For customers validating v34 pipeline, here is a list of updates vs v33.1
Annotations | Add PrimateAI-3D annotation
Annotations | Add gnomAD v4 for SNVs
Variant Data | Make REVEL score available for filtering and export
Variant Data | Make DRAGEN VCF FILTER field available for filtering
Case Quality | Update fail & skip logic on case quality and push case quality data to Lab Tab
Case Quality | Add contamination results from Peddy
DRAGEN 4.2 | For customers using the Emedgene DRAGEN pipeline, no post-processing of SV and STR VCFs to add headers, as these are included starting in DRAGEN 4.2.
Emedgene supports case ingestion from VCF for customer variant callers, as defined in customer’s implementation plans. Two new customer callers were added in this version.
Fixed Issue | Add New Case | Check that BSSH files are fully uploaded before initiating case.
Fixed Issue | Don’t fail a case if non-mandatory files are not present for some samples.
Fixed Issue | Export | MiniVCF | VCF format field fixes for broader compatibility with downstream tools
Fixed Issue | Export | MiniVCF excel file creation will no longer fail for some field types
Pipeline version naming changed to match workbench version.
Annotation | Ensembl Variant Effect Predictor (VEP) updated to version 108
Refseq transcripts updated to version 110
The following effect modifications are updated in Filters > Severity > Simple mode
New effect types: splice_donor_5th_base_variant, splice_donor_region_variant, splice_polypyrimidine_tract_variant, start_lost, start_retained_variant
Modified effect types:
nc_transcript_variant ==> non_coding_transcript_variant
nmd_transcript_variant ==> NMD_transcript_variant
non_coding_exon_variant ==> non_coding_transcript_exon_variant
High severity CNV duplication calculation was expanded to include splice_polypyrimidine_tract_variant_, coding_sequence_variant & intron_variant&_feature_elongation in the severity calculation
Added support for DRAGEN Expansion Hunter's latest default catalog of 60 pathogenic STR loci (including 30 from gnomAD).
Added support for DRAGEN 4.0 for VCF cases (with disabled Machine Learning pipeline).
Labs running small panels can define gene list threshold below which case will deliver even without AI Shortlist results.
AI Shortlist | In a previous version, the algorithm for defining compound heterozygous variants was broken for pedigrees with additional samples. There is now support for compound heterozygous variants in any pedigree in the Autosomal Recessive - Compound Heterozygotes Inheritance Filter and Auto Analysis User Filter.
ACMG Automation | SNVs | Automatic PM5 ACMG tag calculation for SNVs is now more precise.
Annotation | REVEL | Updated REVEL scores with GRCh38 positions.
Annotation | mtDNA | APOGEE and MitoTIP mtDNA variant missense prediction scores are displayed again.
Annotation | ClinGen | Consistent annotation for CNVs classified as Uncertain by ClinGen in GRCh38 cases.
Variant Page | Format of dbSNP link is fixed.
Population Statistics | Fixed the issue with CNV population data being displayed incorrectly in some cases.
User access policy allows organization to select whether invited Illumina support teams will have access to case data and meta data.
New ordering role with access only to create a case on Emedgene.
Visualization | Fixed bug of visualization failing when a large pedigree contains members with and without samples.
Visualization | A display issue that affected some CNV/SV variants has been fixed.
Variant Page | Related Cases | CNV overlap calculation logic has been updated to comply with Curate. The overlap percent is calculated by dividing the number of common base pairs between variants from different cases by the size of the variant under investigation
Population Statistics | Fixed the issue with CNV population data being displayed incorrectly in some cases.
If case is resolved and case status is changed, case resolution will not be updated
Feature | New XAI for CNVs and compound heterozygous SNV-CNV variants
Feature | New and more accurate phenotypic match model, Phenomeld
Feature | Support for DRAGEN 4.0 with ML for customers running their own DRAGEN and through Emedgene
Feature | Lab Page | Gene Coverage - Region coverage statistics will now be calculated based on the case’s kit associated BED file
Feature | Default BED files for coding regions, clinical regions (used for exome) and genomes were updated with latest RefSeq Curated and Gencode versions.
Feature | Re-including Polyphen annotation, and update to consider most severe value
Feature | Support for DRAGEN Force Genotyping caller
Bug Fix | Quality metrics for duplications when CN > 3
Feature | ACMG SNV | Add note
Feature | Add report service activity in dashboard
Feature | Add template name change activity in dashboard
Feature | Add template upload activity in dashboard
Feature | Import Gene Interpretation from Curate
Feature | Enable kit management in organization settings
Feature | New Phenomeld filter added
Feature | Presets | Gene list | Search for gene list name
Feature | Var page | Add Genomenon linkout to clinical significance
Feature | Display varcaller in varpage
Feature | Varpage | Enrich related cases
Feature | Gene list | add NCBI ID to genes in gene list in database
Feature | Validation of variant retrieval. When system is degraded this will alert users not to work on cases with incomplete variant data.
Enhancement | Visualization - add tracks order
Enhancement | Visualization | Change default locus zoom for BigWig
Enhancement | Add more ethnicities
Bug Fix | Display chr number for finalized cases in finalize tab
Bug Fix | Add new case | Reactivate batch mode using HPO IDs
Support for interpreting SV insertions, including compound heterozygous
STR enhancements - new pathogenicity filter, allele frequency added to visualization
New visualization tracks for ClinVar, ClinVar SV and BigWig
Emedgene Curate supports CNVs
Selectable overlap in related cases
Export from Analyze to Curate
Workflow improvements
Gene-related disease card improvement
Edit interpretation summary
Variant page sidecar redesign
Analysis table enhancement - when variant has conflicting classifications it will be displayed in black
DRAGEN QC metrics available for download on lab page
Input sample file errors exposed in the cases page
Support for ACMG 78 genes in filter
Admins can add tags in management page
Header design change to match Illumina software
Added organization setting activity log, viewable from dashboard page on all activity including by ILMN support teams on the backend
Enable lossless compression on PDF reports (a support request)
API | Ability to get detailed version information via API calls
Analysis Tools | Preset Filters | Apply gene list on the fly - validate gene symbols with NCBI ID
mtDNA visualization on GRCh37 bug fixes
Lab Page | Warning when mtDNA were called on wrong reference and no data is presented
Curate | SNV variants include alt validation
Curate | Support Indels and mtDNA
Var Page | Visualization | Instability issues fixed
Var Page | Remove related disease for genes of unknown significance
Var Page | Fix broken OMIM links for genes associated with multiple diseases
Var Page | STR | Allow selection of existing interpretation paragraph
Analysis Tools | Fix zygosity other family members
Analyze | Export to Curate | Fix disease export field
Support for Dragen 3.10 (support for Graph coming in 5.30)
Support for SV insertions called from Manta
Compound heterozygous filter supports SVs (in addition to CNV/SNV/indel)
Compound heterozygous feature for duos (single parent and proband)
Annotate cases with Emedgene Curate data
Support for DRAGEN repeats with ExpansionHunter. For customers using their own pipeline, custom header needs to be added to file.
Added STR annotation engine for 1K Genomes and gnomAD
Support for DRAGEN SV caller. For customers using their own pipeline, custom header needs to be added to file.
Retrieve and annotate with variant interpretation from Emedgene Curate
Support for ingesting files from ICA2 storage
Improvement of de novo variant quality from DRAGEN
Enhancement | Update revel generation script, change revel file path to fix GRCh38 bugs in revel data
Support for interpreting STRs - annotation with 1K genomes and gnomAD, custom visualization, related cases
Support for interpreting SV deletions and duplications. ACMG automated classification tool applies to SV del/dups.
Emedgene Curate supports gene curation - save and view gene interpretations, save preferred transcripts.
Emedgene Curate - new private networking component for opted in laboratories
ACMG classification improvements
In analysis tools disease column, hover to view see all related diseases
New Filter under Variant Effect, Advanced, Curate - select pathogenicity
View allele frequency full decimal number
Var Page | Quality Tab | Add tooltip for quality parameter threshold
Var Page | Option to import variant interpretation summary from Curate
Header update - added Illumina logo
Export variant to Curate bug fix
Organization Settings | Management | Fix broken create group and add users link
Analysis Tools | Filters | Compound heterozygous filter now supports CNV del/SNV
Analysis Tools | Filters | ACMG | VUS renamed Uncertain
Reporting | View reports for past cases even if template has been archived
API | Fixed error where case type wasn’t saved