Emedgene
Illumina Connected Software
  • Get Started with Emedgene
    • Get started with Emedgene
    • How can Emedgene help you solve a case?
  • Emedgene analyze manual
    • Getting around the platform
      • Top navigation panel
      • Emedgene Applications menu
      • Dashboard
      • Settings
      • User roles
      • Help
      • Okta identity management
    • Managing data storage
      • Manage data storages
      • Manage Azure Blob data storage
      • Manage S3 credentials
      • Manage BaseSpace storage
      • Manage GCS storage (V37.0+)
      • Bring Your Own Bucket
      • Bring Your Own Key
    • Cases tab
      • Cases tab
      • Cases table
      • Case status
      • Browse and select cases
      • Case details
    • Creating a single case
      • Add a new case
      • Select sample type
      • Create a family tree
      • Family tree legend
      • Add a sample
      • Supported Variant callers
      • Adding patient info for the proband
      • Adding patient info for the non-proband samples
      • Secondary findings
      • Labeling a case
      • Gene list
      • Supported parental ethnicities
    • Creating multiple cases
      • Batch case upload from platform
      • CSV format requirements
      • Batch case upload via CLI
    • Reviewing a case
      • Individual case page
      • Individual case page: Top bar
      • Individual case page: Top bar
      • Candidates tab
      • Most Likely Candidates and Candidates
      • Genome Overview
      • Analysis tools tab
      • Variant table columns
      • Variant table
      • Variant search
      • Multiselection of variants and bulk actions (34.0+)
      • Download variants
      • Manually add variants to a delivered case
      • Filters/Presets panel
      • Filters
      • Presets
      • Preset groups
      • Variant Type Filters
      • Variant Effect Filters
      • Quality Filters
      • Polymorphism Filters
      • Gene Filters
      • Phenomatch Filters
      • Inheritance Filters
      • Zygosity Filters
      • User Filters
      • Evidence page
      • Phenotypic match strength
      • Lab tab
      • Versions tab
      • Editing an existing case
      • Finalizing a case
      • Clinical Report
      • Reflex genetic testing
      • Variant zygosity notations
      • STR calling and interpretation
    • Variant page
      • Variant page
      • Variant page top bar
      • Variant tagging widget
      • Variant activity panel
      • Desktop apps panel
      • Clinical Significance section
      • Summary section
      • Quality section
      • Visualization section
      • Population Statistics section
      • Related Cases section
      • CNV overlap percentage
      • Evidence section
      • ACMG SNV Classification wizard
      • Logic behind ACMG classification of SNVs
      • ACMG CNV Classification wizard
      • Variant page sidebar (2.29+)
    • Variant visualization setup
      • Enabling visualization for a VCF case
      • Integration between emedgene and desktop IGV
      • Loading alignment files to your desktop IGV (32.0+)
    • Analyze Network
      • Analyze Network Setup
      • Network sharing configuration
      • Case subject consent for extended sharing
      • Public vs Private network
      • Create a network
      • Set network data sharing policy
      • Leave a network
      • Delete a network
    • Settings
      • My settings
      • Management
      • User Management
      • Network
      • Organization Settings (33.0+)
    • Integrations
      • API Beginner Guide
      • Advanced API Implementations
      • API Key Generation
      • BSSH Integration
      • ICA Integration
      • Webhook Integration
  • Emedgene Curate Manual
    • Curate overview
      • Curate overview
      • Emedgene Applications menu
      • Curate navigation panel
      • Genome assemblies supported by Curate
    • Curate Variants
      • Curate Variants overview
      • Curate Variant table
      • Curate Variant page
      • How to add a variant to Curate
      • Curate Variant annotations in the case
    • Curate Genes (2.28+)
      • Curate Genes overview
      • Curate Gene table
      • Curate Gene page
      • How to add a gene to Curate
    • Import Curate annotations to the case (30.0+)
      • Import Curate Variant annotations to the case (30.0+)
      • Import Curate Gene annotations to the case (30.0+)
  • Frequently Asked Questions
    • All FAQ
      • Which browser should I use with Emedgene?
      • Emedgene annotations and update frequency
      • How do I use developer tools to collect logs?
      • Can I analyze Illumina Complete Long Reads in Emedgene?
      • How do I prepare VCF files generated by DRAGEN MANTA to be used as input for Emedgene?
      • Source of gnomAD data for small variants on GRCh38
      • How are MNVs handled on the platform?
      • Support for gene lists with up to 10,000 genes
      • Genomic Regions by Case Type
      • How do I analyze mtDNA variants?
      • Can I use exome data for CNV detection?
      • How does joint calling work on Emedgene?
      • What is the required format for a BED file defining a kit?
      • Which reference genomes can I use?
      • How do I move between organizations?
      • How do I check the version of my environment?
      • "Failed to generate report". What should I do?
      • How do I prepare VCF files generated by Dragen STR (ExpansionHunter) to be used as input?
      • How does Emedgene Analyze prioritize transcripts?
      • How does Emedgene Analyze merge variants from different sources?
      • Performance issue troubleshooting
      • How does Emedgene calculate variant effect and severity ?
      • How to I prepare metrics files generated by DRAGEN to be used as input for Emedgene
      • How are timekeeping and log timestamps kept accurate and consistent?
  • Release Notes
    • Workbench & Pipeline Updates
      • New in Emedgene V37.0 (February 20, 2025)
        • V37 Patches
      • New in Emedgene V36.0 (October 8 2024)
        • V36 Patches
      • New in Emedgene V35.0 (May 22nd 2024)
        • V35 Patches
      • New in Emedgene V34.0 (January 28th 2024)
        • V34 Patches
      • New in Emedgene V33.0 (September 6th 2023)
        • V33 Patches
      • New in Emedgene V32.0 (June 8th 2023)
        • New pipeline 32 (June 8th 2023)
        • V32 Patches
      • More release notes
        • New in emedgene 31 (March 1st 2023)
        • New in emedgene 30 (January 8th 2023)
        • New in emedgene 2.29 (August 25 2022)
        • New pipeline 5.29 (May 1st 2022)
        • New in emedgene 2.28 (May 1 2022)
        • New in emedgene 2.27 (March 7, 2022)
        • New in emedgene 2.26 (Dec 14, 2021)
        • New in emedgene 2.24-2.25 (Aug 11, 2021)
        • New in emedgene 2.23 (Jun 15, 2021)
        • New in emedgene 2.19-2.22 (Apr 8, 2021)
        • New in emedgene 2.16-2.19 (Dec 7, 2020)
        • New in emedgene 2.12-2.16 (Oct 18, 2020)
    • Knowledgebase Updates
      • 2025
        • Variant Databases (March 30th 2025)
        • Zoidberg 77 (March 17th 2025)
        • Zoidberg 76 (February 3rd 2025)
        • Zoidberg 75 (January 6th 2025)
      • 2024
        • Variant Databases (December 8th 2024)
        • Zoidberg 74 (December 2nd 2024)
        • Zoidberg 73 (October 21th 2024)
        • Variant Databases (September 22nd 2024)
        • Zoidberg 72 (September 10th 2024)
        • Variant Databases (July 21st 2024)
        • Zoidberg 71 (July 24th 2024)
        • Zoidberg 70 (June 3rd 2024)
        • Zoidberg 69 (April 19th 2024)
        • Variant Databases (April 9th 2024)
        • Zoidberg 68 (March 18th 2024)
        • Variant Databases (February 5th 2024)
        • Zoidberg 67 (January 28th 2024)
        • Variant Databases (January 5th 2024)
      • 2023
        • Zoidberg 66 (December 24th 2023)
        • Variant Databases (December 3rd 2023)
        • Zoidberg 65 (November 21th 2023)
        • Variant Databases (November 5th 2023)
        • Zoidberg 64 (October 24th 2023)
        • Variant Databases (October 8th 2023)
        • Zoidberg 63 (September 18th 2023)
        • Variant Databases (September 5th 2023)
        • Zoidberg 62 (August 23th 2023)
        • Zoidberg 61 (August 16th 2023)
        • Variant Databases (August 6th 2023)
        • Zoidberg 60 (July 30th 2023)
        • Variant Databases (July 2nd 2023)
        • Zoidberg 59 (June 18th 2023)
        • Variant Databases (June 4th 2023)
          • Variant Databases (May 7th 2023)
        • Zoidberg 58 (May 21th 2023)
        • Zoidberg 57 (April 16th 2023)
        • Variant Databases (April 2nd 2023)
        • Zoidberg 56 (March 19th 2023)
        • Variant Databases (March 11th 2023)
        • Zoidberg 55 (February 19th 2023)
        • Zoidberg 54 (January 16th 2023)
    • Change log
      • Change log pipeline v34
      • Change log pipeline 31
      • Change log workbench 31
      • Change log pipeline 30
      • Change log workbench 30
      • Change log workbench 2.29
      • Change log pipeline 5.29
      • Change log workbench 2.28
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On this page
  • New AI Models
  • Shortlist CNVs and Compound Heterozygous SNV-CNV Variants
  • Improved Phenotypic Match Model
  • Support for DRAGEN 4.0
  • Workflow Improvements
  • Related Cases Enrichment
  • Bulk Translation of Reports
  • Emedgene Curate Improvements
  • Enhancements

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  1. Release Notes
  2. Workbench & Pipeline Updates
  3. More release notes

New in emedgene 30 (January 8th 2023)

PreviousNew in emedgene 31 (March 1st 2023)NextNew in emedgene 2.29 (August 25 2022)

Last updated 2 months ago

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New AI Models

This version was primarily focused on introducing new AI innovation, with the goal of streamlining workflows and further reducing time-per-case.

Shortlist CNVs and Compound Heterozygous SNV-CNV Variants

Our AI Shortlist now compiles CNVs with evidence, along with compound heterozygous SNV-CNV variants. We expect this exciting new capability to drive significant time savings.

The model expands our core AI Shortlist model to CNV variants, and similarly considers dozens of features used by geneticists to interpret a case. The model was validated in a cohort of 51 singletons previously solved by a CNV variant. In 92% of cases (n=47 / 51) the solving variant was identified in a short list of 10 variants. In 6% (n=3), the solving variant was present in the candidate list. Only 2% (n=1), or a single case, was missed by the new AI Shortlist.

Due to the challenging quality nature of CNV variants, the conventional successful AI Shortlist model for SNV is not affected by newly added CNV results. CNV and compound heterozygous variants shortlisted variants are cumulative to SNV/indels, and the default short list for your organization will be extended by 5 variants on average.

The model supports deletions and duplications called both by the DRAGEN CNV read-depth caller and DRAGEN SV caller.

Improved Phenotypic Match Model

We have a new and improved phenotypic match model, Phenomeld. Phenotypic match algorithms estimate the concordance between patient phenotypes and an associated disease, and are a critical component in the AI Shortlist model.

Phenomeld, which achieves an AUC of 0.94, is used both as part of the AI Shortlist model, and as an independent filter in the analysis tools. The improvement was achieved with ensemble machine learning, which utilizes several phenotypic match models to improve model performance.

The Phenomeld model was validated against two data sets.

Internal Validation Set

A second validation used a set of 4648 ClinVar cases, and compared Phenomeld with phen2gene, where Phenomeld demonstrated improved results.

ClinVar Validation Set

For exploration of phenotypic match results outside of the AI Shortlist models, you can use the Phenomeld filter in the analysis tools.

Support for DRAGEN 4.0

This version supports DRAGEN 4.0 with ML and graph mapper, both for customers using the Emedgene DRAGEN pipeline and customers bringing their own DRAGEN.

DRAGEN 4.0 improves accuracy and reduces analysis time by ~26%.

Workflow Improvements

Related Cases Enrichment

The table now includes: solved/unsolved status, zygosity and affected and overlap % (for CNVs only).

When a case is selected, additional data is displayed: interpretation, phenotypes, proband ID, demographics, ACMG tags and case type.

Bulk Translation of Reports

Our reporting system now enables customers to upload custom data sets to reports. This enables customizable and flexible bulk translation and augmentation of reports with proprietary data.

Emedgene Curate Improvements

  • Private Networks now support CNV variants, with selectable % overlap.

  • Store gene interpretations and auto-populate to reports

  • New gene metrics card for easier gene curation

Enhancements

  • Lab Page | Gene Coverage - Region coverage statistics will now be calculated based on the case’s kit associated BED file. If none is defined, a default clinical exome BED will be used.

  • Variant Page | ACMG - You can now write and store notes on ACMG tags for SNV variants (previously available only for CNV variants).

  • Analysis Tools | Presets - New search bar in gene lists, for faster addition of gene lists to preset filters.

  • In organization settings, you can now view and manage Enrichment Kits.

    • Standard users can view the BED file used for any kit

  • PolyPhen2 is back! Illumina has acquired a license to include this data in tertiary analysis platforms.

  • Gene Lists | When creating a gene list, the platform will save the NCBI ID for any gene in order to maintain compatibility with future gene symbol updates without the need for a lab gene list audit.

  • Expanded ethnicity list to support an increasingly global and diverse customer base.

Utilizing an internal dataset of 314 well characterized cases, Phenomeld was compared to the open source model, as well as to the previous Emedgene Phenomatch model, outperforming both.

Learn more about the .

The component in the variant page has been enriched with interpretation and classification data, in order to streamline use of lab curated data.

Users with permissions can upload new BED files for any reference, both for existing and new kits. Please follow the for BED files (link accessible only to Emedgene platform users).

phen2gene
DRAGEN 4.0 release
Related Cases
file format guide
New AI Models
Shortlist CNVs and Compound Heterozygous SNV-CNV Variants
Improved Phenotypic Match Model
Support for DRAGEN 4.0
Workflow Improvements
Related Cases Enrichment
Bulk Translation of Reports
Emedgene Curate Improvements
Enhancements