Organization DB management

The Organization Database Management feature gives users better visibility and control over the databases (DBs) created and uploaded within their organization. These DBs help improve variant interpretation and are commonly used for filtering known variants (historic or noise) or storing curated findings.

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

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

Adding a New Database

Users with the Managing Organization DB role can add/edit existing databases within their organization. To create or upload a new Database, please contact your Illumina support representative.

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.

Audit Logging

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