Configure a QC System

Follow these steps to configure the out-of-the-box QC solution to meet the needs of your lab:

• Remove unnecessary QC steps. (See Remove QC steps )

• Configure master step fields for QC aggregation. (See Configure Master Step Fields for QC Aggregation)

• Configure QC evaluation criteria. (See Configure QC Evaluation Criteria)

• Specify QC master step field values to copy up to aggregation. (See Copy Master Step Fields)

Remove QC steps

Clarity LIMS includes preconfigured RNA Initial QC, DNA Initial QC, and Library Validation QC protocols, each containing a sequence of steps. You can modify these protocols, and remove steps that your lab does not use.

1. On the main menu, click Configure.

2. On the LIMS configuration screen, click the Lab Work tab.

   The Workflow, Protocol, Step, and Master Step navigation panel displays.

3. In the Protocol list, select the protocol you want to modify.

   The Workflow, Protocol, Step, and Master Step navigation panel displays.

4. To delete a step, select it and click the Delete button.

You cannot remove a step if it contains samples that are currently in progress, or if there are samples queued for it.

In this scenario, you must move the samples before proceeding with the deletion. For details, see Manually Moving Samples to the Next Step.

Configure Master Step Fields for QC Aggregation

In the default BaseSpace Clarity LIMS configuration, the Aggregate QC step aggregates the results of all QC steps in the protocol—if they are available.

If a step has been removed from a QC protocol, it is ignored and aggregation still occurs for the remaining steps. No error is generated.

QC Aggregation Logic

The following flowchart shows the logic behind the default configuration of QC aggregation.

Often, this default configuration is acceptable and there is no need to make any changes. However, you can configure alternate QC master step field values that overwrite these defaults. For example, you may want to:

• Make a particular step required for aggregation.

• Increase the priority of the results of a particular step – a step whose results are considered more accurate, for example.

• Make one/both of the changes listed above, and then lock down values so that users cannot modify them.

Aggregation Master Step Fields

The Aggregate QC master step includes a master step field for each QC step to be considered for aggregation.

The value for the QC master step field may be one of two values:

• Use if available: If the QC step was run run for a sample, its value will be used in the aggregation calculation; if the QC step was not run, it will be ignored.

• Required: The step is required for aggregation. If it has not been run for a sample, the QC value cannot be calculated and aggregation will not proceed.

The default setting for all QC steps is Use if available.

Aggregation Priority

The Required and Use if available master step field values can have an additional (Priority n) suffix.

Acceptable Values

To be an acceptable value, the value for 'n' may be any value between 1–99, where 1 is the highest priority and 99 is the lowest priority. Master step fields without a priority value defined are assigned a priority of 99.

Default Value

The default priority value for all QC steps is (Priority 5).

How It Works

If sample measurements exist for multiple QC steps, all of which have been assigned the same level of priority (as is the case in the default system) the QC flags are evaluated such that any failure results in an overall fail flag for QC aggregation.

Sometimes, however, a particular QC technology may be considered more accurate and you may want its results to take precedence.

For example, a lab may run Bioanalyzer and NanoDrop QC steps on all samples. If one of these steps results in a QC fail, a PicoGreen assay is run on the failed sample and its result is then considered more accurate. In this case, set Bioanalyzer and NanoDrop at priority 5 and PicoGreen at priority 3.

All QC aggregations are logged in an Excel workbook log file and attached to the Aggregate QC step.

Subsequent invocations of the aggregation script results in a new sheet being created in the workbook, in the first sheet position. This new sheet automatically becomes the active sheet.

Configuring alternate master step fields for QC aggregation

The best practice method for configuring alternate master step field values for QC aggregation is to create a group of defaults. The fields defined in the group overwrite the default configuration values.

For details, see Add and Configure Custom Fields.

The aggregate QC script treats any custom field that does not begin with 'Copy' as a priority master step field. Therefore, you are restricted from adding fields that are not priority fields. Any new priority fields must contain default values of Required and Use if available.

Locking down master step fields

If you do not want lab scientists to be able to manually edit a master step field value, lock it down by setting the Custom Entries toggle switch to No. At run time, the lab scientist must select a value from the predefined drop-down list.

Configure QC Evaluation Criteria

In the default Clarity LIMS system, each QC master step has two sets of QC evaluation criteria defined. These are displayed in the Record Details screen when the QC step is run.

Each set of criteria comprises three master step fields: Source Data Field, Operator, and Threshold Value.

When the QC protocol step is run, the lab scientist selects from the prepopulated drop-down lists of Source Data Field and Operator values, and then types a numeric value into the Threshold Value field.

Configuring QC criteria fields

You may want to restrict the values available for selection from the Source Data Field and Operator lists, or set default criteria values that cannot be changed.

The best practice method for configuring the criteria used to evaluate QC protocol steps is to create a group of defaults. The master step fields defined in the group overwrite the default configuration values.

For details, see Configure Groups of Defaults.

Copy Master Step Fields

In the default Clarity LIMS system, when QC aggregation is executed, the Record Details screen allows lab scientists to (optionally) select one or two master step field values to be copied up from a QC protocol step.

Generally, this is a concentration value.

If necessary, you can specify the master step field values to be copied.

The best practice method of setting master step fields to be copied up to aggregation is to create a group of defaults. For details, see https://github.com/illumina-swi/clarity-core-docs/blob/main/docs/clarity-lims-v6.3-reference-guide/automated-quality-control/broken-reference/README.md.

Setting QC master step fields to copy up to aggregation is an optional step. If you do not require this feature, leave the default system as is. Note also that if the Copy task fields are left empty, no values are copied up and no errors are generated. Similarly, if you specify a QC step that has not been run or a field that contains no value, no errors are generated.