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
  • Legal
    • Privacy, Security & Compliance
    • Release Policy
Powered by GitBook
On this page
  • New Variant Types Supported
  • SV Insertions
  • STR Improvements
  • New Visualization Tracks
  • Curated Data Tracks
  • BigWig Track for CNV Visualization
  • Additional
  • Emedgene Curate + CNVs
  • Additionally:
  • Additional new features
  • Gene-related disease card update
  • Edit interpretation summary
  • Variant page sidecar redesign
  • Enhancement to Analysis Table
  • Lab Page Enhancement
  • ACMG 78
  • Expose input file errors

Was this helpful?

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

New in emedgene 2.29 (August 25 2022)

PreviousNew in emedgene 30 (January 8th 2023)NextNew pipeline 5.29 (May 1st 2022)

Last updated 5 months ago

Was this helpful?

New Variant Types Supported

SV Insertions

Emedgene now supports calling and interpretation of SV insertions called by the DRAGEN Manta SV caller.

Calling:

The DRAGEN Manta SV caller detects simple insertion/deletion events , and detects both fully-assembled and partially-assembled (inferred) insertions. Minimum size of SV insertion is 50bp. Indels smaller than 50bp are called by the regular SNV caller and annotated as SNV.

Known caller limitations:

  • The maximum fully-assembled insertion size should correspond to approximately twice the read-pair fragment size, but note that power to fully assemble the insertion should fall off to impractical levels before this size.

  • Note that Manta does detect and report very large insertions when the breakend signature of such an event is found, even though the inserted sequence cannot be fully assembled.

  • In the case of partial assembled insertions, the size of the variant displayed does not reflect its true size.

Note that for customers bringing their own DRAGEN pipeline into Emedgene, specific VCF headers in the SV file need to be added before sample ingestion. Contact support for more information.

Annotation:

SV insertions are annotated with gnomAD SV and ClinVar SV data, for population frequencies and known pathogenicity. Insertion annotation is performed on the basis of the insertion start position; the sequencing content is not considered.

Interpretation:

Variant page and analysis tools have been adapted to support SV insertions.

  • Variant type will be clearly marked in the header

  • New filters added for filtering SV insertions, quality filtering for both length and bin count can be applied (see remark above regarding the INS size).

STR Improvements

  • New pathogenicity filter

  • Allele frequency is now viewable in the proprietary STR visualization

Summary Table of Variant Types Supported by Test Type and Version

Variant Type

WGS

WES

Panel

Emedgene DRAGEN

Bring your own DRAGEN

Platform Version

SNV

Yes

Yes

Yes

All

All

All

Indel

Yes

Yes

Yes

All

All

All

CNV

Yes

Yes

Yes

All Need PON - exome/panel

5.24+ Need PON - exome/panel

2.22+

mtDNA

Yes

Yes

Yes

All

5.26+

2.25+

SV del/dup

Yes

Yes

Yes

Yes

5.28+ Needs adjustment

2.28+

SV insertion

Yes

Yes

Yes

Yes

5.29+ Needs adjustment

2.29

STR

Yes

No

No

Yes

5.29+ Needs adjustment

2.28+

New Visualization Tracks

Curated Data Tracks

You can now add ClinVar and ClinVar SV tracks to the in-platform visualization. Pathogenicity corresponds to the ClinVar color scheme, with black denoting a conflict.

BigWig Track for CNV Visualization

BigWig visualization is now available for WGS cases, specifically the tangent normalized signal points view. This visualization helps interpret CNVs by clearly showing the bins and breakpoints.

For customers bringing their own DRAGEN output, a VCF and BigWig data can be shared via the API and batch upload tool.

These new tracks are available in both simple and advanced modes, allowing you to configure the visualization tab as needed.

Additional

A known mtDNA visualization discrepancy on GRCh37 was fixed in this version.

As always, we support synchronization with IGV desktop, and all settings in the platform can be mirrored to the IGV desktop environment which continuously displays the current selected variant data.

Emedgene Curate + CNVs

CNVs are now supported in Emedgene Curate! Including streamlined annotation and analysis flow integration, all the way through to auto-populating report template fields.

  • Add a CNV variant directly to Emedgene Curate, or import during your case analysis;

  • Search for a CNV by range, type or gene;

  • Variant header, info card and gene’s related disease components have been adapted for CNVs;

  • Select a disease for a curated CNV variant;

  • Explore the related cases table - filter by % annotation overlap.

  • In your Curate navigation, you will notice a new column denoting Variant Type. For labs with enabled private networks, the icon will denote pathogenicity by color, with a hover showing more details.

Additionally:

  • Once you have curated a CNV variant, all future cases including in your private network if enabled, will be annotated with your data.

  • Once a variant is reviewed, curated data can be imported and used to automatically populate a report template field.

Additional new features

Gene-related disease card update

The gene-related disease has always shown a numeric summary of phenotypic match, for patient phenotypes found in the disease out of all patient phenotypes.

This card now shows a numerical match between patient phenotypes and disease phenotypes. The full list of disease phenotypes is displayed, with the phenotypic match strength for each. A link to the full list of patient phenotypes will open the side car for an easy view and comparison.*

Edit interpretation summary

Edit the interpretation summary at the top of the page, in addition to the edit capability in the evidence tab.*

*Note that both of these new capabilities are only available for variants tagged by the AI Shortlist or users as most likely or candidates.

Variant page sidecar redesign

The variant page sidecar has been redesigned.

  • Includes a default view:

    • Sample names of proband and family members.

    • Proband phenotypes, and family if available

  • Allows you to configure your desktop IGV and Alamut connections, including the new Alamut API.

  • The sidecar can be collapsed and expanded, and does not cover active window

Enhancement to Analysis Table

In the analysis tools, the known variant column colors had previously ignored VUS (variants of unknown significance) classifications if appearing in conjunction with P/LP or B/LB.

This has now been updated and if a variant has both P/LP and VUS classifications or B/LB and VUS classification, the appropriate mixed colors will appear.

If a variant has conflicting classifications it will appear in black.

Lab Page Enhancement

For labs using the Emedgene DRAGEN pipeline, QC metrics are now available for download.

ACMG 78

Updated filters to support full ACMG 78 gene list.

Expose input file errors

The majority of case pipeline failures are due to errors in customer input files. We now expose explicit and detailed input file errors on the cases page.

This update follows the latest recommendation from ACMG for reporting secondary findings: .

https://www.acmg.net/PDFLibrary/Secondary-Findings-v3.1.pdf
New Variant Types Supported
SV Insertions
STR Improvements
New Visualization Tracks
Curated Data Tracks
BigWig Track for CNV Visualization
Additional
Emedgene Curate + CNVs
Additional new features
Gene-related disease card update
Edit interpretation summary
Variant page sidecar redesign
Enhancement to Analysis Table
Lab Page Enhancement
ACMG 78
Expose input file errors