupported placeholder token, or a field nested under the wrong section); an invalid configuration can be accepted without an error. (9856)
* When a saved variant filter includes a criterion that is not compatible with the case being viewed (for example, a sample metric or VCF INFO attribute not present in that case), the incompatible criterion is silently dropped instead of showing an error. (13233)

## Product Limitations

The following limitations apply to this release.

### Variant Review and Interpretation

* Uploading a preferred transcript list does not verify that each transcript belongs to the gene it is associated with. (5133)
* The SpliceAI score is computed per transcript but is shown and applied at the gene level; variants with multiple transcripts may not reflect the score for the transcript you are reviewing. (6200)
* OncoKB and CKB may choose different default transcripts for the same variant, so the transcript shown can differ between knowledge-base sources. (7336)
* Selecting "None" in a Biological or Actionability filter may not exclude variants the way other filter values do. (9926)
* For cases ingested in 4.0, 5.0, and 5.1, numeric quick-filter fields (for example, Tumor VAF or Read Depth) do not offer dropdown suggestions, and selecting a suggested example such as "< 0.5 Tumor VAF" returns an error. (12023)
* A fusion without a Nirvana "inframe" annotation can be shown with an Inframe unidirectional gene fusion consequence. (11151)

### Knowledge Base and Assertions

* Genome equivalence (matching the same assertion across GRCh37 and GRCh38) is not supported for nucleotide-level assertions. (3451)
* COSMIC frequency and occurrence data can be inconsistent for some variants across the variant grid and variant details. (6584)
* Some CKB clinical trials for CD274-positive disease are not available in Connected Insights. (12771)
* Some annotation transcript IDs are outdated and their transcript links do not resolve at NCBI. (14724)
* When a knowledge base's classification for a variant is inferred from a similar variant or from the variant's position in a hotspot, rather than curated for that specific variant, Connected Insights does not match it to the variant. For example, OncoKB reports BRCA1 R71M as Likely Oncogenic on the basis of BRCA1 R71G, so no OncoKB biological classification or associated findings are shown for R71M in Connected Insights. This is intentional: current oncogenicity guidelines do not treat variant similarity or hotspot location as sufficient evidence on their own. See [Biological Classification Assertions](/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-biological-classification-assertions.md) in the user guide. (13076)

### Visualization

* For some genes such as ESR1, the coverage plot may use a different transcript than the one displayed for the variant. (5491)
* In the IGV viewer, read order in the BAM track can change after zooming, and the SV track can show only one SV when several are present at the same locus. (1298, 5494)

### Reporting

* Reopening an approved report does not notify reviewers that associated assertions were updated. (3934)
* Retrieving a report can fail if the report service has already initialized the case-report record under certain timing conditions. (5263)
* Rerunning report automation without updating assertions can leave the assertions added to the report out of sync with the assertions shown in variant detail, for a case ingested from a previous release. (11900)

### API and Data

* The structural variant caller can also call insertion, deletion, or delins events that the small variant caller has already reported. Those overlapping calls appear as duplicate variants in the Variants page. Opening variant details or visualization for either copy can display the other copy instead of the one you selected. (3723)
* After the Ontology NV 29 update, some genes and transcripts are not returned because of a change in feature-type classification. (3777)

## **Revision History**

| Version | Description of Change |
| ------- | --------------------- |
| 00      | Initial Release       |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/connected-insights/resources-and-references/rar-release-notes/5.5-release-notes/5.5.1-release-notes.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.