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Settings

My settings

The My settings page can be accessed by clicking on the corresponding tab under Settings.

The My settings page features the following panels:

1. Professional Credentials

Add or modify your details, including: a. Full name, b. Title, c. Specialty, d. License number.

2. Contact Information

a. **Add or modify your contact details including:**<br/>
    i. Personal phone number,<br/>
    ii. Office phone number,<br/>
    iii. Office address.<br/>
b. **Check the box to receive updates regarding case status via email**<br/>
![](../../\_files/images/emedgene_analyze_manual/settings/my_settings_2_image.png)

3. Organization

a. **Choose one of your organizations,**<br/>
b. **Add or modify organization details including:**<br/>
    i. Organization address,<br/>
    ii. Department.<br/>
![](../../\_files/images/emedgene_analyze_manual/settings/my_settings_3_image.png)

4. Roles and Permissions

Starting with version 38, in Illumina environments only, Roles and Permissions management has been migrated to IAM. All Emedgene roles are now defined as IAM scopes and can be assigned to users through predefined IAM roles or custom IAM roles.

Please note: In legacy environments, user management remains unchanged.

5. Profile Picture

Upload or change your profile picture.

Management

The Management page can be accessed by clicking on the corresponding tab under Settings. Note: The Management page is accessible only for users having a Manager role.

The Management page features the following panels:

  1. Illumina Support Access

Enable case access for our support team via a slider button to provide billing, administrative, and support services. You can also disable it afterward to ensure maximum security.

  1. Storage

Connect a new storage, edit its details, check connection, or delete a storage. Please check out a dedicated Managing data storage article collection for instructions.

  1. S3 credentials

Manage API credentials (an access key ID and a secret access key) used to connect to the default AWS S3 storage bucket (32.0+): create, deactivate, activate or delete.

  1. Test Statuses

    a. #### Case Statuses

    Create Case statuses, remove Case statuses that haven't been in use and change order of Case statuses by drag and drop. The order will be reflected in the Case Status dropdown featured in Cases table and Individual case page Top bar.

    Be sure to scroll down and click Save!

b. #### _Stale Days_

Define the number of days that must pass without the case [being finalized](../reviewing_a_case/finalizing_a_case.md) for it to be classified as "stale" and subsequently factored into the _Stale Cases_ statistics on the [_Dashboard_](../getting_around_the_platform/dashboard.md)_._

**Be sure to scroll down and click&#x20;**_**Save**_**!**
c. #### _Variant Tags_

Create custom [_Variant tags_](../variant_page/variant_tagging_widget.md) and remove _Variant tags_ that haven't been in use. If you're using our reporting solution, please avoid using spaces in the _Variant tag_ name.

**Be sure to scroll down and click&#x20;**_**Save**_**!**

5. #### Test Settings

a. #### _Case Labels_ Create, edit, and remove [_Case labels_](../creating_a_single_case/labeling_a_case.md) that haven't been in use. Once you're done, don't forget to click _Save_ at the bottom of the _Test Settings_ section\*.\*
b. #### _Gene lists_ Create [gene lists](../creating_a_single_case/gene_list.md) from scratch or from existing ones, edit, remove, hide, unhide, and download. Adding and removing genes to the list is only available for gene lists that haven't been in use; editing the list name is not restricted.
c. #### _Enrichment kit BED files_ (30.0+)

Add enrichment kits defined by [BED files](../../frequently-asked-questions/all-faq/what_is_the_required_format_for_a_bed_file_defining_a_kit.md) and hide/unhide custom kits.
33.0+: **Improved BED validation errors** 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.

6. #### Groups

Create and delete user groups as needed, aligning them with your case review workflow. Each user group is represented by its dedicated column in the Cases table.

  1. Webhooks

Set up webhooks. You might need assistance from your IT team.

Network

The Network page is accessible via the dropdown menu under Settings. Note: The Network page is accessible only for users having a Manager role.

Here, the dedicated network manager can:

For detailed instructions on network analysis, refer to the Network section.

Organization Settings (33.0+)

The Organization Settings page (33.0+) is accessible via the dropdown menu under Settings. Note: The Organization Settings page is accessible only for users having a Manager role.

Workbench & Pipeline

1. AI shortlist (38.0+)

The AI Shortlist Module, located in the Workbench & Pipeline section of Organization Settings, allows you to refine variant prioritization based on analysis type.

Organization settings > Workbench & Pipeline > AI shortlist

1.1 Rare Diseases

The AI shortlist prioritizes genes of known and unknown significance within the shortlist, which will contain a fixed number (10 SNV, 5 SV) of variants.

  • Discovery Mode: The AI shortlist will prioritize known and unknown genes, and will be limited to likely solving variants.

  • Focused Mode: The AI shortlist will prioritize known genes and unknown genes separately, and will be limited to likely solving variants.

1.2 Carrier

The AI shortlist will prioritize variants reported as pathogenic or likely pathogenic in any known variant databases or variants with high severity.

  • Known Pathogenic: The AI shortlist will prioritize variants reported as pathogenic or likely pathogenic in any known variant databases.

  • High Severity: The AI shortlist will prioritize variants with high severity.

  • Both: The AI shortlist will prioritize variants reported as pathogenic or likely pathogenic in any known variant databases or variants with high severity.

2. Pipeline versions

To set the versions for the secondary analysis pipeline, case pipeline, DRAGEN, and human reference. An user can also configure whether to include reference homozygous genotype calls in cases. Read more.

Pipeline versions card

2.1. Sample

To set versions for the human reference, DRAGEN, and the secondary analysis pipeline to process individual samples in cases, including mapping alignment and variant calling.

2.2 Variant caller mapping (38.0+)

Manage the variant callers used for the secondary analysis pipeline.

Required role - 'Manage pipeline versions'. Without the role the user will not be able to select/unselect variant callers from the table.

Various variant callers along with the sequencing type, methodology and compatibile sample, dragen and case pipeline version information is shown in the table. Upon save, after selecting the specific varcallers, an user can expect the successive case runs to follow the user selections.

2.3. Sample pipeline arguments (38.0+)

To view your sample pipeline arguments for mapping and calling. If the arguments are not set, they will be displayed as ‘N/A’.

2.4. Case

To set case pipeline version.

3. Organization DB management (38.0+)

To manage your organization’s databases:

  1. Go to Organization Settings

  2. Select the Workbench & Pipeline tab

  3. Scroll to the new section called Organization DB Management

3.1 Viewing Existing Databases

All users can view a table listing the current databases configured for their organization. If no DBs are present, a message will inform you that none are available.

Table Information Includes:

  • DB Name

  • DB Type (Historic, Noise, or Curated)

  • DB File Name

  • Human Reference (e.g., GRCh37, GRCh38)

  • Variant Type (SNV or CNV)

  • Fields:

    • Historic/Noise: AF, HET, HOM, HEM

    • Curated: Pathogenicity

  • Overlap Details (for CNVs only):

    • C: Candidate Overlap

    • A: Annotation DB Overlap

    • Example: C: 70%; A: 70%

    • SNVs will show “N/A” in this column

  • AI Shortlist: On/Off

  • Active: On/Off

  • Last Edited Date

Additional Features:

  • Search: Use the search bar to filter the table by DB name

  • Download: Click the download icon to export a DB as a VCF file

3.2 Adding a New Database

Users with the role Managing Organization DB can add/edit new databases.

Steps to Add a DB:

  1. Click Add New in the Organization DB Management section.

  2. Complete the form:

    • Active (On/Off)

    • DB Name

    • DB Type: Historic or Noise

    • Variant Type: SNV or CNV

    • Human Reference: GRCh37 or GRCh38

    • AI Shortlist: On/Off

    • Fields will be auto-populated and not editable

  3. Upload the DB file using the file browser.

  4. Click Save to finalize. A success message will confirm the addition.

Steps to Edit:

  1. Click the Edit button next to the database you want to update.

  2. Modify the available fields.

  3. Click Save to apply the changes. A confirmation message will appear.

Note: Legacy databases cannot be edited. A notification will indicate if a DB is legacy.

3.3 Audit Logging

All changes (adding or editing a DB) are automatically recorded in the organization’s audit log for transparency and traceability.

4. SV annotation threshold (38.0+)

Present under Workbench & Pipeline in Organization Settings, this module enables configuration of annotation overlapping thresholds for structural variants with external and internal databases.

Organization settings > Workbench & Pipeline > SV annotation threshold

Value Constraint: Comprised between 0 to 1, with 2 decimals allowed.

4.1 One Side Pathogenic

CommentShare feedback on the editorThe One Side Pathogenic setting allows to set a threshold for identifying structural variants classified as pathogenic, such as those in ClinGen Pathogenic, ClinVar Pathogenic, DDDSyndromes, and Curate Pathogenic databases. It starts at a default of 0.7, and accepts value between 0 and 1.CommentShare feedback on the editor

4.2 One Side Uncertain

CommentShare feedback on the editorThe One Side Uncertain setting allows to set a threshold for identifying structural variants classified as uncertain, such as those in ClinGen VUS, ClinVar VUS, and Curate VUS databases. It starts at a default of 0.7, and accepts value between 0 and 1.CommentShare feedback on the editor

4.3 Two Sided

CommentShare feedback on the editorThe Two Sided setting allows to set a threshold for identifying structural variants classified as benign, such as those in ClinGen Benign, ClinVar Benign, DECIPHER, DGV, gnomAD SV, 1000 genomes, and Curate Benign databases. It starts at a default of 0.7, and accepts value between 0 and 1.

Environment

Environment settings

1. Organization URL (ILMN clouds only)

Associating URLs with your workgroup on ILMN Cloud

On ILMN Cloud, customers can easily associate URLs with their current workgroup by selecting from a list of predefined URL patterns. These URLs play a crucial role in organizing and accessing workgroup-specific resources.

Key Points to Remember:

  • URL Selection: You can choose from a set of predefined URL patterns.

  • Multiple Associations: A single URL can be associated with one or several workgroups.

  • Activation Time: After selecting the URL for your workgroup, please allow 1 to 15 minutes for the changes to take effect.

Need a Custom URL?

If you would like to create a new custom URL pattern within your domain, please reach out to our technical support team at techsupport@illumina.com for assistance.

2. Platform version

Select a platform version for your organization from the options available in your region. Please allow 1-15 minutes for changes to become active. Keep in mind that this selection will not alter your pipeline version, only the software version. To change a pipeline version please contact techsupport@illumina.com.

Important! If you switch to a version older than 33.0, the feature will be removed from your Organization Settings, and you will need to reach out to support for platform version changes.

3. Case identifier

By default, Emedgene displays the Case ID in the "EMGXXXXXXXXX" format*.* However, you have the choice to use the Proband ID instead. Please note that the Proband ID has a visible 13-character limitation, with the remaining characters visible upon hovering.

4. Default page (34.0+)

The default page upon entering a case can be customized. You can choose between:

  1. Candidates - default option;

  2. Analysis/filters

  3. Analysis/presets

  4. Lab

5 . Analysis tools columns order (34.0+)

You can customize the default order of Variant table columns. Just rearrange the columns by dragging and dropping them to your preferred sequence.

Lab Workflow

Lab Workflow settings (34.0+)

1. Presets

Here you can review and manage organization filter Presets.

1.1. Create Preset

Upon clicking on Add new, you will be redirected to Analysis tools page where you can create a Preset from active filters.

1.2. Review logic behind the Preset

Click on an downward arrow icon left to the Preset's name.

1.3. Edit Preset

  1. Click on the ✏️Edit icon;

  2. Make the necessary changes. Editing the Preset requires basic understanding of JSON data format;

  3. Click Save. The software will perform schema validation on the edited Preset. &#xNAN;Note: you can modify the Preset's content but not its name. Note: the Preset can't be edited if it's locked.

1.4. Lock/unlock Preset

Locking the Preset prevents any user from changing it.

  1. Click on the ��Lock/Unlock icon;

  2. Click on Lock/Unlock in the popup window.

1.5. Delete Preset

  1. Click on the 🗑️Delete icon;

  2. Confirm your decision by clicking Delete in the popup window.

Note: Only unused Presets can be deleted.

2. Preset groups

Here you can review and manage filter Preset groups.

In versions prior to 34.0, creating Preset groups required technical support. With 34.0+, Preset groups can be easily created by combining different Presets. Alternatively, you can upload a JSON file that defines the Presets in a Preset group. The file name and schema will be validated upon upload.

The section has two tabs:

  • V2 (new)

Here you can create (from Presets/from a JSON file, view, edit, hide/unhide and download your organization's Preset groups.

  • V1 (legacy)

Here you can view and download legacy Preset groups.

Migrating V1 Preset groups to the improved V2 methodology

Legacy Preset groups can be migrated to the new methodology via two simple steps: downloading the Preset group JSON file in the V1 (legacy) tab, then uploading it on the V2 (new) tab.

2.1. Create Preset group from existing Presets:

  1. Click on Add new;

  2. From the dropdown, select New;

  3. Enter a name for the Preset group. Note: The Preset group can't be renamed later!

  4. Select Presets to include in the Preset group. Click Add after selecting each Preset;

  5. Drag and drop Presets to change the order;

  6. Click on Save.

2.1. Create Preset group from JSON file:

This is the second step in the migration of the V1 (legacy) Preset group, after you have downloaded the Preset group JSON file.

  1. Click on Add new;

  2. From the dropdown, select From file;

  3. From the file browser, select a JSON file that defines a Preset group;

  4. The system will thoroughly validate the file;

  5. If validation is successful, a Preset group will be created. Any underlying Presets that are missing from your organization will be added as well.

2.3. Review contents of the Preset group (V2 and V1)

Click on an downward arrow icon left to the Preset group's name.

2.4. Edit Preset group

  1. Click on the ✏️Edit icon; 2a. Add Presets to the group as needed. Select Presets to include in the Preset group from the dropdown. Click Add after selecting each Preset; 2b. Remove Presets from the group as needed. Click on the ��Remove icon on right to the right of the Preset name. 2c. Drag and drop Presets to change the order;

  2. Click Save.

2.5. Hide/unhide Preset group

When you hide a Preset group, it will no longer appear in the Preset groups list offered at case creation (Select preset group step).

Click on the 👁️Hide/Unhide icon.

Note: A default Preset group cannot be hidden.

2.6. Download Preset group file (V2 and V1)

This is the first step in the migration of the V1 (legacy) Preset group to V2 methodology. A Preset group file contains preset names and the filters used to define each Preset in JSON format.

Click on the ⬇️Download icon.

2.7. Revert *Preset group (*V1)

If a V1 Preset group that has undergone migration is set to revert, the corresponding V2 Preset group will be deleted.

Click on the ↩️Revert icon to undo the migration.

Note: If a migrated Preset group has been assigned as default, it cannot be reverted.

3. Default Preset group

You can set a Preset group as default. The case is assigned to the default Preset group if no Preset group is selected or the default value is selected in the Add New Case Preset group selection step.

  1. Click on the dropdown arrow;

  2. Select the Preset group;

  3. Click Save.

Note: A default Preset group cannot be hidden and cannot be reverted.

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.

Quality parameters (38.0+)

Quality parameters section allows users to configure quality thresholds for the organization. Users with 'Manage Quality Parameters' role can edit the thresholds.

NGS Quality

  • Set the Gene list threshold for your organization. Case validations will not be applied for cases with gene list containing fewer than the gene list threshold.

  • Default value for the Gene list threshold is 50.

  • Values above 0 and whole numbers are accepted.

Array Sample Quality

  • Set the Array quality thresholds for your organization. If a sample’s quality values meet the criteria below, it will be classified as ‘High’; otherwise, it will be classified as ‘Low’.

  • Default thresholds are Call Rate >= 0.99 and LogR Dev <= 0.2

  • Values between 0 to 1 are accepted.

NGS quality & Array sample quality section in Quality Parameters