The "My Cases" tab displays all cases you've created, whether by uploading a VCF, FASTQ files or by manually selecting variants.
Within the 'My Cases' screen, each case is represented by a tile, featuring the case name, workflow icon, and dedicated assay information.
To start your analysis click on the chosen case from the list or use the search bar to directly find it by case name.
Franklin is designed to help you manage the case analyses and to highlight the suspected case variants in a workbench view, which is the homepage when entering a case.
The interpretation workflow begins with automatically prioritized variants in the workbench. For a more comprehensive assessment, you can then explore variants using either preserved filters or a dynamic filtering strategy. Finally, you can manually prioritize variants to the workbench for their final assessment and reporting.
First quality assurance step is available through the sample Quality Control tab before initiating the case analysis process.
Case data, such as patient information, case phenotype, selected panels, and family pedigree (if applicable), are accessible within the workbench.
In the Analysis Results section, Franklin displays a shortlist of the most relevant variants, found by the Franklin A.I. prioritization engine.
For more information about variant priority in Franklin please visit "Franklin's AI-based variant prioritization engine" article.
💡 Adding case phenotypes, helps Franklin to improve the accuracy of the prioritization algorithm and to display better analysis results.
After screening the sample parameters and updating the case data it is time to review Franklin’s suggested variants in the analysis results.
For more information about the workbench tab in Franklin please visit "Working in the Workbench" article.
To review the full variant list of the case, click on the "Variants" tab in the sidebar menu on the left or the link to the variant list at the bottom of the page.
In tha variants assessment tab use filters to narrow down the results by relevance, or search via specific gene or phenotype to discover additional relevant variants.
For more information about filtering variants in Franklin, please visit "Franklin's Advanced Filtering System " article.
Saved filter sets can be created for your organization to unify filtering strategies across your team, improving workflow and meeting specific needs.
For more information about filtering strategies, visit " Creating and Managing Quick Filter Presets for Variant Triage in Franklin " and “Creating and Managing Filter Decision Trees “articles.
To assess variants thoroughly and access all relevant information click on the gene name in the variant tile to open the "Variant interpretation hub" popup.
Here, you can find multiple annotations and evidence, associated with the variant, including Franklin's suggested ACMG based classification, relevant articles, phenotypes, and more.
If you find any other relevant variants for the case, add them to the workbench for further discussions and review. You can manually add variants to the workbench, using the action widgets at the right side of the variant tile:
or in the Variant interpretation hub popup:
After exploring the variant data and to complete the variant interpretation, Classify the variants according to your findings and conclusions.
Access the classification tab from the action widgets or from the variant interpretation hub.
💡 Embrace the power of the Franklin community, use the variant community feed. Share your classification, browse the data other members added, and consult with the community members to improve your classification.
Now you can finalize the case and choose the variants to report from the workbench. For more information about reporting from Franklin please visit "Including Variants in the Report " article.
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