To open a case, mouse over the corresponding row in the Cases table and click on the Open case text next to the Case ID (first column). Alternatively, once a row is selected, clicking on it again will open the case as well.
Go to Filters, select the field under Field, then choose or manually input value under List and click on Apply. To add another filter, click on Add new.
To remove a filter, under Active filters, click on the cross icon on the right of the filter setting. To clear filters altogether, click on the cross icon on the right of Filters.
Available filters include:
Case Id
Status: Issue reported, Uploading, In progress, Reanalysis, Archived, Delivered, Confirmed, Approved, Pending Sequencing, or any other customized case status
Participants - users involved in the case submission, analysis, finalizing, or those who subscribed to receive updates on the case.
Type: Custom Panel, Exome, Whole Genome
Sample Id
Resolved: Resolved, Not Resolved
Label: any customized Case label
You can sort cases by:
Creation date, or
Due Date.
To do this, hover over the column name and click on the up or down arrow to sort ascending or descending, respectively. The current sorting order is depicted as a single up or down arrow symbol next to the column's name.
Alternatively, you can click on the name of the column and select Sort ascending or Sort descending in the dropdown menu.
You can use the Case search tab in the top bar to search for cases by the Case ID or Proband ID.
To group cases by Case Status, go to Group and select Status; to undo grouping, select None.
A. Select fields to be displayed: go to Fields and set a toggle switch next to each field name in on or off position per your desired view.
B. Hide the currently displayed field: click on its title and select from the dropdown menu Hide column.
A. Drag and drop columns: hover over the column title cell, click on the six-dot icon on the left to the text, drag to the desired location and drop.
B. Set column order under Fields: go to Fields, hover over the field name, click on the six-dot icon on the left to the text, drag to the desired location and drop.
C. Move a particular column: click on the column title and select from the dropdown menu Move left or Move right.
Grab the right or left border of the column title cell and drag it with your cursor to the desired width.
Case details panel is divided into three tabs:
Case Info
Family Tree
Activity
Information on the currently selected case is displayed in the window that pops up when you click on the corresponding row of the . To close the window, click on the cross icon.
Case ID
Case Type: Custom Panel, Exome, Whole Genome
Sample Type: FASTQ, Project VCF, VCF, BAM
Gene List - all genes or a particular gene list used to filter the analysis results
Human Reference - the genome reference used during case analysis
Ordered by - user who created the case by default, and creation date
Signed by - user who finalizes the case
Related cases - lists the Case IDs for all the cases that share one or more samples with the one currently selected
Due Date - a deadline for finalizing the case. You can enter or edit the Due Date by clicking on the calendar icon under the Due Date section.
Participants - names of the users involved in the case submission, analysis, finalizing, or those who subscribed to receive updates on the case. To receive email notifications on your colleagues' activities in the particular case, click on the Subscribe icon.
Patient Information: Sex (33.0+) / Gender (32.0 and older), Age
Clinical Information:
Proband Phenotypes - HPO terms used to describe clinical findings in the proband
Suspected Disease: Suspected disease (if provided), Penetrance (%) and Severity (mild, moderate, severe, or profound)
Parental Consanguinity
Report secondary findings (Yes, No or N/A)
Clinical Note: any notes on proband's phenotypes, family history, or other critical points of the case.
Here you can find:
Sample information for each family member:
Phenotypes: proband phenotypes and phenotypes reported for other family members (related and unrelated)
Medical Condition (Healthy or Affected)
Sex
Age
BAM file location
You can choose All activities, Comments, or Case-related activities from a dropdown menu. To add a comment to the case, write it in the Write a new comment text field and click Add.
Case status indicates the current stage of case processing by the Emedgene platform or a genomic analyst.
Status column of the ;
The sequencing file is being uploaded on the platform.
Note: The Uploading status cannot be manually altered.
Case is running.
Note: The In Progress status cannot be manually altered.
The running stage completed, and the case is now available for users for analysis and review.
Analysis and review completed.
Status Finalized by design should be assigned manually after summarizing the analysis findings through the Case Interpretation widget. Specifically, when finalizing a case, you should indicate its end result:
Confidently Solved (Positive),
Likely Solved (Positive),
Further Investigation (Uncertain), or
Unsolved (Negative).
Confidently Solved, Likely Solved and Further Investigation end result categories correspond to the Resolved case status supercategory, and Unsolved obviously falls into Not resolved (together with all the non-finalized cases). The indicated case analysis outcomes are used to calculate the diagnostic yield.
Indicates that the case is not subject to further review. Changing Case status to Archived requires technical support (pre-34.0 flow).
Note: The Archived status cannot be manually altered.
Makes the case unaccessible. This status is only assigned manually.
Note: Once moved to trash, the Case status cannot be altered without technical support.
The case has been created, but is not connected to any genetic data.
Note: The Pending Sequencing status cannot be manually altered.
The case failed to run. Please check the integrity of the files used and verify that the variant caller is on our accepted variant caller list.
Note: The Issue Reported status cannot be manually altered.
The system is re-running the AI Shortlist algorithm for the case.
Note: The Reanalysis status cannot be manually altered.
In the Individual case page Top bar, click on a dropdown icon next to the current case status.
Select the status from the menu.
In the Cases table, click on the current case status.
Select the relevant status from the dropdown menu.
Maternal and Paternal
Graphic representation of the pedigree. More information about the symbols can be found .
Maternal and Paternal
This tab logs actions related to the selected case such as changes, variant tagging, ACMG pathogenicity, changes to an evidence graph, evidence notes, transcript changes for a specific variant, and comments added by users. Each log includes the date and time that each action was performed. We keep all logs for at least six years for full traceability.
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Note: access to applying or Finalized status could be restricted to specific users, such as organization managers and directors, who possess corresponding .
Note: You can change statuses Delivered and (provided you have the necessary ) Finalized, as well as custom statuses. However, the default case statuses Uploading, In Progress, Archived, Move to trash, Pending Sequencing, Issue Reported and Reanalysis cannot be manually altered.
From Settings>Management>Test Statuses>, you can create custom Case statuses, remove unused Case statuses, and rearrange their order.
Cases table lists all the genomic sequencing cases submitted by your organization. It is the primary component on the left-hand side of the Cases tab.
A unique ID assigned to a case by Emedgene.
Proband's sample ID submitted by creating the case in the platform.
Current Case Status in the system. You can change Case Status without leaving the Cases table via a convenient dropdown.
Custom Case Statuses can be added in Settings>Management>Test Statuses>Case Statuses. Additionally, you can rearrange statuses by using drag and drop, and the order will be reflected in the Case Status dropdown featured in Cases table and Individual case page Top bar.
Automatically saved.
Can be set, changed or removed on the spot. To set a date, click on the calendar icon and select a date of interest. To change it, click on the previously set due date and select a new one. To remove the due date, click on the cross button next to it.
Proband phenotypes as submitted by the user.
Users involved in the case submission, analysis, finalizing, or those who subscribed to receive updates on the case. To receive email notifications on your colleagues' activities in the particular case, click on Subscribe icon. To unsubscribe, hover over your initials and click on the cross button.
Case Type (Custom Panel, Exome, Whole Genome).
Custom Case labels.
User groups as defined in Settings > Management.
The Cases tab provides a bird's-eye view of all the previously submitted genomic sequencing cases.
Case details window that pops up on the right when activated
Case navigation panel on top
