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Getting around the platform

Emedgene applications menu

The Emedgene platform is divided into two applications:

  • Analyze—genomic analysis workbench

  • Curate—the knowledge management system

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To switch from Analyze to Curate:

Go to the nine-dot app launcher icon located on the and select Curate from the dropdown menu.

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To switch from Curate to Analyze:

Go to the nine-dot app launcher icon located on the Curate navigation panel and select Analyze from the dropdown menu.

Top navigation panel

The top navigation panel serves as a guide to the platform. It includes:

  1. Case search bar

  2. tab

  3. tab

top navigation panel

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

  • Dashboard
    Cases

    Dashboard tab

    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.

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    Lefthand panel

    • 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.

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    Righthand panel

    • 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.

    Case status

    Help

    Click on the circle-question 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.

    How to filter cases

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    Available filters

    You can filter cases using the following :

    • Case ID

    How to customize Cases table view

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    How to select columns to be displayed

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    A. Show or hide columns via the Fields menu

    How to search for cases

    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

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    How to apply filters

    1

    Go to the Filters menu in the Cases table navigation panel

    2

    Under Field, select the field you want to filter by

    3

    Under List, select a value from the dropdown or manually enter one

    4

    Click Apply to activate the filter

    5

    To add another filter, click Add new under the active filter and repeat steps 1-4

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    How to remove a filter

    1

    Go to the Filters menu in the Cases table navigation panel

    2

    To remove a specific filter, click the X icon next to it

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    How to clear all filters

    In the Cases table navigation panel, click the X icon next to the Filters menu

    fields

    How to open a case

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    To open a case:

    A. Hover over the corresponding row in the Cases table and click on the Open case link next to the Case ID in the first column

    B. Alternatively, double-click the row

    1

    Click Fields

    2

    In Fields menu, use the toggle switch next to each field name to show or hide columns based on your preferred view

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    B. Hide a column directly from the Cases table

    1

    In the Cases table, click the column title you want to hide

    2

    From the dropdown menu, select Hide column

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    How to change column order

    You can reorder columns in three ways.

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    A. Drag and drop the column

    1

    Hover over the column title

    2

    Click the six-dot icon that appears on the left to the title

    3

    Drag and drop the column

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    B. Reorder columns via the Fields menu

    1

    Click Fields in Cases table navigation panel

    2

    In Fields menu, hover over the field name

    3

    Click the six-dot icon that appears on the left to the title

    4

    Drag and drop the field

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    C. Move a column using a dropdown menu

    1

    Click the column header

    2

    From the dropdown menu, select Move left or Move right

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    How to adjust column width

    1

    Hover over the left or right border of the column header cell

    2

    When the resize cursor appears, click and drag the border to your desired width

    Activity

    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.

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    The Activity tab logs the following actions:

    Category
    Activities

    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.

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    Important notes

    1. Edits are permanent. Even if a change is undone, the original action remains recorded for traceability

    Cases table navigation panel

    The Cases table navigation panel provides several tools to help you customize your table view and manage cases. It includes the following components:

    • Filters menu Use this to narrow down the list of cases.

    • Group by menu Organize your cases by case status

    • menu Choose which columns are visible in the table and define their order

    • button

      Permanently delete cases currently in the trash. Use with caution, as this action cannot be undone

    Cases table

    Cases table lists key details of all genomic sequencing cases submitted by the organization.

    You can the table by hiding, showing, rearranging fields, or adjusting column widths, except for Case ID, which is fixed as the first column and always visible.

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    Cases table fields

    Field
    Description

    Family tree

    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

    Fields
    Empty trash
    Phenotypes. For family members other than the test subject, phenotypes are categorized as:
    • 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

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    Okta identity management

    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.

    ​

    How to sort cases

    You can sort cases by Creation date, Due date, or Quality.

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    To sort cases:

    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.

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    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).

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    Cases tab

    The Cases tab provides an overview of genomic sequencing cases submitted by the organization, as well as individual case details.

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    The Cases tab includes:

    1. Cases table—displays a list of cases along with key details

    2. —enables customization of the table view, including grouping and filtering of cases

    3. —opens when a case is selected, providing additional information

    Case details

    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

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    How to access the Case details panel

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    From the Cases table

    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.

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    From an individual case page

    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.

    Cases table navigation panel
    Case details 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 xmark 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.

    single case creation
    batch case creation
    case status
    Management

    Case info

    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:

    How to delete cases

    In order to prevent accidental data loss, deleting cases in Emedgene includes a staging step before permanent case deletion.

    1

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    Move a case to trash

    to Move to trash (≤v37.0) or Trash bin

    Whole Genome
  • 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].

    (v38.0+).

    Once moved to trash, the case becomes inaccessible. This can be reversed by replacing Move to trash or Trash bin with a different status.

    2

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    Empty trash folder (v37.0+)

    Authorized users can permanently delete all items in the trash. To do this:

    1. Click Empty trash on the .

    2. Review the warning message showing the number of cases pending deletion.

    3. Confirm to permanently delete all cases in the trash.

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    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

    Update the case status
    Parental consanguinity—indicates whether the parents are related by blood
  • Report secondary findings—specifies whether secondary findings analysis was requested

  • ethnicity
    Cases table navigation panel

    How to group cases

    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.