The integration includes the following:
Automated beadchip accessioning in Clarity LIMS upon beadchip creation on Illumina Connected Analytics (ICA).
Automated verification of beadchip status. Samples are automatically created upon successful verification.
Automated beadchip imaging status tracking (imaging run started; errored out; completed successfully; or ended by user events).
Manual invocation of analysis on ICA.
Automated analysis status (for completed successfully or errored out events) tracking.
The integration utilizes the following pre-configured workflows in IPP:
iLASS Infinium Genotyping Assay v1.0
Last Updated: November 2024
Release Date: September 2023
Document Version: 2
These release notes describe the key changes to software components for the Clarity LIMS iScan Integration Package version 1.1.0.
Refer to under Instruments & Integrations.
Updates to the Java and third-party dependency libraries used in the integration.
Fixed the SIS core service not being properly registered in systemctl.
Warning log message displays when the ImagingAborted and ImagingFailed events are processed.
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:
Version
Changes
2
Updated Compatibility section to reference Compatibility matrix table.
1
Initial release.
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)
This step is automated and must not be started manually.
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
ℹ Automatically populated when imaging is started
Text
Read Only
Instrument
ℹ Automatically populated when imaging is started
Text
Read Only
Run Start Time
ℹ Automatically populated when imaging is started
Text
Read Only
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.
Field Name
Field Type
Options
Additional Options and Dropdown Items
Analysis Complete Time
ℹ Automatically populated when analysis is completed or aborted
Text
Read Only
Analysis Run Name
Text
Required
Analysis Configuration ID
Text
Required
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.
Data Path
ℹ Automatically populated when imaging is started
Text
Read Only
Instrument Run ID
ℹ Automatically populated when imaging is started
Text
Read Only
Run Status
ℹ Automatically populated when imaging is started, completed, aborted, or has failed
Text
Read Only
DMAP Location
ℹ Automatically populated when imaging is started
Text
Read Only
Instrument Type
ℹ Automatically populated when imaging is started
Text
Read Only
Failure Reason
ℹ Automatically populated when imaging fails
Text
Read Only
Log
ℹ Automatically populated when imaging is started, completed, aborted, or has failed
Multiline Text
Read Only
ICA Run ID
ℹ Automatically populated when imaging is started
Text
Read Only
Run Complete Time
ℹ Automatically populated when imaging is completed or aborted
Text
Read Only
Analysis Start Time
ℹ Automatically populated when analysis is started
Text
Read Only
Analysis Report
ℹ Automatically populated when analysis is completed
Text
Read Only
Analysis Status
ℹ Automatically populated when analysis is started, completed, aborted, or has failed
Text
Read Only
Analysis Run ID
ℹ Automatically populated when analysis is started
Text
Read Only
Log
ℹ Automatically populated when analysis is started, completed, aborted, or has failed
Multiline Text
Read Only
