BeadChip Accessioning, Imaging, and Analysis
Last updated
Last updated
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.
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.
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)
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.
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.
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.
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.
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.
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.
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.
This step is automated and must not be started manually.
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
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
Automatically populated when imaging is started
Automatically populated when imaging is started
Automatically populated when imaging is started
Automatically populated when imaging is started
Automatically populated when imaging is started
Automatically populated when imaging is started, completed, aborted, or has failed
Automatically populated when imaging is started
Automatically populated when imaging is started
Automatically populated when imaging fails
Automatically populated when imaging is started, completed, aborted, or has failed
Automatically populated when imaging is started
Automatically populated when imaging is completed or aborted
Automatically populated when analysis is completed or aborted
Automatically populated when analysis is started
Automatically populated when analysis is completed
Automatically populated when analysis is started, completed, aborted, or has failed
Automatically populated when analysis is started
Automatically populated when analysis is started, completed, aborted, or has failed
