The Workbench is the main view from a case, which includes the most important information for the analysis of the sample. As soon as a case has completed processing, you will start your evaluation from this page.
On the top area, right by the case name, there are a few interesting options for a user regarding case management:
Date of creation and user that uploaded the sample
Assigne and status, where you can modify accordingly
A button to Follow Case, in which case you would get automatic emails every time a variant in the Workbench has new evidence that can lead to its reclassification. This is one of the streamlined reanalysis features integrated into Franklin.
A drop-down menu to export several files, such as the VCF, FASTQ, or BAM for the case.
The Workbench is divided into three main sections:
Quality Control
The Quality Control section appears collapsed by default, but you can expand it by clicking on "See details". Depending on the case type and the assay configuration, the QC metrics shown in this section may differ.
When analyzing family cases, each family member will get a tab with the corresponding QC metrics for their sample, as well as several automatically calculated metrics such as Consanguinity Check, Family Relationship Check, and UPD Check.
Franklin's bioinformatics team has set up default thresholds for the most common QC metrics. If a value is outside of the appropriate range, Franklin will show a warning sign in red. You can also place the cursor over the metric result to see a short explanation of each metric.
Pro tip: Did you know that Franklin Professional supports more than 50 out-of-the-box QC metrics, and most custom ones as well? We can even adjust the thresholds to fit the pass/fail criteria for your specific organization.
Analysis Results
The Analysis Results section shows the variants that were selected by Franklin's AI-driven prioritization engine as clinically relevant for the case. This allows you to start your case analysis by reviewing the variants that are more likely to be causal for the conditions, to reach faster results.
Franklin's prioritization algorithms are complex, but in essence, they take into account:
The variant's ACMG classification, automatically calculated by Franklin
The variant's Confidence metric, which takes into account QC, calling, and alignment metrics, as well as allele balance.
The relation between phenotypic and genotypic information, considering the HPO terms introduced by the user in the Case Details section.
The inheritance mode of the diseases associated with the gene.
To learn more about Franklin's prioritization engine, check out this article.
The variant tile shows us different high-level information depending on the type of variant. For SNPs, we can visualize (from left to right):
Franklin's automatic ACMG classification (color-coded band)
Aggregated frequency from gnomAD
Internal frequency, from your own repository of cases
Confidence, with allele balance
Aggregated prediction from in silico prediction tools
Gene inheritance
ClinVar classifications (color-coded world icon)
For CNVs, we can visualize (from left to right):
Franklin's automatic ACMG classification (color-coded band)
Occurrences from DGV and gnomAD
Internal occurences, from your own repository of cases
Confidence
Gene inheritance, for all the genes/regions included in the variant.
Upon clicking on the arrow located on the right-most edge of the tile, Franklin shows an expanded view of the metrics, with more details regarding the different insights from a wide range of databases.
Upon clicking on the gene name or the "Full detail view" button, you can access the Variant Interpretation hub. In this popup window, you find all the evidence available for the variant, the gene(s), and the condition(s), centralized in Franklin from more than 100 different databases, as well as the unique information only available for the Franklin Community.
For more information regarding this view, go to this article.
Finally, by clicking on the "Classify" button for the variant to issue your classification within the case. You can save that classification as internal, or share it with the rest of the Franklin Community (which is not required but highly encouraged). You can learn more about Franklin's sharing policy in this article.
Case Details
The Case Details section shows you all the metadata from the case you inputted into Franklin when creating the case. It also lets you edit this information, including phenotypic information, and apply virtual panels at the case level. For more information regarding virtual panels, check out this article.
The Case Details section shows:
Patient information, including sex, date of birth, ethnicity, family history, and physician comment.
Sample details, including ordering physician and specimen type
Phenotypes, divided by body system
Case comments, where any one of the users from the organization can document case-level observations
Panels, both soft and hard
Family members, in the context of Family Cases
By clicking on the "Edit" button on the top right, a user can edit any of the details during the case analysis.
Pro tip: did you know that these fields are customizable? Franklin Professional users can choose what type of information to include in the Case Details section, as part of their Onboarding process!
Still have questions? Reach out to our Support Team, they'll be happy to help!