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

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

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

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

  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.

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