The Illumina MiSeqDx Integration Package v1.10.0 supports the integration between Clarity LIMS and MiSeqDx instruments.
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.
The following protocols are included in MiSeqDx Integration Package v1.10.0:
CF 139-Variant Assay Library Prep 1.2
CF Clinical Sequencing Assay Library Prep 1.2
Illumina SBS MiSeqDx (CF 139-Variant Assay) 1.2
Illumina SBS MiSeqDx (CF Clinical Sequencing Assay) 1.2
Illumina SBS MiSeqDx (Universal Kit) 1.2
Universal Kit Library Prep 1.2
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) 1.2
MiSeqDx Validation (CF Clinical Sequencing Assay) 1.2
MiSeqDx Validation (Universal Kit) 1.2
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 Illumina SBS MiSeqDx protocols:
Extension-Ligation of Bound Oligos (Library Prep step)
PCR Amplification (Library Prep step)
Library Pooling (MiSeqDx) (Illumina SBS MiSeqDx step)
Denature, Dilute and Load Sample (Illumina SBS MiSeqDx step)
MiSeqDx Run (MiSeqDx) (Illumina SBS MiSeqDx step)
Variant Calling (MiSeqDx) (Illumina SBS MiSeqDx step)
For instructions on user interaction for each step and using the MiSeqDx Validation (CF 139-Variant Assay) 1.2 protocol to validate automated sample sheet generation, refer to MiSeqDx Integration v1.10.0 User Interaction, 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
Step
Automations on Step
CF 139-Variant Assay Library Prep 1.2
Universal Kit Library Prep 1.2
PCR Amplification (CF 139-Variant Assay/Universal Kit) 1.2
Auto Place Indexes
Validate Index Placement
Illumina SBS MiSeqDx (CF 139-Variant Assay) 1.2
Illumina SBS MiSeqDx (CF Clinical Sequencing Assay) 1.2
Illumina SBS MiSeqDx (Universal Kit) 1.2
Library Normalization (MiSeqDx) 1.2
Create Normalization CSV
Illumina SBS MiSeqDx (CF 139-Variant Assay) 1.2
Illumina SBS MiSeqDx (CF Clinical Sequencing Assay) 1.2
Illumina SBS MiSeqDx (Universal Kit) 1.2
MiSeqDx Validation (CF 139-Variant Assay) 1.2
MiSeqDx Validation (CF Clinical Sequencing Assay) 1.2
MiSeqDx Validation (Universal Kit) 1.2
Denature, Dilute and Load Sample (CF 139-Variant Assay / CF Clinical Sequencing Assay / Universal Kit) 1.2
Generate MiSeqDx Sample Sheet
Validate Container Name
Validate Single Input
Illumina SBS MiSeqDx (CF 139-Variant Assay) 1.2
Illumina SBS MiSeqDx (CF Clinical Sequencing Assay) 1.2
Illumina SBS MiSeqDx (Universal Kit) 1.2
MiSeqDx Validation (CF 139-Variant Assay) 1.2
MiSeqDx Validation (CF Clinical Sequencing Assay) 1.2
MiSeqDx Validation (Universal Kit) 1.2
MiSeqDx Run (MiSeqDx) 1.2
AUTOMATED - Run Report Generation
Verify Report Status
This section discusses the index placement and validation automations configured on the PCR Amplification 1.2 Library Prep steps.
The example workflow uses the CF 139-Variant Assay Library Prep 1.2 protocol.
By default, in the CF 139-Variant Assay Library Prep 1.2 and the Universal Kit Library Prep 1.2 protocols, the PCR Amplification 1.2 step includes two automations. Both automations invoke the place_indexes script with different options.
Auto Place Indexes — Automatically invoked on entry to the Add Reagents screen.
⚠ For the Auto Place Indexes automation, if an 8-sample reagent category/label group is selected, index placement must be performed manually.
ℹ The CF Clinical Sequencing Assay Library Prep 1.2 protocol only uses 8-sample reagent categories/label groups. Hence, index placement must be performed manually.
Validate Index Placement — Automatically invoked on exit from the Add Reagents screen.
A list of reagents installed with this configuration is provided in Installed Components.
Good laboratory practices mandate that a positive control DNA sample and a negative (no-template) control sample are included in every run. The positive control DNA sample should be a well-characterized sample with a known CFTR mutation.