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DRAGEN Array Cytogenetics Analysis

DRAGEN Array - Cytogenetics Analysis

Cytogenetics Threshold Adjustment

When using DRAGEN Array – Cytogenetics analysis or DRAGEN Array - Cytogenetics analysis + Emedgene interpretation cloud analysis types, additional customization options will appear after product files are selected within Configuration Settings. Adjustments to these thresholds will be saved as part of the Configuration Setting. Thresholds can be adjusted based on results objectives. Adjusting thresholds will impact the number of events called and thus, the output in the VCF and JSON files.

The recommended thresholds/settings are pre-set within the software for any new configurations:

Threshold
New Config
Min Value
Max Value

GTC Output

False

N/A

N/A

SNV VCF Output

False

N/A

N/A

CNV minimum size (kb)

0

0

250000

CNV minimum probes

10

0

250000

LOH minimum size (kb)

3000

0

250000

LOH minimum probes

500

0

250000

CNV Smoothing window size

5

0

1000

DRAGEN Array - Cytogenetics analysis + Emedgene interpretation

This analysis type integrates with Emedgene to display results in a user-friendly interface.

Prerequisites

  • You'll need an additional Emedgene subscription to be either "Array", "Professional", or "Enterprise" tier. You can also follow the Illumina Software Registration Guide to obtain that subscription.

  • To ensure proper integration with Emedgene (EMG), ICA notifications must be enabled for the specific ICA BSSH-managed project. EMG relies on these notifications to detect when an analysis has successfully completed. To configure SNS (Amazon Web Services Simple Notification Service) events in your managed ICA BSSH-managed project, follow these steps:

    • In the ICA portal, in the ICA BSSH-managed project (e.g. "BSSH Your Workgroup Name") navigate to the Notifications section via the left-hand menu.

    ICA Notifications Menu

    • Click + Create, then select ICA Event.

    ICA Event

    • Fill in the required fields as follows:

      • Event: Analysis Success

      • Type: SNS

      • Address: Provide the correct address based on your region (contact [email protected] if unsure).

      • Payload Version: v4

      • AWS Region: This will be auto-populated based on the provided address.

      • (Recommended) Click Send Test Message to verify the configuration.

      • Click Save to complete the setup.

Create Subscription

For more details on the prerequisites for this analysis, see the Automatic Case Creation from ICA section in the Emedgene User Guide. For more details on limitations for this analysis see the release notes

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