We are happy to introduce several enhancements and new features in our latest update:
Broader Support for Snippet Library Across Franklin
The Snippet Library is now available in more places throughout Franklin, making it even easier to reuse standardized text across workflows. You can now insert snippets into gene summary, case details, somatic interpretations, variant comments, and all variant interpretation fields (including custom ones) - all with the same familiar interface introduced in interpretation fields, allowing quick insertion and editing of predefined content.
For more information on snippets, please refer to our Help Center article.
To enabled the Snippet Library for your organization, please contact our support team ([email protected]).
Custom Transcript-Based Gene Filtering in Family Cases
In Family cases, the Variants tab now supports searching for variants from the search bar, as well as filtering on variants using the Panel filter, based on organization-preferred transcripts of the variants’ genes. This capability was previously available in single cases, and is now available in family cases as well. Reminder: organization-preferred transcripts can be configured by contacting our support team ([email protected]).
Tumor Cases: Internal Sample Count Filter
In tumor (somatic) cases, we have added the “Internal Sample Count” filter to the Frequency filter section. The new filter allows for filtration of SNV variants by the number of tumor samples in your organization in which the variants appear. Variants returned by this filter are those that have VAF > 1% and a Confidence level other than Failed. If the “Include N/A” filter option is selected, then variants with VAF < 1% and a Confidence level of Failed will return as well.
Additionally, the “Internal Frequency” filter in tumor cases has been renamed to “SNV Internal Frequency” to better explain its function. An updated view of the Frequency filter section:
Tumor Cases: Extra VCF Annotations
Extra VCF Annotations are VCF fields that are not extracted and displayed by default in Franklin; our support team can be contacted to set up Extra VCF Annotations for an assay. Once configured, these annotations are displayed in a dedicated section on the expanded variant tile, and can be included in the Report. Previously available only in germline cases, Extra VCF Annotations are now available in tumor (somatic) cases for SNP, CNV, fusion and RNA variants. These annotations appear to the right of the Clinical Evidence section (see below) and can be included in the report.
Contact out support team ([email protected]) to set up Extra VCF Annotations for your assay.
Tumor Cases: Additional Fusion Variant Details in Exports
In tumor (somatic) cases, export of fusion variants from the Variants tab or the Workbench now include additional columns for fusion breakend gene, exon, and supporting reads.