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.
iScan
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.
iScan System
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.
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.
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.
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.
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
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.
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
If there is an analysis error event, the Analysis Complete Time field is not populated.
Properties Installed
Refer to for the properties installed with Illumina iScan Integration Package v1.2.0.
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
Comment
Multiline Text
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
Analysis Timedout
Analysis Errored
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
Field Name
Field Type
Options
Additional Options and Dropdown Items
Analysis Complete Time
ℹ Automatically populated when analysis is completed or aborted
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
BeadChip Accessioning, Imaging, and Analysis
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)
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 (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.
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.
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.
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.
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
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.
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
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
Analysis Timedout
Analysis Errored
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
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
iScan System 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
Set Array Secondary Analysis
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Routing Script - GenomeStudio
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
