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:
GTC Output
False
N/A
N/A
SNV VCF Output
False
N/A
N/A
DUP minimum size (kb)
50
0
250000
DUP minimum probes
10
0
250000
DEL minimum size (kb)
25
0
250000
DEL minimum probes
10
0
250000
LOH minimum size (kb)
3000
0
250000
LOH minimum probes
500
0
250000
GAINLOH minimum size (kb)
500
0
250000
GAINLOH minimum probes
300
0
250000
mDUP minimum size (kb)
50
0
250000
mDUP minimum probes
10
0
250000
mDEL minimum size (kb)
25
0
250000
mDEL minimum probes
10
0
250000
mLOH minimum size (kb)
3000
0
250000
mLOH 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.
Note: Support for each DRAGEN Array version begins with a specific Emedgene release and continues with later versions. For more details see the compatibility table on the Emedgene help site. In that table, "EMG version" refers to the combination of the Platform minor version (Organization Settings > Environment > Platform minor version) and the case pipeline version (Organization Settings > Workbench & Pipeline > Pipeline versions > 4. case). Both must be updated. The Secondary Analysis Pipeline setting (Organization Settings > Workbench & Pipeline > Pipeline versions > 1. Sample) is not related to DRAGEN Array integration with Emedgene.
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), Platform Core notifications must be enabled for the specific Platform Core 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 Platform Core BSSH-managed project, follow these steps:
In the Platform Core portal, in the Platform Core BSSH-managed project (e.g. "BSSH Your Workgroup Name") navigate to the Notifications section via the left-hand menu.
Platform Core Notifications Menu Click + Create, then select Platform Core Event.
Platform Core Event Fill in the required fields as follows:
Event: Analysis Success
Type: SNS
Address: Provide the correct address based on your region (contact techsupport@illumina.com 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.
For more details on the prerequisites for this analysis, see the Automatic Case Creation from Platform Core section in the Emedgene User Guide. For more details on limitations for this analysis see the release notes.
Applicable Arrays
For specific product compatibility, see the Product & Analysis Compatibility table.
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