BeadChip Accessioning, Imaging, and Analysis

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)

⚠️ 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 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 ℹ️ Automatically populated when imaging is started	Text	Read Only
Instrument ℹ️ Automatically populated when imaging is started	Text	Read Only
Run Start Time ℹ️ Automatically populated when imaging is started	Text	Read Only
Data Path ℹ️ Automatically populated when imaging is started	Text	Read Only
Instrument Run ID ℹ️ Automatically populated when imaging is started	Text	Read Only
Run Status ℹ️ Automatically populated when imaging is started, completed, aborted, or has failed	Text	Read Only
DMAP Location ℹ️ Automatically populated when imaging is started	Text	Read Only
Instrument Type ℹ️ Automatically populated when imaging is started	Text	Read Only
Failure Reason ℹ️ Automatically populated when imaging fails	Text	Read Only
Log ℹ️ Automatically populated when imaging is started, completed, aborted, or has failed	Multiline Text	Read Only
ICA Run ID ℹ️ Automatically populated when imaging is started	Text	Read Only
Run Complete Time ℹ️ Automatically populated when imaging is completed or aborted	Text	Read Only
Comment	Multiline Text

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.

Field Name	Field Type	Options	Additional Options and Dropdown Items
Analysis Complete Time ℹ️ Automatically populated when analysis is completed or aborted	Text	Read Only
Analysis Run Name	Text	Required
Analysis Configuration ID	Text	Required
Analysis Start Time ℹ️ Automatically populated when analysis is started	Text	Read Only
Analysis Report ℹ️ Automatically populated when analysis is completed	Text	Read Only
Analysis Status ℹ️ Automatically populated when analysis is started, completed, aborted, or has failed	Text	Read Only
Analysis Run ID ℹ️ Automatically populated when analysis is started	Text	Read Only
Log ℹ️ Automatically populated when analysis is started, completed, aborted, or has failed	Multiline Text	Read Only

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

Refer to Integration Properties Details for the properties installed with Illumina iScan Integration Package v1.2.0.