We are happy to introduce several enhancements and new features in our latest update:
Tumor Cases: Clinical Trial Selection for the Report
In tumor (somatic) cases, the Case Summary tab now includes a dedicated Clinical Trials section, allowing you to select specific clinical trials to include in your report. This section displays trials that are relevant to the variants selected for reporting. The listed trials can be filtered by Location, Phase, or Status. Multi-selection of trials is supported, and a toggle is available for displaying only the trials currently selected for inclusion in the report.
More Precise Variant Prioritization using “Major Phenotype” Matching
A dataset of main phenotype categories per disease has been integrated into the genotype-phenotype model. This dataset was derived from the MONDO disease hierarchy, HPO phenotype terms, manual curation, and large language model (LLM)-generated output. It enhances the specificity of variant prioritization by lowering the genotype-phenotype score when none of the major phenotype categories associated with a condition are present in the patient’s phenotype data. As a result, genes with weaker clinical relevance may receive lower priority scores - potentially excluding them from the variant shortlist - while phenotype filtering remains unaffected.
Coverage Uniformity QC Metric
The Quality Control tab of the Workbench can now include a new metric for assays involving kit regions - Coverage Uniformity. This metric is defined as the percent of the kit regions covered with a depth that is 20% or more of the average kit region coverage depth. For example, if the average kit region coverage depth is 200, 20% would be 40; if 85% of the kit regions have a coverage depth of 40 or more, than the Coverage Uniformity would be 0.85. This QC metric may be required for complying with regional regulatory requirements, and is now available in Franklin. Contact our support team ([email protected]) to configure this QC metric for a relevant assay.
“See VCF Line” Available for Repeats and LOHs
The “See VCF” feature now supports Repeats and LOH variants. Reminder: this feature lets you quickly view the raw VCF line for a specific variant without the need to download the full VCF file or search manually. Contact our support team ([email protected]) to enable this feature for your organization.
Gene Summary in Variant Classification
The Gene Summary field is now included by default (i.e. not requiring configuration) when classifying a variant. This content appears in the classification and can be included in the final report. If your organization maintains curated gene summaries, they will be auto-filled. Otherwise, Franklin will display a summary sourced from RefSeq. The text is fully editable during classification, and any updates you make will be reflected in the report.
Case Automatically Refreshes upon Completion of a Family Re-analysis
In family cases, following the completion of Rerun family analysis, or when the process of changing the Affected status of a family member completes - the case will automatically update, not requiring a browser tab refresh if the case remained open during the re-analysis process.