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The Emedgene platform is divided into two applications:
Analyze—genomic analysis workbench
Curate—the knowledge management system
Go to the nine-dot app launcher icon located on the and select Curate from the dropdown menu.
Go to the nine-dot app launcher icon located on the Curate navigation panel and select Analyze from the dropdown menu.
The top navigation panel serves as a guide to the platform. It includes:
Case search bar
tab
tab
Add new case button
Emedgene applications dropdown menu to switch between Analyze and Curate
Help dropdown menu under a question mark icon
Settings dropdown menu activated by clicking the username or profile picture
The Dashboard tab depicts an overview of the user activity on the Emedgene platform and provides a glance at key performance indicators for an organization.
Diagnostic Yield card presents the proportion of "solved" cases out of the total number of the organization's cases of the same type.
Status Diagram card displays the total number of the organization's submitted cases as well as the numbers of cases under each status.
Stale Cases card highlights the cases that are stuck at one of the intermediate stages of the analysis, and are not finalized.
Network Activities panel displays a timeline of activities performed by multiple users within the organization. This log includes activity like creating a case, verifying a filter preset, changing a , generating a report, and more.
Click on the icon in the top navigation panel to open the Help dropdown menu.
From there, you can access:
Help Center: Find feature guides, step-by-step instructions, and tips to help you get the most out of the platform.
Walkthroughs: View short interactive demos of workflows (in development).
Feature requests: Share your ideas and feedback.
What's new: Stay updated with the latest release notes.
About: View general information such as your organization name and platform version.
You can use the Case search tab in the top bar to search for cases by the Case ID or Proband ID.
Sample ID (Proband ID)
Status
Type
Label
Resolved: Resolved or Not resolved
Participants
Go to the Filters menu in the Cases table navigation panel
Under Field, select the field you want to filter by
Under List, select a value from the dropdown or manually enter one
Click Apply to activate the filter
To add another filter, click Add new under the active filter and repeat steps 1-4
Go to the Filters menu in the Cases table navigation panel
To remove a specific filter, click the X icon next to it
In the Cases table navigation panel, click the X icon next to the Filters menu
Click Fields
In Fields menu, use the toggle switch next to each field name to show or hide columns based on your preferred view
In the Cases table, click the column title you want to hide
From the dropdown menu, select Hide column
You can reorder columns in three ways.
Hover over the column title
Click the six-dot icon that appears on the left to the title
Drag and drop the column
Click Fields in Cases table navigation panel
In Fields menu, hover over the field name
Click the six-dot icon that appears on the left to the title
Drag and drop the field
Click the column header
From the dropdown menu, select Move left or Move right
Hover over the left or right border of the column header cell
When the resize cursor appears, click and drag the border to your desired width
The Activity tab offers a timeline of case actions and enables users to leave comments. It supports key functions that enhance case management and review:
Traceability—Maintains a complete, time-stamped history of case actions
Error recovery—Allows users to identify and trace changes, such as variant edits or disease associations, made in error
Real-time collaboration – Enables teams to monitor each other’s updates as they happen, ensuring transparency
Training & quality control – Helps identify patterns in variant interpretation and supports consistent application of evidence criteria
Audit compliance – Supports clinical and laboratory documentation standards (e.g., CAP/CLIA) by providing a verifiable action history
Each activity entry includes:
Timestamp (date + time)
User name of the person who performed the action
Action description
Activity logs are kept for at least six years for full traceability.
Viewing activity logs
In the Cases table, the Activity tab within the Case details panel displays only comments and case-related activities. To view the full list of all activities, open the Case details panel directly from the individual case page.
The Cases table navigation panel provides several tools to help you customize your table view and manage cases. It includes the following components:
The Family tree tab includes the following information:
Pedigree diagram. Pedigree legend can be found .
Sample details for each family member:
ACMG pathogenicity
ACMG evidence updated (logs any changes made via the ACMG classification wizard) — this log entry includes a link to the relevant variant page for immediate review
Transcript changes
Reference transcript updated
Logs are case-specific. Activity entries do not reflect changes made in other cases or in the Curate database
Time zone awareness. Timestamps follow the system’s configured time zone, which may differ from your local time—especially in international collaborations.
Case-related
Case created Case status changed Case participants updated Case labels modified Report created Case moved to trash Case data edited, no reanalysis initiated Case data edited and reanalysis launched
Comments
Comments left in the Activity tab
Variant tagging
Variant tag updated — this log entry includes a link to the relevant variant page for immediate review
Evidence notes
Evidence notes updated — this log entry includes a link to the relevant variant page for immediate review
Evidence pathogenicity
Variant pathogenicity updated — this log entry includes a link to the relevant variant page for immediate review
Evidence graph
Evidence graph updated — this log entry includes a link to the relevant variant page for immediate review
Related—directly match one of the proband’s phenotypes
Unrelated—do not match any of the proband’s phenotypes
Medical Condition – Indicates whether the individual is considered Healthy or Affected in the case
Sex. Specified by the user
Age. Automatically calculated in years based on the provided date of birth
Maternal and Paternal ethnicity—ethnic background of the proband’s parents
BAM file location. Shown where relevant
The Emedgene platform utilizes the Okta Identity Management solution to control user access. This improves user management, enhances access and authentication security, and allows organizations to implement single sign-on for their users.
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You can sort cases by Creation date, Due date, or Quality.
A. Hover over the column header and click the up or down arrow to sort in ascending or descending order
B. Alternatively, click the column name and select Sort ascending or Sort descending from the dropdown menu
The current sort direction is indicated by a single arrow icon next to the column name.
Only one column can be used for sorting at a time.
Case ID
A unique identifier assigned to each case by Emedgene, formatted as EMGXXXXXXXXX. This field is fixed and cannot be hidden or repositioned in the table. Share this code with Tech Support when reporting issues.
Proband ID
The identifier of the proband. For , this corresponds to the Sample Name; for , it corresponds to the BioSample Name of the test subject.
Phenotypes
Proband phenotypes as submitted by the user.
Status
The current in the system. Custom statuses can be added in the tab under Settings, and their order can be rearranged via drag-and-drop.
You can update the status directly from the Cases table by clicking the status badge and selecting a new status from the dropdown menu.
Creation date
The date the analysis was initiated. This is saved automatically. The field is sortable.
Due date
A customizable field that allows you to set, change, or remove a due date.
Click the calendar icon to set a date. To change it, click the existing date and select a new one. To remove it, click the cross icon next to the date. The field is sortable.
Quality
Indicates the overall case quality. Hover over the icon for a brief summary, or view detailed results in the Lab tab.
The field is sortable.
Type
Indicates the case type (whole genome, exome, custom panel, array).
The Cases tab provides an overview of genomic sequencing cases submitted by the organization, as well as individual case details.
Cases table—displays a list of cases along with key details
—enables customization of the table view, including grouping and filtering of cases
—opens when a case is selected, providing additional information
The Case details panel provides comprehensive information about a particular case.
The Case details panel is organized into three tabs:
Case info—displays technical, operational, and clinical information about the case
Family tree—shows a graphical pedigree and sample details for each family member
Activity—provides a timeline of all actions taken within the case for audit and collaboration
Click on the row of the case you want to view. A pop-up side Case details panel will appear on the right. To close the panel, click the X icon in the top right corner.
To expand the Case details panel, click the left-pointing arrow icon on the right edge of the screen. To collapse it, click the right-pointing arrow icon at the top left of the panel.
Label
A customizable field that allows you to assign custom case labels. Click the pencil icon to add a new label, select an existing one, or remove a label from the case.
Participants
Users involved in the case who subscribed to updates.
To receive email alerts for case updates, click the Subscribe icon. To unsubscribe, hover over your avatar and click the button.
Lab directors and other authorized roles can assign cases directly to analysts, making workload management easier.
User groups
User groups as defined in Settings. Each group appears as a separate column in the table.
The Case info tab includes the following information:
Case ID—a unique identifier assigned to each case by Emedgene, formatted as EMGXXXXXXXXX
Case type—the type of analysis performed:
Exome
Custom Panel
Array
Sample type—the format of the sample files used in the case:
FASTQ: *.fastq.gz, *.fq.gz, *.bam, *.cram.
Project VCF: *.pvcf, *.vcf, *.vcf.gz, *.pvcf.gz
VCF: *.vcf, *.vcf.gz, *.targeted.json, *.gt_sample_summary.json
Gene list—defines whether gene list was used during analysis and how it was applied:
All genes—AI Shortlist was neither confined to nor prioritized a specific gene list
Virtual panel (In silico panel)—AI Shortlist was limited to only the genes in the gene list
Boosted gene list—AI Shortlist analyzed variants in all genes, but variants in the gene list were given higher priority
Analysis type:
If field is not present—carrier analysis was not performed
Carrier—carrier analysis was performed for the selected gene list
Human reference—the genome reference used during case analysis
Ordered by—the user who created the case and the case creation date
Signed by—the user who finalized the case
Related cases—the Case IDs of other cases that share one or more samples with the selected case
Due Date—the user-defined deadline for finalizing the case. To enter or edit the Due Date, click the calendar icon in the Due Date section
Participants—Users involved in the case, whether in submission, analysis, finalization, or those subscribed to updates. To receive email notifications, click the Subscribe icon. To unsubscribe, hover over your avatar and click the X icon
Patient Information—basic demographic details:
Sex. Specified by the user
Age. Automatically calculated in years based on the provided date of birth
Clinical Information:
Proband phenotypes—HPO terms used to describe clinical findings in the proband
Suspected disease—if provided, includes the suspected condition, penetrance (%), and severity (mild, moderate, severe, or profound)
Maternal and Paternal —ethnic background of the proband’s parents
Clinical note—free-text notes provided at the time of launching the analysis
Additional case information can be added using custom fields, either via the API or by including extra columns in your CSV during batch case creation. This allows you to extend the case details panel with project-specific data. To enable this feature or learn more, please contact [email protected].
Once moved to trash, the case becomes inaccessible. This can be reversed by replacing Move to trash or Trash bin with a different status.
Authorized users can permanently delete all items in the trash. To do this:
Click Empty trash on the .
Review the warning message showing the number of cases pending deletion.
Confirm to permanently delete all cases in the trash.
Warning: Once trash folder is emptied, this action cannot be undone. Review cases pending deletion before proceeding!
After deletion is confirmed:
All cases marked Move to trash are permanently removed
An activity entry is recorded
Email notifications are sent to users who have opted in
Report secondary findings—specifies whether secondary findings analysis was requested
To organize cases by status, navigate to the Cases table, click on Group on the navigation panel, and select Status. To remove the grouping, select None.
