Franklin Solutions for Virtual Panels Overview
Franklin offers powerful solutions for managing and filtering variant data according to gene lists or pre-defined panels. In this article, we will explore the two types of virtual panels supported in Franklin, how to manage them in Franklin’s knowledge base, and the additional features of panels analysis.
Two Types of Virtual Panels Supported in Franklin
Franklin supports two types of virtual panels:
Hard Panels: This panel filters analysis results as part of the sample processing step and presents only variants that pass the panel filtering. It cannot be removed or changed by the user during the analysis process and is intended to avoid unwanted incidental findings. The panel can be configured by a list of genes or using a bed file.
Soft Panels: This panel consists of a list of genes and filters the variant list according to the gene list. Soft panels can be edited, removed, or added during the analysis process. For each gene, both panels can be set to use a specific transcript or use all transcripts.
Managing Virtual Panels in Franklin's Knowledge Base:
Both panels are managed in Franklin’s knowledge base. Creating a new gene panel can be done by following the instructions provided. There are two ways to create a case with a hard panel in Franklin:
Selecting a hard and soft panel during the case creation process - learn more here
Configuring default panels (hard and soft) as part of the assay configuration. This is done as part of Franklin's implementation program specifically designed for virtual panel workflows.
Utilizing Hard and Soft Panels Together for Optimal Results:
One way to utilize these features is to set an assay with both a hard panel and a soft panel. For example, configuring an assay for a long QT syndrome test over a whole exome sequencing that will have a hard panel called “Arrhythmia and Cardiomyopathy Comprehensive” that includes 168 genes and a core virtual panel called “Long QT syndrome.” The analyst can start working on the variants in the ‘core virtual panel,’ and only if no reportable variants found, he will be able to remove the virtual panel and analyze all of the genes in the expanded hard panel.
Case panels as displayed in the Workbench
Additional Features of Panels Analysis:
Evaluating Gene Coverage in the Panel: To evaluate the coverage of the genes in the panel, navigate to the coverage report that will be filtered according to the soft or hard panel.
Influence of Panels on Quality Control Metrics and Final Reports: The panels also influence the Quality Control metrics and the final report by displaying the genes analyzed and calculating regions of limited coverage.
Conclusion:
Franklin's solutions for virtual panels offer a powerful tool for managing and filtering variant data according to the gene list or pre-defined panels. Hard panels prevent unwanted incidental findings, while soft panels can be edited, removed, or added during the analysis process. By utilizing both hard and soft panels together, analysts can achieve optimal results. Franklin's knowledge base provides all the information needed to create new gene panels, select panels during the case creation process, and configure default panels as part of the assay configuration. Additionally, the coverage report provides a way to evaluate gene coverage in the panel, while the Quality Control metrics and final reports display the genes analyzed and calculate regions of limited coverage.
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