MiSeqDx Integration v1.9 Configuration and User Interaction

The Illumina MiSeqDx Integration Package v1.9 supports the integration between Clarity LIMS and MiSeqDx instruments. The integration allows for automated tracking of an Illumina sequencing run in Clarity LIMS and includes the following functionality:

• Tracking instrument run status.
• Generating a run report.
• Capturing and parsing run statistics.
• Uploading variant call files to the LIMS.

In addition, this integration provides automated generation of a sample sheet file for use with the MiSeq Operating Software (MOS).

This documentation describes the integration between Clarity LIMS and the MiSeqDx system. It includes information about protocols and automations, configuration options, installed components, and rules and constraints.

• MiSeqDx RPM that supports Diagnostic (Dx) mode.
• MiSeq RPM that supports Research (RUO) mode.
• Preconfigured Clarity LIMS protocols that map to library prep and sequencing lab protocols and instrument runs.
• Preconfigured protocols that allow for validation of the sample sheet generation and index placement functionality.
• Automatic generation of:
– A sample sheet file for use with the MOS (Diagnostic mode) instrument software.
– A run report, which includes the current run statistics.
• Automated tracking of the following information in Clarity LIMS:
– Progress and metrics of a MiSeqDx sequencing run
– Per-instrument sequencing runs
– Sequencing run parameters
– Real-Time Analysis (RTA) run directory location and other run specific information
• The ability to monitor the run status (cycle number) across multiple instruments from within Clarity LIMS.
• The ability to attach Variant Call Format (VCF) files to Clarity LIMS.

The following protocols are included in MiSeqDx Integration Package v1.9:

• CF 139-Variant Assay Library Prep 1.1
• CF Clinical Sequencing Assay Library Prep 1.1
• Universal Kit Library Prep 1.1
• SBS MiSeqDx (CF 139-Variant Assay) 1.1
• SBS MiSeqDx (CF Clinical Sequencing Assay) 1.1
• SBS MiSeqDx (Universal Kit) 1.1

There are three validation protocols. Each protocol is included in a workflow with the same name. The protocols are as follows.

• MiSeqDx Validation (CF 139-Variant Assay) 1.1
• MiSeqDx Validation (CF Clinical Sequencing Assay) 1.1
• MiSeqDx Validation (Universal Kit) 1.1

In Assay workflows, include a QC validation protocol between the Library Prep and Illumina SBS protocols. The default workflow does not include a QC protocol.

Each validation protocol includes the following steps from the Library Prep and SBS MiSeqDx protocols:

• Extension-Ligation of Bound Oligos (Library Prep step)
• PCR Amplification (Library Prep step)
• Library Pooling (MiSeqDx) (SBS MiSeqDx step)
• Denature, Dilute and Load Sample (SBS MiSeqDx step)
• MiSeqDx Run (MiSeqDx) (SBS MiSeqDx step)
• Variant Calling (MiSeqDx) (SBS MiSeqDx step)

For instructions on using the MiSeqDx Validation (CF 139-Variant Assay) 1.0 protocol to validate automated sample sheet generation, see MiSeqDx Integration v1.9 Validation and Troubleshooting.

The following table lists the automations included in this integration, and the steps on which they are configured.

MiSeqDx Integration Default Automations

Protocol

Steps & Automations
• CF 139-Variant Assay Library Prep 1.1
• Universal Kit Library Prep 1.1

On PCR Amplification (CF 139-Variant Assay / Universal Kit) 1.1 step:

• Auto Place Indexes
• Validate Index Placement
• Illumina SBS MiSeqDx (CF 139-Variant Assay) 1.1
• Illumina SBS MiSeqDx (CF Clinical Sequencing Assay) 1.1
• Illumina SBS MiSeqDx (Universal Kit) 1.1

On Library Normalization (MiSeqDx) 1.1 step:

• Create Normalization CSV
• Illumina SBS MiSeqDx (CF 139-Variant Assay) 1.1
• Illumina SBS MiSeqDx (CF Clinical Sequencing Assay) 1.1
• Illumina SBS MiSeqDx (Universal Kit) 1.1
• MiSeqDx Validation (CF 139-Variant Assay) 1.1
• MiSeqDx Validation (CF Clinical Sequencing Assay) 1.1
• MiSeqDx Validation (Universal Kit) 1.1

On Denature, Dilute and Load Sample (CF 139-Variant Assay / CF Clinical Sequencing Assay / Universal Kit) 1.1 step:

• Generate MiSeqDx Sample Sheet
• Validate Container Name
• Illumina SBS MiSeqDx (CF 139-Variant Assay) 1.1
• Illumina SBS MiSeqDx (CF Clinical Sequencing Assay) 1.1
• Illumina SBS MiSeqDx (Universal Kit) 1.0
• MiSeqDx Validation (CF 139-Variant Assay) 1.1
• MiSeqDx Validation (CF Clinical Sequencing Assay) 1.1
• MiSeqDx Validation (Universal Kit) 1.1

On MiSeqDx Run (MiSeqDx) 1.1 step:

• AUTOMATED - Run Report Generation
• Verify Report Status

As of Clarity LIMS v5, the term user-defined field (UDF) has been replaced with custom field in the user interface. However, the API resource is still called UDF.

There are two types of custom fields:

• Master step fields—Configured on master steps. Master step fields only apply to the following:
• The master step on which the fields are configured.
• The steps derived from those master steps.
• Global fields—Configured on entities (eg, submitted sample, derived sample, measurement, etc.). Global fields apply to the entire Clarity LIMS system.