Cases Page

Overview

Connected Insights creates a case for each imported secondary analysis result and then populates the case with the variants called for the sample.

Use the Cases Page to track and manage your lab’s cases, including monitoring case status, identifying cases needing attention, and starting new cases.

Case, subject, and sample metadata can be entered through the UI (see Case Metadata Upload), in the metadata.csv file picked up via the data uploader (see Data Upload), or via API (see Case APIs).

Typical Actions

• View and customize the Case List.

• Assign case participants and tags.

• Click on a case ID to navigate to the Case Page.

Case List Columns

• Case ID — Indicates the unique ID for the case. Select a case to open it.

• Created Date — Indicates the date that the case was created. The default sort is descending.

• Status — Indicates the status of the case.

  • Awaiting Molecular Data — Analysis files not added.

  • Missing Required Data — The case is missing fields like disease or the required test definition.

  • Ready for Processing — The case has all required information and is ready for ingestion.

  • Processing — Annotation and ingestion of the case is in process.

  • Has Issue — The upload case failed. Select the case for details. Contact Illumina Technical Support for guidance.

  • Ready for Interpretation — Variants are ingested and ready to be interpreted.

  • Report(s) Signed Off — Report is approved and signed off.

• Workflow Type — Indicates the type of analysis available for this case: DNA, RNA, or DNA+RNA.

• [Optional] Sex — The biological sex of the subject: male, female, or unknown.

• Disease — The disease associated to the case. It is a required field for processing the case. You can provide disease information from a SampleSheet.csv, a custom case data file, or add it via the user interface.

• Tags — Free text labels associated to the case. You can create new labels by entering a value or use autocomplete to select existing values.

• Participants — The users assigned to the case. You can add users from a dropdown of all users that are a member of the workgroup.

❗ If the case data definition is configured, the case and subject level fields display as columns by default.

Customize the Case List

Show, hide, and reorder columns in the Cases List as follows:

• To search across all columns, the global search box in the top right can be used.

• To move a column, drag the column to a position in the grid.

• Select the menu button next to the column name to change any of the following options:

  • Pin a column to a position or to the left or right sections of the grid.

  • Automatically resize the column to display all of the content in the selected column.

  • Auto-size all columns to display all content for all displayed columns.

• Select the filter icon to filter by a specific column by keywords and information.

• Select the display icon to check or uncheck columns that appear.

Delete a Case

To delete a case from the Case List grid as follows:

1. Navigate to the case to be deleted.

2. Right of the Case Id, select the "..." menu. This menu is only visible to the Lab Director role with the required Illumina Connected Analytics (ICA) permissions. See note below.

3. Select Delete Case.

4. Confirm the delete.

❗ The case and any associated subject or sample data, if the subject or sample is not associated to any other cases, is deleted (ICA files, case data, audit log data, variant data, and report data). Case deletion is restricted by role. The user must have the Connected Insights role of Lab Director and the user or the workgroup must have an "ADMINISTRATOR" role in the ICA project associated with the Connected Insights workgroup. The generic format for the ICA Project associated with Connected Insights Workgroup is ICI_[region]_[workgroup_name]_Project.

Connected Insights - Local

For Connected Insights - Local, the Cases page also displays the following notifications:

• If your Genome Equivalent Sample balance is low, a notification to contact your administrator or Illumina Technical Support displays.

• If the storage space in the /staging/ or external mounted directory is below the required space threshold for case ingestion, a notification displays, and ingestion stops after reaching capacity. To continue ingestion, free up space.

• If the external drive is not accessible, a notification displays and ingestion or case processing will fail. To continue, ensure the external storage drive is accessible.

Do not delete or alter content at the following locations to free up space:

/staging/ici

/<mountedDrive>/d53e4b2d-0428-4b3e-92bf-955f7153c360

/<mountedDrive>/ici_<ServerHostname>/

These locations contain Connected Insights-generated files. If these files are deleted, new cases cannot be processed, or case results may not be available.