New in Emedgene V33.0 (September 6th 2023)
Release Highlights
Platform: Organization Settings - New self-serve features available to customers
Emedgene customers can select their preferred version out of any of the past 5 releases. Customers on v29.0 should select an upgrade path at this time.
The software release includes the following components, which can be selected independently:
Platform 33
Pipeline 33
Pipeline: Support for DRAGEN 4.2 Release
All supported DRAGEN callers can now be run with DRAGEN 4.2, for customers starting from FASTQ or VCF.
DRAGEN 4.2 includes enhanced multigenome (graph) reference and Machine Learning (ML) models that improve small variant calling accuracy. Emedgene supports the new graph and ML while maintaining backward compatibility for customers on previous DRAGEN versions.
Improved CNV calling accuracy achieved through joint CNV/SV detection is available for customers starting from VCF (FASTQ support coming in 34.0). In order to minimize duplication, SV variants that are not merged with CNVs are removed from the CNV_SV VCF, and are ingested separately via the SV VCF.
Supported DRAGEN 4.2 outputs in 33.0:
Limitations
Discrepancies between DRAGEN callers supported from VCF and FASTQ, where some are only supported from FASTQ and some from VCF, will be addressed in Emedgene 34.0 (Q4 23).
Not all DRAGEN 4.2 callers are supported.
High sensitivity caller will be supported in 34.0.
Additional targeted callers will be supported in mid-2024 with the release of DRAGEN 4.3.
Platform: Organization Settings. New self-serve features available to customers
A new Organization Settings page will enable customers to progressively control their organization settings without requesting ILMN support. To access the page: Click on the user initials or profile picture > Settings > Organization Settings.
In 33.0 we’ve added the following self-serve capabilities:
i. Select your own URLs from the available URLs in your domain
Customers on ILMN clouds can now select their preferred URLs. It takes 1-15 minutes for URL changes to go live.
ii. Select a platform version for your organization from officially released versions
This feature is available for both Emedgene and Illumina cloud customers. It takes 1-15 minutes for changes to go live.
Note:
This is available only on 33.0 and up. If you select a previous version the feature will disappear from your organization settings, and you will need to contact support to change platform versions.
Note that this will not change your pipeline version, only the software platform. To change a pipeline version please contact techsupport@illumina.com.
iii. Set your own case identifier to display on the case and variant page
Emedgene by default displays the EMGXXXXXXXXX case identifier. Customers can now choose to display the proband ID instead. The proband ID has a visible 13-character limitation, and the remaining characters will be visible on hover.
Candidate page displaying a proband ID:
Variant page displaying a proband ID:
Each of these new features requires a unique role. Contact your support team or techsupport@illumina.com to add these roles to your organization.
IV. Improved BED validation errors
When attaching a BED file to a kit in the Management tab, the system will generate clear and actionable error messages for any exceptions that may occur.
Limitations
Proband ID field is limited to 13 characters.
Changing a preferred URL or a platform version takes 1-15 minutes to go live.
Platform: Workflow enhancements
Support for ACMG Secondary Findings v3.2
The ACMG secondary findings v3.2 gene list has been updated in both the XAI and the filters.
For the XAI, when a user selects to receive secondary findings, we will apply the v3.2 gene list (requires pipeline 33).
The All ACMG genes filter has also been updated to this new list of 81 genes.
Edit a case label after case creation from the UI
Case labels can now be edited after case creation through the UI in the Cases table, in addition to the existing capability via the API. This is role-based, please contact your support team or techsupport@illumina.com to add these to your organization.
New export capabilities
Added CNV annotations to the mini VCF – Emedgene produces a lightly annotated VCF that is available for customers to download for every case. In this version the following CNV annotations were added to this file: decipher_sv, dgv_sv, GnomAD_SV, clinvar_benign_sv, clinvar_uncertain_sv, clinvar_pathogenic_sv, clingen_benign, clingen_uncertain, clingen_pathogenic and DDD (requires pipeline 33).
Export/report on the gene list associated with the case HPO terms. This gene list is produced with the Phenomeld phenotypic match algorithm. The capability was added in 32.0 but now customers can include the gene list in their report.
Limitations
Analysis Tools | Sort by phenomatch score and tags is not yet available
Curate | Some HGVS p-values not accepted yet, discrepancy between Curate and Analyze
Fixed issues
ClinVar sanity check fails case if there are no known variants in ChrY with wrong message. Cases will still fail but with the correct error message.
Variant Page | Fixed an issue where a manually added transcript would display twice.
Analysis Table | Filters | Polymorphism Filters | Fixed an issue where a filter was mislabeled Het or Het Count instead of Allele Count. No variants were missed due to this mislabeling, as the Allele Count filter is more inclusive.
Analysis Table | Preset Filters | Fixed bug where updated gene lists were resulting in a case incompatible error message.
Analysis Table | Fixed an issue where manually added variants were sorted incorrectly causing them to ‘disappear’ from the UI.
Add New Case, Lab Tab, Cases Sidecar | Gender changed to Sex.
Add New Case | Fixed a bug where users couldn’t edit cases that failed due to bad inputs.
Lab Tab | Fixed an issue where % mapped reads was always 0.
Export/Report | Fixed an issue where synonymous variants were exported with ‘%3D’ instead of ‘=’.
Notification | Fixed a bug where case delivery email notifications included organization parameters based on the user creating a case rather than the organization.
Known issues
Organization Settings | Set mandatory fields - does not work from the UI. Please contact support if you’d like to configure these fields for your account.
Gene Lists | Very large gene lists (>6700 genes) may return a false error message during creation, despite being successfully created.
Visualization is not supported for users storing VCF and CRAM on ICA V1 and BSSH. Only VCF and BAM are supported.
Variant Page | Visualization | Chromosome ideogram visualization is missing for mtDNA variants in VCF case run on GRCh37.
Variant Page | Visualization | Simple/Advanced selectors will not work for locally uploaded BAM files.
Variant Page | Visualization | Zoom out of BigWig/TTS displays mean data.
Variant Page | ACMG SNV Score | Incorrect score for mtDNA variants, although classifier behaves as expected.
Analysis Tools | Preset Filters | Preset containing a gene list ID will display filtered data when an organization has configured a base gene list filter.
Analysis Tools | ‘Last’ button on pagination does not work.
Candidates Page | Compound het SNV-CNV variants will not display the automated CNV classification. Workaround – view variants from analysis table.
Candidates | When clicking on See all candidates link, variant filters are inactivated. Workaround: Reset filters to default.
Candidates | SV Insertions information partially displayed. Work around: View from a preset filter.
Network | GRCh37<-->GRCh38 Liftover not available for older components of Network infrastructure, as a result, [Variant Page | Clinical Significance | Networks Classified] may remain erroneously empty while [Variant page | Related cases section] shows relevant information. Same gap for manually classified variants.
Network | Zygosity, even when set in extended sharing, may remain blank for older cases. Once you click on a case missing zygosity it will be saved for all future views.
Manually Added Variants | STRs -When manually adding an STR variant it cannot be tagged or reported.
Manually Added Variants | Users without the role can add variants but not save them. Button should be disabled.
Cases Page | Contact support link for failed cases does not work. Please use techsupport@illumina.com.
ILMN Clouds | Help Center | Some links may not work. Work around: Paste the title into the help center search.
Add New Case | Batch Upload | Analysis Type field is not available with this version of Batch Upload, and it cannot be used to initiate the new Carrier workflow.
Add New Case | Create a case from case creation summary does not work, please click on top Add New Case button from cases page.
Reanalysis | If HPO terms were updated between analyses, the reanalysis will not automatically map previous HPO terms to new ones.
Lab Tab | Reanalyzed cases will show up with duplicated insufficient gene regions. Fix planned for 34.0 .
Lab Tab, Sidecar | Pedigree | In very large pedigrees some family members can’t be clicked to view quality.
Lab Tab | STR repeats number for parents does not exist, proband values displayed.
Curate | ILMN cloud users need to be logged in to the organization from which they are trying to access Curate.
API | Assign users to case fails with no error if faulty emails used.
API | Creation of large gene lists may return an error (due to timeout) despite the creation of the gene list.
Report/Export | For variants tagged as ‘Most Likely’ order is not preserved when pushing to the report. Work around – use another tag, e.g. ‘In Report’.
Activity | Editing interpretation paragraph yields an erroneous activity labeled reanalysis.
Dashboard | Diagnostic Yield includes Uncertain as Resolved.
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