The integration includes the following:

• Automated beadchip accessioning in Clarity LIMS (via Illumina Connected Analytics during pre-imaging verification).

• 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 Illumina Connected Analytics.

• Automated analysis status (for completed successfully or errored out events) tracking.

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)

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.

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.

1. iScan Control Software verifies the BeadChip container is queued to the imaging step in Clarity LIMS.

2. 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.

Configure and Start an Analysis Run

1. 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.

2. Enter the Analysis Configuration ID. To retrieve the configuration ID that is associated with the analysis, contact Illumina Support.

3. 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.

The Illumina iScan integration provides preconfigured workflows that map to established lab protocols and steps used with the iScan system. The integration also supports the associated consumables and assays used in these protocols.

Last Updated: November 2024

Release Date: July 2024

Document Version: 2

These release notes describe the key changes to software components for the Clarity LIMS iScan Integration Package version 1.2.0.

Compatibility

Refer to under Instruments & Integrations.

New Features

• Updated iScan integration to support 'ILASS Infinium Genotyping Assay v1.1' and 'ILASS Infinium Genotyping Assay with PGx v1.1' workflows

• Supports the new 'Infinium Methylation Array EX-48' beadchip

• Removed unused Analysis Result column from Sample Details table in Infinium Analysis step.

• Integration-related properties can now be accessed and updated via System Setting in Clarity v6.3. Refer to for configurable properties.

• Updated integration properties to be extensible to future array projects

  • Replaced supportedImagingWorkflowStepNames with supportedImagingWorkflowStepNamePattern

  • Replaced supportedAnalysisWorkflowStepNames with supportedAnalysisWorkflowStepNamePattern

• Added analysis run ID in analysis run logging to improve troubleshooting.

Defects fixed

• Fixed imaging result not reflecting correctly in the "Infinium Array Imaging on iScan" step upon re-imaging of beadchip.

• Updated iScan install details to table retrieved by getInstallHistory script.

Known issues

• Warning log message displays when the ImagingAborted and ImagingFailed events are processed.

Revision History

The Illumina iScan Integration Package v1.2.0 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 v2.9.0:

• iLASS Infinium Genotyping Assay v1.1

• iLASS Infinium Genotyping Assay with PGx v1.1

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

Beadchip are auto accessioned for the workflows listed in Supported Workflows. The beadchip containers are created in Clarity by iLASS at the hybridization step of the post-lab protocol. Prior to imaging, a verification is performed and beadchips that are not accessioned prior to start of the workflows will be automatically accessioned by Illumina Connected Analytics (ICA). 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 v1.2.0:

• GCRA-24v1-0

• GDA_PGx-8v1-0

• GSA-48v4-0

• MSA-48v1-0

Image Infinium BeadChip on iScan Step

Master Step: Image Infinium BeadChip on iScan (iLASS Infinium Genotyping Assay v1.1) or Image Infinium BeadChip on iScan (iLASS Infinium Genotyping Assay with PGx v1.1)

Master Step Custom Fields

The following table lists field configuration details defined on the Image Infinium BeadChip on iScan master step. These fields are located under Configuration, on the Master Step Fields tab.

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.

1. iScan Control Software verifies the BeadChip container is queued to the imaging step in Clarity LIMS.

2. 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.

Invoke Infinium Analysis Step

Master Step: Invoke Infinium Analysis (iLASS Infinium Genotyping Assay v1.1) or Invoke Infinium Analysis (iLASS Infinium Genotyping Assay with PGx v1.1)

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 master step. These fields are located under Configuration, on the Master Step Fields tab.

Configure and Start an Analysis Run

1. 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.

2. Enter the Analysis Configuration ID. To retrieve the configuration ID that is associated with the analysis, contact Illumina Support.

3. 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.

Properties Installed

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.

Compatibility

Refer to under Instruments & Integrations.

New Features

• Updates to the Java and third-party dependency libraries used in the integration.

Defects Fixed

• Fixed the SIS core service not being properly registered in systemctl.

Known Issues

• Warning log message displays when the ImagingAborted and ImagingFailed events are processed.

Revision History

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

Overview

The iScan workflow includes the following functionality:

• Preset protocol.

• Ability to attach the scan log to the samples.

Protocol 1: Infinium Array Imaging (iScan v1.0)

Protocol Type = Other

Next Steps Configuration

Step 1: Image Infinium BeadChip (iScan v1.0)

• Master Step Name = Image Infinium BeadChip - iScan v1.0

• Step Type = No Outputs

Automations

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if (input.::Infinium Kit Name:: == ::Infinium MethylationEPIC Kit:: ) { input.::Array Secondary Analysis:: = ::GS-METHYLATION::} ; if (input.::Infinium Kit Name:: != ::Infinium MethylationEPIC Kit:: ) { input.::Array Secondary Analysis:: = ::GS-GENOTYPING::}' -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Array Secondary Analysis' \
--FIELD_VALUE 'GS-GENOTYPING' \
--WORKFLOW 'GenomeStudio v1.0' \
--STEP 'Create Infinium Genotyping Analysis Sample Sheet (GenomeStudio v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
--FIELD_NAME 'Array Secondary Analysis' \
--FIELD_VALUE 'GS-METHYLATION' \
--WORKFLOW 'GenomeStudio v1.0' \
--STEP 'Create Infinium Methylation Analysis Sample Sheet (GenomeStudio v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

  • Scan Log - Manually uploaded

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields