> 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/emedgene/release-notes/workbench-and-pipeline-updates/new-in-emedgene-v100.39.0-october-16th-2025/v100.39-patches.md).
# V100.39 Patches
Patches
Date
V100.39.700
September 22, 2026
V100.39.600
June 24, 2026
V100.39.500
May 6, 2026
V100.39.300
February 26, 2026
V100.39.2
December 28, 2025
V100.39.1
November 12, 2025
### V100.39.700 Update (September 22nd, 2026)
#### Features
* Lab Tab | The gene coverage section now returns all genes, with a clear visual distinction between genes that have coverage and those that don’t and new columns for weighted mean coverage, weighted % bases >=3x and weighted % bases >=20x.
* Lab Tab | The gene coverage summary row also includes weighted mean coverage, weighted % bases >=3x and weighted % bases >=20x.
* Add New Case, Organization Settings | ICA is now rebranded to Illumina BioInsight Platform Core, and the storage configuration, PON selection and add new case flow reflect this name change.
* Curate | Made significant improvements to variant loading speeds.
#### Fixed Issues
* Add New Case | Fixed an issue where selecting a Preset Group was disabled after adding a new gene list.
* Pipeline | General infrastructure robustness improvement.
* Pipeline | Fixed an issue where variants that are annotated with snpEFF can get a wrong HGVS.
* Pipeline | Fixed a rare issue where SV annotations when two variants share a chr:pos:ref:alt might not get VEP annotation.
* Lab Tab | Fixed a rarely occurring rerun issue that results in no coverage data displayed due to a pipeline failure.
* Lab Tab | Fixed an issue where DRAGEN report for arrays could be missing data.
* Analysis Tools, Variant Page | Fixed an issue where some tags viewable from Settings weren’t viewable from tag drop-down.
* Analysis Tools, Variant Page | Visualization | Fixed a rarely occurring issue where wrong variant was displayed in visualization when scrolling through variants.
* Analysis Tools | Fixed an issue where it was possible to add a manually added variant to a finalized case.
* Analysis Tools | Fixed issue so variants tagged as Not Relevant will always remain black.
* Variant Page | Summary | Fixed an issue where the historicDB population summary card wasn’t displaying the last 10 for CNVs.
* Variant Page | Summary, Population Statistics | Fixed an issue where organization DBs containing mtDNA variants were displayed incorrectly in the summary tab and not displayed at all in the population statistics.
* Variant Page | Connected Variants | Fixed an issue where compound heterozygous variants including a CNV spanning multiple genes displayed an incorrect variant list.
* \[Hotfix - Revert ] ~~Variant Page | ACMG Automation | Fixed an issue bringing Curate ACMG annotations to analyze when some tags are empty in Curate.~~
* Curate | Fixed a rare issue where variants were exported in the wrong genome build.
* Curate | Fixed an issue where sometimes the NCBI ID of a gene could not be found.
* Report | Fixed an issue where download button for ODT report template was not visible (although download was available).
* Report/Export | Fixed a rarely occurring issue where report/export failed for variants with no ACMG tags.
* Report/Export | Fixed multiple issues related to gnomAD fields:
* Fix for SNVs where MID and AMI where not part of calculation of max fields export.
* Changed rounding to including 7 digits after decimal.
* Added ‘GnomAD\_sv\_N\_HOMALT’, ‘GnomAD\_sv\_Max\_AF’, ‘GnomAD\_sv\_Max\_AF\_pop’, ‘GnomAD\_sv\_max\_AC’, ‘GnomAD\_sv\_max\_AN’ fields for CNVs.
* Added GnomAD\_All\_Hom, GnomAD\_All\_HomHemi, GnomAD\_All\_Hemi, GnomAD\_Max\_AF\_pop fields for SNVs.
* Organization Settings | Fixed an issue where when editing Preset Filters after sorting, save is inactivated.
### V100.39.600 Update (June 24th, 2026)
* General | Fixed an issue with session time out on V100.39, where users were redirected to Cases Page and not the case they were working on when performing a refresh.
* Candidates | Evidence | Fixed an issue with variant tagging.
* Analysis Tools | Manually Added Variants | Fixed an intermittent issue where interpretation text can’t be edited.
* Variant Page | Fixed an issue where related cases display could be displaying data for a previous variant when moving quickly between variants.
* Variant Page | Evidence | When writing notes in the ACMG component, using the arrow key will move in the text as expected and not between variants.
* Versions Tab | Fixed an intermittent failure to display all input data in a case.
* Report/export | Fixed a rarely occurring issue where export of SNVs is failing due to missing SpliceAI10K data for ACMG calculation.
* Propagations from 38.4.200
### V100.39.500 Update (May 6th, 2026)
* Add New Case | Fixed a rarely occurring issue where DRAGEN 4.4 targeted.json files cannot be accessioned.
* Add New Case | Rarely occurring issue where DRAGEN array json files cannot be accessioned.
* Pipeline | Fixed intermittent case failures for organizations using ICA Runner.
* Variant Page | Summary | Fixed an issue where patient phenotypes were also shown in the matching disease phenotypes box.
* Variant Page | Visualization | Improved visualization performance when deletion/duplication distinguishing patterns are displayed for clinical significance tracks.
* Variant Page | Visualization | Improved visualization performance of SV BND track.
* Variant Page | Evidence | Added warning when ACMG tags from Curate (occurs sometimes from V38 variants) cannot be applied due to versioning issues.
* Variant Page | Evidence | Fixed an issue where PP5 exclusion in organization setting isn't applied to score, only to overall ACMG pathogenicity calculation.
* Curate | Fixed an issue where duplicate variants may appear if importing a variant from a case on a previous VEP version.
* Propagations from 38.4.100
### Hotfix (March 1st, 2026)
* Export/Report | Fix an intermittent bug causing cases to fail on export/report.
### V100.39.300 Update (February 26th, 2026)
* Variant Page | Evidence | Fixed an issue in ACMG automation for SNVs so that BP4 excludes variants that are high severity.
* Case Interpretation | Fixed an issue where newly tagged variants aren’t loaded without a refresh.
* Integrations | Fixed a bug where webhooks weren’t triggered for cases with Issue Reported and Reanalysis statuses.
* Propagations from 38.4.0
### Hotfix (January 27th, 2026)
* Pipeline | Fixed a rarely occurring issue where cases that were interrupted in the normalization step can sometimes have the wrong [variant merging logic](https://help.emg.illumina.com/emedgene-analyze-manual/tertiary-analysis-pipeline/how-does-emedgene-analyze-merge-variants-from-different-sources).
### Hotfix (January 21st, 2026)
* Propagations from V38 Jan 21st 2026 hotfix.
### Hotfix (January 11th, 2026)
* Pipeline | Fixed pipeline case failures due to "customized\_data\_float" error.
* Lab Tab | Fixed a rarely occurring issue where gene coverage data isn’t loading.
* Variant Page | Visualization | Turned off patterns for distinguishing between deletions and duplications by default, as this feature is causing severe performance issues for some users. It can be turned on via a support request and we are working on a performance fix.
* Curate | Fixed the error message for partially successful batch uploads.
* Curate | Fixed an issue causing export APIs to fail. Emdg-10796
* Propagations from V38 hotfix on Dec 31st, 2025.
### V100.39.2 Update (December 28th, 2025)
#### Features
* Analysis Tools | Filters | Added a description tooltip for every filter.
#### Fixed Issues
* \[Hotfix November 24, 2025] Add New Case | Fixed flow for accessioning carrier analysis on parental samples in a trio.
* Pipeline | Fixed a rarely occurring V100.39 annotation issue for CNVs with the same chr:pos:ref:alt but different SV length.
* Pipeline | Fixed a rarely occurring bug that resulted in negative variant length for array cases.
* Lab Tab | Improved error messages on insufficient gene coverage query. Error message will clearly indicate whether no coverage file was available for the case or coverage is not available for a specific gene.
* Lab Tab | Gene coverage will be generated even when gene list includes a gene with no coding genomic regions, although no coverage can be generated for genes with no start position in the Emedgene knowledge graph.
* \[Hotfix November 24, 2025] Variant Page | Summary, Evidence | Fixed an issue where interpretation text and ACMG evidence were not editable.
* Variant Page | Summary, Quality | Allele frequency rounded to 4 decimal points as in analysis tools. Export data is not rounded at all.
* Variant Page | Quality | Fixed a rounding error that could cause a slight error in the allele bias pie chart.
* Variant Page, Analysis Tools | Visualization | Fixed an issue where the Curate track did not display pathogenicity colors.
* Variant Page | Related cases | Fixed an issue that resulted in duplicate entries in the related cases component.
* Variant Page | Evidence | Fixed an issue where ACMG component was erroneously marking all tags as curated, even when only a few were activated in Curate.
* Variant Page | Evidence | Fixed a bug in the BP2 calculation that caused rare errors.
* Variant Page | Evidence | Fixed an issue where multi tagging functionality causes variant interpretation template to fail to generate.
* Analysis Tools | Fixed an issue occurring for organizations with variant multi-tag turned on that causes variants tagged by AI to appear as tagged by user.
* Analysis Tools | Fixed an issue where CADD score filter was hidden on the UI.
* Analysis Tools | Fixed an issue on the new combo page where a pagination warning was missing.
* Case Interpretation | When clicking close on Case Interpretation box without saving, text will not be saved as expected.
### V100.39.1 Update (November 12th, 2025)
#### Features
* Variant Page, Analysis Tools | Improvements to follow ISCN nomenclature. Examples:
* arr \[GRCh38] Xq26.2-q26.3(133042525\_136149357)x2
* seq \[GRCh37] 6p11.2(57801514\_57827028)x3.
* Variant Page | Visualization | Deletions and duplications are now visually distinct in IGV. While colors in our embedded IGV are reserved for pathogenicity, users can now distinguish between deletions and duplications using patterns. Dashed variants are deletions. Pathogenicity colors are preserved.
* Variant Page | Visualization | BND from the DRAGEN SV caller can now be displayed in IGV (proband only) as a track called ‘BND’.
* Case Interpretation | Changed order of default displayed variants to prioritize customer tags before system tags. Customer tags can be sorted via a support request.
#### Fixed Issues
* Pipeline | Improved multiple pipeline infrastructure issues to reduce case processing time.
* Pipeline | Fixed multiple issues causing case failures including when SMN targeted caller outputs null values.
* Pipeline | Fixed an issue in transcript prioritization logic for gene lists that contain genes with deprecated symbols (using NCBIs).
* Cases Page | Fixed an issue where non-admins could move cases in ‘Trash Bin’ status to other statuses.
* Lab Tab | Improved insufficient regions error messages when no coverage information is available for the case/gene.
* Variant Page | Fixed a rare issue where variant interpretation template was not reloaded when moving between variants.
* Variant Page | Variant Interpretation Template (VIT) |Load from related cases or Curate – fixed an occasional issue where templates loaded were from the previous variant viewed.
* Variant Page | Variant Interpretation Template | Removed auto-load of VIT for CNVs, as the selection was the first annotated CNV rather than an exact match.
* Variant Page, Curate | Variant Interpretation Template now supports the special characters ‘&’ and ‘<>’ which were causing some report generation to fail.
* Curate | Analyze and Curate now share the same variant validation.
* Curate | Export now includes transcript.
* \[Hotfix Oct 30] Curate | Fixed a role issue preventing access to Curate.
* Curate | Fixed a role issue preventing deletion from UI/API for some users.
* Report | Report PDF download is visible again.
* Report | Add an inheritance field to JSON export/report that supports multiple inheritance modes for a disease, as seen on the UI.
* Organization Settings | Fixed an issue editing Preset Filters that contain splice scores. The presets showed an error in the UI, while being saved correctly in the DB.
* Organization Settings | Time Zone added for Newfoundland (GMT-2:30).
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