Version 91 Updates

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

In Variants tab, the gnomAD Exome and gnomAD Genome filters, which belong to the Frequency filter section, are now grouped into dedicated sub-sections. Each sub-section displays a blue dot badge when at least one of its filters has a value.

In addition, the Frequency filters “gnomAD (Exome)” and “gnomAD (Genome)” have been renamed to “gnomAD (Exome) Freq” and “gnomAD (Genome) Freq”, respectively.

Both changes can be viewed in the following illustration:

This more compact and organized layout helps you find and manage filters more efficiently.

The Curated Gene Data tab is now available in the popup of SVs (in addition to SNP variants). For multi-gene SVs, the tab displays the number of genes included with easy navigation between them.

In a germline SNV variant page in both case and the search, a new Confidence column is now available in the Internal Frequency widget:

This column shows the confidence of the variant call for each sample it was called in across the organization’s repository.

Excel exports from the Variants tab now include additional information. The "Quality" column is now included not only for germline SNP, but also for somatic SNP and germline and somatic SV. A new “Filter tree labels" column has been added to the export for germline SNP, providing all Filter Decision Tree labels assigned to a variant during annotation. The “Internal Sample Count” and “User Classification” columns in the email export have been populated similarly to their counterparts in the immediate “online” download export, but using the variant information available during annotation, and without the internal frequency information for the “Internal Sample Count” column. Columns related to case actions (“Include in Report” and “Clinically Irrelevant”) have been removed from the email export as they do not contain information during case annotation; these columns remain available in the immediate download export.

You can now create hidden Single cases using Franklin’s API. This allows you to add single cases that remain hidden after creation, helping keep your My Cases view uncluttered when the single cases are not of direct interest, e.g. when only a Family case created from these cases is of interest. Furthermore, Franklin’s API now also allows to retrieve hidden analyses, making it possible to programmatically check for the existence of hidden cases, e.g. when validating that a hidden case has been created. For more details, please visit Franklin API documentation (https://api-docs.genoox.com/).

In Assets, under the Samples section, you now receive more informative warnings when deleting samples. Before deleting a sample, a confirmation popup displays any associated single cases that will also be deleted:

If the sample is linked to family cases and hence cannot be deleted, the popup instead lists the associated family cases:

After the closing the popup, the sample that could not be deleted remains visible in the sample list. This enhancement helps you understand the impact of deleting a sample.

In tumor (somatic) cases, the Transcript IDs for both genes involved in a fusion (e.g., NM_...) are now displayed for fusion variant. In Variants tab, both Tile View and Table View include this display:

In tumor (somatic) cases, when searching for a fusion in Variants tab by gene name or panel, the search also considers now the fusion’s gene 3’ gene (fusion mate), and not only the 5’ gene. Hence, searching either of the fusion’s genes will include the fusion in the search results. This enhancement therefore provides more comprehensive information when searching for gene fusions.

In CMA Family cases, the "Number of probes" annotation is now available for SV. In Variants tab, you can view this information on the expanded tile and use for filtering, similar to single CMA cases.

Fixed an issue in Case Details and New Case pop-ups, where a pasted phenotype that includes commas and contains two valid HPO terms (e.g., "Intellectual disability, mild") was incorrectly split into multiple phenotypes. When pasting a list of phenotypes, only semicolons are now recognized as separators between the phenotypes.