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
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    • Managing data storage
      • Manage data storages
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      • Manage BaseSpace storage
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      • Bring Your Own Bucket
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    • 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
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    • 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
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      • Multiselection of variants and bulk actions (34.0+)
      • Download variants
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      • Filters/Presets panel
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      • Variant Type Filters
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      • Evidence page
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      • Clinical Report
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    • Variant page
      • Variant page
      • Variant page top bar
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      • Desktop apps panel
      • Clinical Significance section
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      • Quality section
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      • Population Statistics section
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      • 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
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    • Settings
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      • Organization Settings (33.0+)
        • Quality parameters (38.0+)
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    • Integrations
      • Automatic Case Creation from ICA - Cyto Array Analysis
      • API Beginner Guide
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  • Emedgene Curate Manual
    • Curate overview
      • Curate overview
      • Emedgene Applications menu
      • Curate navigation panel
      • Genome assemblies supported by Curate
    • Curate Variants
      • Curate Variants overview
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      • 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+)
  • Integrations
    • API Beginner Guide
  • 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 V38.0 (June 3rd, 2025)
      • 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
      • More release notes
        • 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
        • 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
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On this page
  • Panels Of Normals (PON) (37.0+)
  • Attaching a PON to a Kit
  • Creating a PON for Emedgene Using BaseSpace Baseline Builder

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  1. Emedgene analyze manual
  2. Settings
  3. Organization Settings (33.0+)

Kit Management

Panels Of Normals (PON) (37.0+)

For detecting copy number variation (CNV) in targeted panel and exome cases, DRAGEN utilizes a Panel of Normals (PON) approach. This method leverages a set of matched normal samples to establish a reference baseline for CNV event detection.

A PON file is typically a text file listing absolute paths to 'target counts' files of individual matched normal samples. However, a PON can also be in the form of a combined counts file, which is a column-wise concatenation of individual target counts files (either GC-corrected or not).

The Illumina BaseSpace Baseline Builder App can generate this combined counts file (see the section "Creating a PON for Emedgene Using BaseSpace Baseline Builder").


Attaching a PON to a Kit

Starting from version 37, users can attach a PON to an existing Kit BED.

A new PON Management section is available in the Organization Settings page: PON Management.

This section includes a table displaying:

  • Kit Name

  • Kit ID

  • GC Corrected Status

  • Human Reference

  • DRAGEN Version

  • Maximum Interval Size

Additionally, there is an ‘Add PON’ button to initiate the PON addition process.\

Prerequisites

Before adding a PON, ensure the following requirements are met:

  • The PON file must be a combined counts file.

  • The file must be stored in a supported cloud storage (AWS S3, ICA, or BaseSpace Storage). Direct uploads are not allowed.

  • Users must have the “Manage PON” role.

  • The Enrichment Kit and its human reference BED must already exist. The BED file must match the one used to generate the PON.

  • Only one PON per unique combination of Enrichment Kit, Human Reference BED, and DRAGEN Main Version is allowed.

  • PONs cannot be added for DRAGEN sub-versions.

Compatibility

To use the PON for CNV calling, the sample pipeline version must be set to 37.0 or higher. Otherwise, CNV calling will not use the newly added PON.

Existing PONs

Previously existing PONs will not appear in the PON table. However, a notification will indicate the presence of existing PONs within the workgroup.

PON Migration

Previously existing PONs will continue to function, and CNV calling will remain unaffected. If migration to the new PON table is required, please contact techsupport@illumina.com or your bioinformatics support team.

Adding a new PON

  1. Click ‘Add PON’ to open a pop-up window.

  2. Select values for the required fields:

    1. Enrichment Kit: Lists all unique kits within the organization (excluding common kits). To add a PON for a common Kit BED, create a separate Kit with the same Kit BED (refer to Kit Management for details).

    2. DRAGEN Version: Only versions 3.6 and later are supported.

    3. Human Reference: Choose GRCh37 or GRCh38.

  3. Based on the selected DRAGEN version, the system will display the expected maximum interval size:

    1. DRAGEN 4.2 and below: 250bp

    2. DRAGEN 4.3 and above: 500bp (default for DRAGEN 4.3)

  4. Click Next go to file selection window:\

  1. On next window select a combined counts file from a supported cloud storage service (AWS S3, ICA, or BaseSpace Storage). Ensure the file is available in storage before proceeding.

  2. Only one file with the extension “.combined.counts.txt.gz” can be selected.

  3. Click ‘Next’ to validate the file.\

Automated Validations

Before adding a PON, the system performs the following checks:

1. Maximum Interval Size Validation

  • The system inspects the first 1000 rows of the combined counts file to ensure that no target exceeds the threshold interval size.

  • Using a combined counts file with the expected maximum interval size is strongly recommended.

2. GC Correction Validation

  • The system determines GC correction status by checking the cnv-enable-gcbias-correction field in the file headers:

    • 0: Non-GC corrected

    • 1: GC corrected

  • If this field is missing, the system analyzes target value types:

    • Integer values: Non-GC corrected

    • Float values: GC corrected

  • Users must ensure the combined counts file has the intended GC correction status.

Viewing Added PONs

Once a PON is successfully added, it appears in the PON table with details based on the selected inputs. Value for Maximum Interval Size and GC Corrected Status are inferred from validation results.\

Deleting PON from table

If user wants to delete a PON for a combination listed in table for any reasons, then user with role “Manage Pon” shall be able to delete it. This deletion will be a soft deletion i.e. linkage between combined counts file and Kit BED will be removed and there will be no impact on combined counts file itself.\

Creating a PON for Emedgene Using BaseSpace Baseline Builder

Introduction

As of Emedgene V37, users of Emedgene can supply their own panel of normal (PON) to enable CNV calling on gene panels and WES samples. This guide details the process using BaseSpace.

The DRAGEN Baseline Builder application in BaseSpace can be used to build PONs that are compatible with Emedgene:\

Users without BaseSpace can receive a free trial BaseSpace account along with compute (250 iCredits) and storage (1 TB) by registering here (https://basespace.illumina.com/). The compute is allocated for 30 days upon trial commencement and will be sufficient to generate a PON.

Alternatively, Illumina Connected Analytics (ICA), DRAGEN servers and DRAGEN in cloud are also capable of generating Emedgene compatible PONs.

Requirements

  • ~ 50 normal samples 50/50 male:female split, originating from the same library prep protocol, ideally from the same sequencer.

  • The sample fastq files need to be in one or more Projects in your Basespace account.

  • iCredits

  • Compatible BED file

Uploading a BED file:

The BED file used must match that uploaded to Emedgene, any discrepancy may cause a failure during case processing. See Emedgene Help Center Articles for more information on creating an Enrichment Kit in Emedgene.

Uploading a BED file to a project in BaseSpace can be done within the project:\

Note that hg19/grch37 BED files are not directly compatible with hs37d5 (the reference used within Emedgene) and will require their region contigs being renamed from "chr1", "chr2", "chr3"... etc. to "1", "2", "3" etc.

Running the app

1) Select the application "DRAGEN Baseline Builder" with the latest version that matches your Emedgene secondary analysis pipeline (4.3 in example) and click launch:\

2) Select output project and Baseline Mode "CNV":

3) Select input FASTQ Biosamples to use. \

50 samples is a rough guideline as the degree of correlation between normals and case sample is more important than quantity.

4) Select correct reference genome, matching that used in Emedgene.

Chose the multigenome version of the genome build.

For GRCh38/hg38:\

For GRCh37/hg19 choose the hs37d5 build (remember to rename contigs in BED file if using hs37d5):

5) Select BED file you uploaded to your Basespace project in Step 2.1 above:\

6) Configure Emedgene specific settings:

Emedgene CNV calling has DRAGEN settings that must also be used during PON creation. In the app, this can be done in the advanced settings section at the bottom of the page:

Tick "Ignore Duplicate Reads in CNV Baseline Files" and change "Generated Combined Counts file for CNV" to "GC Corrected" 7) Tick the BaseSpace Labs App Acknowledgement box. \

8) Launch the app.

Downloading Results

Once the analysis is complete, open the output files and look for the *.combined.counts.txt.gz file. It may be within a folder called "pon".

It can be downloaded from analysis results manually, by clicking on the file and selecting "Download", via the Basespace CLI (https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview), or if the output project is connected to Emedgene - loaded directly into the platform.

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