BeadChip Accessioning, Imaging, and Analysis
The Illumina iScan Integration Package v1.1.0 supports the integration of Clarity LIMS to iScan systems. The package includes the following workflows, which are included in the Illumina Preset Protocols (IPP) Package v2.6.0:
iLASS Infinium Genotyping Assay v1.0
iLASS Infinium Genotyping Assay with PGx v1.0
This integration enables you to do the following tasks:
Accession the BeadChip.
Handle the imaging run event (including pre-imaging verification for the imaging step).
Handle the analysis run event for the analysis step.
⚠️ The configuration used in this integration supports iScan lab processes. Any changes to the configuration (including renaming protocols, steps, and fields) can cause issues with these processes.
Accession the BeadChip
In the iScan workflows, BeadChips are accessioned into Clarity LIMS before the hybridization step of the post-lab protocol. The BeadChip container type is defined based on the BeadChip product type (eg, PGx) and the product version. Because every BeadChip has a unique barcode, Clarity LIMS can track usage throughout the entire workflow. The following BeadChip names are supported in iScan Integration v1.1.0:
GCRA-24v1-0
GDA_PGx-8v1-0
GSA-48v4-0
If you need help accessioning your BeadChip, contact Illumina Support.
Image Infinium BeadChip on iScan Step
Master Step: Image Infinium BeadChip on iScan (iLASS Infinium Genotyping Assay v1.0) or Image Infinium BeadChip on iScan (iLASS Infinium Genotyping Assay with PGx v1.0)
⚠️ This step is automated and must not be started manually.
Master Step Custom Fields
The following table lists field configuration details defined on the Image Infinium BeadChip on iScan (iLASS Infinium Genotype Assay/with PGx v1.0) master step. These fields are located under Configuration, on the Master Step Fields tab.
⚠️ Do not delete, rename, or modify. These actions will break the integration.
Field Name | Field Type | Options | Additional Options and Dropdown Items |
BeadChip Barcode | Text | Read Only | |
Instrument | Text | Read Only | |
Run Start Time | Text | Read Only | |
Data Path | Text | Read Only | |
Instrument Run ID | Text | Read Only | |
Run Status | Text | Read Only | |
DMAP Location | Text | Read Only | |
Instrument Type | Text | Read Only | |
Failure Reason | Text | Read Only | |
Log | Multiline Text | Read Only | |
ICA Run ID | Text | Read Only | |
Run Complete Time | Text | Read Only |
Pre-Imaging Verification
When BeadChips are loaded onto the iScan system, the iScan Control Software (iCS) with LIMS mode enabled performs pre-imaging verification to make sure that user loads the correct BeadChip. This verification is done as follows.
iScan Control Software verifies the BeadChip container is queued to the imaging step in Clarity LIMS.
After the verification completes sucessfully, Clarity LIMS iScan integration creates run on ICA and starts BeadChip imaging starts automatically.
Imaging Run Status Tracking
When the BeadChip is scanned with an iScan, Clarity LIMS receives the events of the run status update. Then, the custom fields are automatically populated with information.
The Run Status field can show the following statuses:
Running
Completed
Aborted
Failed
If there is a run error event, the Run Complete Time field is not populated. The Failure Reason field will be populated only when the run error event happens.
Invoke Infinium Analysis Step
Master Step: Invoke Infinium Analysis (iLASS Infinium Genotyping Assay v1.0) or Invoke Infinium Analysis (iLASS Infinium Genotyping Assay with PGx v1.0)
In this step, the iScan Integration handles events related to BeadChip analysis. This step is a manual step that requires data input of Analysis Configuration ID and Analysis Run Name fields to start the analysis run.
Master Step Custom Fields
The following table lists field configuration details defined on the Invoke Infinium Analysis (iLASS Infinium Genotyping Assay/with PGx v1.0) step. These fields are located under Configuration, on the Master Step Fields tab.
Field Name | Field Type | Options | Additional Options and Dropdown Items |
Analysis Complete Time | Text | Read Only | |
Analysis Run Name | Text | Required | |
Analysis Configuration ID | Text | Required | |
Analysis Start Time | Text | Read Only | |
Analysis Report | Text | Read Only | |
Analysis Status | Text | Read Only | |
Analysis Run ID | Text | Read Only | |
Log | Multiline Text | Read Only |
Configure and Start an Analysis Run
On the Record Details milestone, navigate to Step Details and enter the Analysis Run Name. The Analysis Run Name can only contain a maximum of 255 alphanumeric characters, underscores, hyphens, and periods. The name cannot start with the wfr. characters.
Enter the Analysis Configuration ID. To retrieve the configuration ID that is associated with the analysis, contact Illumina Support.
Select Start Analysis v1.0 to start the analysis run.
Analysis Run Status Tracking
When the analysis is started on ICA, Clarity LIMS receives the event and displays related information. The custom fields are automatically populated with information.
The Analysis Status field can show the following statuses:
Analysis Running
Analysis Completed
Analysis Completed with Warning
Analysis Aborted
Analysis Timedout
Analysis Errored
If there is an analysis error event, the Analysis Complete Time field is not populated.
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