| Patches | Date |
|---|---|
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
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:
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.
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:
Customers on ILMN clouds can now select their preferred URLs. It takes 1-15 minutes for URL changes to go live.
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.
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.
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.
Proband ID field is limited to 13 characters.
Changing a preferred URL or a platform version takes 1-15 minutes to go live.
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.
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.
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.
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
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.
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.
| Patches | Date |
|---|
Analysis Tools | Preset filters | Fixed an issue introduced with v33.2 that caused some LOF preset filters to not return variants. Customers impacted by this issue were notified individually and resolution offered for potentially affected cases.
Propagation of fixes included in . See release notes for detail.
Add New Case | NovaseqX added to selectable sequencers.
Add New Case | Fixed a batch uploader issue where sex column was used correctly but also imported in additional data
Pipeline | Fixed an issue where cases running with DRAGEN 4.2 on HG19 fail the pipeline
Pipeline | Added support for multi-allelic CNVs when customers start from joint gVCF
Pipeline | Added support for DRAGEN VCFs where hardware is unknown.
Pipeline | Fixed a bug that caused discordant AI results between a first and second analysis due to model selection.
Pipeline | Fixed an issue causing some reanalysis cases to fail due to insufficient backward compatibility with previous values. This fix will improve pipeline robustness.
Cases Page | A search on this page will only search for EMG ID, sample names, or any string in the test data. This fix will improve performance.
Analysis Tools | Fixed variant count issue for compound heterozygous filters caused by using a single source for what is essentially a two-step process. Only count displayed was incorrect.
Analysis Tools | Fixed preset filter issue where presets were returning more results than expected due to ‘-‘ in the gene name in some preset filters. No data was missed.
Variant Page | Fixed incorrect gnomAD link after the gnomAD v4 release.
Organization Settings | Fixed an issue causing available URLs to become unviewable when changing the platform version from V34 to V33.
Performance: Additional updates to increase performance through infrastructure modifications.
Add New Case | Fixed issue where new ethnicities added in v32 were not supported for reanalysis in subsequent versions.
Batch Upload | Fixed issue for singleton cases uploaded with batch uploader that resulted in inability to edit cases after creation.
Batch Upload | Fixed issue causing Not Authenticated error for customers with more than 100 BSSH projects.
Batch Upload | Improved backward compatibility for Gender changed to Sex field.
Pipeline | Improved error logging for DRAGEN for easier troubleshooting.
Pipeline | Fixed issue where ingesting DRAGEN ExpansionHunter and SV caller VCFs from DRAGEN 4.2 failed cases due to unexpected header.
Pipeline | SMN Caller | Fixed multiple issues causing case failures from FASTQ & BAM.
Pipeline | SMN Caller | Fixed issue for GRCh37 & SMN caller where relatedness isn’t calculated due to Peddy failure.
Pipeline | Enable flow where in a trio only the Proband has Ploidy outputs and parents don’t.
Pipeline | Don’t fail cases where no samples are provided but ignore samples isn’t set.
AI | Include full gene list in Phenomeld for virtual panels, irrespective of phenotypic match.
Cases Page | Search from the cases page is now limited to case ID, sample name and test data fields to improve performance.
Lab Page | Fixed issue of no coverage statistics for cases with missing samples. Coverage appropriately generated for the samples submitted with the case.
Lab Page | Fixed missing average coverage affecting some pipelines.
Analysis Tools | Manually Added Variants | Fixed an issue where STR manually added variants can’t be tagged or reported.
Analysis Tools | Export | Resolved issue in export of some presets and filters due to incomplete customer facing role.
Variant Page | Fixed issue where proband coverage copied to parents for customers starting from joint gVCF.
Variant Page | Fixed all broken gnomAD links after the gnomAD v4 release.
Variant Page | Updated Decipher link after link structure change.
Curate | Fixed issue where selecting a disease associated with a gene for a variant appears to automatically apply it to all variants in that gene in the UI, while data is correctly applied in the backend.
Curate | Enable customers to login to Curate when signed into a different organization on Analyze.
Reanalysis | Fixed backward compatibility issue preventing variants in cases originally analyzed on and before V27.0 to be pushed into a report.
Settings | Fixed issue where S3 credentials couldn’t be generated for long domain names. Character limit is eliminated.
Settings | Fixed issue in kit BED validation for non-canonical chromosomes.
Infrastructure: Multiple improvements of resource allocations to increase robustness and performance.
Feb 18th, 2024
Jan 14th, 2024
V33.3 | June 19th, 2024 |
V33.2 | Feb 18th, 2024 |
V33.1 | Jan 14th, 2024 |
