We are happy to introduce several enhancements and new features in our latest update:

To maintain lab-defined SOP steps and enhance consistency in variant triage across users, Quick Filters now support specific actions without modifying their filter settings. Users can perform gene searches, add panels, change sorting preferences, and modify phenotypes without triggering a new variant search.

As a result, the filter panels on the left side of the screen will now be locked, preventing changes to the filter settings beyond the permitted actions mentioned above.

For users who need to revert to the previous behavior, please contact the Genoox support team ([email protected]).

The number of probes is now included as an annotation for CNVs and LOH. The value is presented in the extended tile, and a filter is added under the Confidence filters. The filtering function allows you to manually enter upper and lower ranges, marking variants without this metric as N/A. If "include N/A" is selected, all variants lacking this value will be shown. This addition enhances your ability to work with AED files, CGH array files, and Alissa CMA migration flow data by offering more precise data management and reporting options.
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You can now add or remove variants from existing organization variant lists directly through the UI. Adding to multiple lists is supported, and removing presently removes a variant from all assigned lists. This functionality is available during variant selection as well as from the variant tile. When adding to a list, you can the apply supplemental actions "Not Relevant" and "Add to Workbench", which affect the current case only. The Variant List filter remains unchanged and continues to filter based on list membership at the time of case creation (annotation). For the initial creation of organization variant lists, please contact our Support team ([email protected]).
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You can now utilize new gnomAD filters in tumor cases with dynamic filtering options. This enhancement supports both hg38 and hg19 reference genomes and introduces the following filters for SNV/indel analysis: gnomAD frequency (Exome-v2.1 hg19, and Genome v4.1 hg38, Allele Count, Hom Number, Hemi Number.

In tumor cases, variant oncogenic classification in line with ClinGen-CGC-VICC classification system is now available:
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Oncogenic classification can be performed from the Variant Interpretation full view, or the sidebar. You can save classifications as draft or final, and once saved, the chosen classification is marked on the variant tile and added to My Organization Assessments and the Knowledge Base. The classifications will be displayed with a special tag, for example “O” for “Oncogenic”:
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As in other classifications in Franklin, you can now edit Franklin's oncogenic computed classification. You can adjust rule properties such as Met/Unmet status and strength, and then preview how these changes affect the classification.
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Finally, you can now effortlessly apply Franklin’s suggested oncogenic classification to a variant in a single click. This will also add the oncogenic classification criteria to the variant assessment
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Resolved an issue with exporting a list of CNVs to Excel where the start positions were displayed incorrectly.

Resolved an issue in the tree builder where filters created from a panel were displaying the panel's UUID instead of its name. Now, the actual name of the panel will be correctly shown.
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