Quality control

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Abbreviations

AP	Assay Plugin
CV	Coefficient of variation
FF	FastFinder
LIMS	Lab information management system
QC	Quality control
SD	Standard deviation

General info

The quality control (QC) module can be used for tracking your control results. Here, an overview of the trackings that are created is found. QC trackings can easily be added or inactivated. Using the filters, it is possible to quickly search a specific (sub)set of tracking(s), e.g. all available trackings for an Assay Plugin.

Activating the Quality Control module

To be able to use QC tracking in FastFinder, the QC module needs to be activated. This is either done automatically (by Velsera) when this module is part of the contract or activated at a later moment. In this case, users can activate the QC module in FastFinder. Velsera will then contact the customer to confirm the activation and perform the necessary actions to start using the QC module.

Setting up Quality Control tracking

To create a new QC tracking for an Assay Plugin, the following steps need to be done:

1. Navigate to the Quality control module.
2. Click Create new tracking. New QC tracking form opens.
   
3. Complete the information required to set up a tracking:

• Tracking type: 
  • Target result tracking: track target-related results over time of a Control sample type. The trackable control sample types include negative, positive controls, and quantification standards. 
  • Standard curve tracking: track parameters related to the standard curve over time.
• Tracking name: the name of the QC tracking.
• Assay: Select the Assay Plugin for which the tracking needs to be set up. 
• Instrument type: Type of the PCR instrument used. Only the instruments applicable for the chosen Assay Plugin are possible. Only one instrument can be selected per tracking. The Assay Plugin version is displayed in brackets.
• Instrument: Tracking can be performed across all available instruments or for a specific instrument.
• Sample type: Sample type to which the tracking is applied. The available options are related to the configured control sample types in the Assay Plugin, including Quantification standards. 
• Targets: Target(s) to which the tracking will be applied. If multiple targets are selected, a QC tracking will be created for each target. The target name will be added as a suffix to the Tracking name.

It is also is possible to define one or more QC setups per tracking. The following parameters need to be defined manually for each QC setup.

• Lot: The specific lot for which QC tracking will be performed.
• Metric: The metric that will be tracked over time.
  • Target result tracking includes the following metrics:
    • Cq 
    • Raw end fluorescence
    • End fluorescence
    • Concentration (available only for quantitative PCR assays)
  • Standard curve tracking includes the following metrics:
    • Efficiency
    • Slope
    • Y-intercept
    • R²
• Mean: Expected mean value of the tracked metric. Mean can have the following values:
  • Fixed: A single, fixed mean value.
  • Floating and fix after <Nr.> analyses: Use a floating mean value until the defined number of analyses is reached, after which a fixed value is used.
• Standard Deviation (SD)/Coefficient of Variation (CV in %): SC or CV boundaries of the tracked metric. Can be defined as:
  
  • Fixed: A single, fixed SD value.
  • Floating and fix after <Nr.> analyses: Use a floating SD value until the defined number of analyses is reached, after which a fixed value is used (only applicable for SD).

To add additional QC setups, click Add QC setup.

Note, it is only possible to set up a single tracking per Assay Plugin per time. If multiple trackings per Assay Plugin are required, they need to be configured individually. 

Within a QC tracking

If completely set up, a tracking can be easily accessed by opening the Quality control module and clicking the specific tracking.

General information about the tracking (configuration) is provided at the top of the screen. For each QC setup that is configured, information can be found in the dedicated block, and the metrics can easily be updated if needed.

The QC data will be visualized using a Levey-Jennings graph. This only includes data from tracked authorized runfiles with this plugin in FastFinder. Note that data is not tracked historically and retrospectively. In the graph, you can click on a certain data point and have the ability to go to the applicable Target Results if desired.  

If a metric is updated during the tracking, in the Historic tracking configurations section there is an overview of the adaptations made during the tracking period. It is also mandatory to add a comment when changing one of the metrics.

It is also possible to activate multiple QC setups (for multiple metrics) per tracking, either during initial setup or later on. These can be activated or inactivated by toggling the button next to the QC setup (metric).

 

Quality control settings

To access Quality control settings for a workflow, go to Settings > Quality control. Inside quality control settings, configure the following options:

• • Automatic failure: If enabled, automatically marks all samples as failed when a QC violation occurs. To enable, select a Failure reason and click Save.
  • Westgard rules: If enabled, applies Westgard rules to all active QC visualizations.

Westgard rules

Alerts in FastFinder Analysis can be set up via Westgard rules. They can be configured either per tracking, or for all trackings simultaneously.

To define Westgard rules for a single tracking, access the settings within the tracking in the QC module. A fly-over screen will open allowing you to activate the relevant rules.

Rules can be activated by toggling the button, after which they will be applied to new analyses. You can choose if you want to implement one or more Westgard rules. If all rules are toggled off, no warning or error messages are received upon tracking. However, in the QC module itself, you can always follow up on the control results.

To set up Westgard rules for all active trackings, see Settings - Quality control.

(In)activate a tracking

When a certain tracking is no longer relevant, it can be inactivated. This can be done as follows:

1. Navigate to the Quality control module in FastFinder.
2. Go to the QC tracking that needs to be inactivated (either by selecting it from the list or by using the search field).
3. Select the tracking.
4. In the top right corner, toggle the Active button to inactivate the QC tracking. 
   

Note: It is always possible to access and/or reactivate a tracking that has been inactivated by accessing the tracking again and toggling the Active button. To see all inactive trackings, open the Inactive tab in Tracking overview:

 

Quality Control integration in Analysis

Quality Control is also integrated in the Analysis module on the FastFinder platform, which allows you to easily access QC tracking data. This includes data per target and per control type for which QC tracking is enabled, for example historic tracking over time and possible violations, etc.

Under the Summary tab of an analysis, the Control Results section shows whether or not the control complies with the conditions specified in the QC module. This is where you can quickly review the status of QC tracking. 

For more detailed information, navigate to the Quality control tab within the Analysis module. This tab contains all details regarding QC tracking. Data is shown for each target per control sample type, including the Levey-Jennings chart displaying the tracked historic data over time. 

In case of a violation of the Westgard rules, this information can be found under the relevant target. A violation is handled as an error notification and therefore always requires manual review. There are two options to handle a violation:

• Confirm
  You agree with the violation, which will result in the control sample that is made invalid. The point in the Levey-Jennings chart will be shown in red. It is up to you to decide whether to mark all samples for this assay for retest because of this violation or not (see explanation below). In the analysis itself, the decision tree will be executed taking into account an invalid control sample. 

• Ignore
  You accept the data as it is and the control will be considered as valid according to the QC. You can proceed to authorize the analysis. In the Levey-Jennings chart, the point will be shown in black. Note: In this case, it is mandatory to enter a comment that is added to the audit trail. 

You can also choose to fail all samples for the particular assay, invalidating all samples in the analysis. This will also be shown in the Analysis results CSV. 

You can export the results of the QC tracking in the Analysis results CSV. Both the quality control results and QC-related notifications on target level can be visualized in the report:

• QualityControlResult
  Outcome of the QC evaluation based on the implemented QC trackings and Westgard rules of control samples. This is indicated as Valid or Invalid. 

• Target_x_QCnotifications
  QC notifications related to Target x (e.g. Warning: Violation of Westgard rule(s) 1:2s)

• ControlValidity
  Both the QualityControlResult (described above) and the control validity of the assigned controls (regular assay target from PCs/NCs in the control results section) are reported. If one of them is invalid, ControlValidity will be reported as invalid.

Customization of the Analysis results CSV (to include or exclude the above parameters) can be done in FastFinder under Settings > Analysis results CSV. As the CSV is exported to the LIMS system, it is important to ensure that any changes made in the CSV are supported by the LIMS platform. It is recommended to contact your local IT department for more information on this topic.

Relevant articles

Settings - Quality control