We are happy to introduce several enhancements and new features in our latest update:
CMA Family Case Creation via UI
We have added a new case type in Franklin - CMA Family. This case allows you to analyze CMA samples in a case structure similar to the Inherited Disease (germline) Family case.
Creation of a CMA Family case is available on the New Case popup:
The Sample Repository only allows to search and select CMA single samples, which were previously created in your organization. Drag-and-drop samples onto family members, similar to a germline family case.
Similar to a germline family case, the CMA Family case includes a pedigree and related information, as well as links to the single cases. Family zygosity is displayed in Variant Assessment tab. Inheritance models are calculated, allowing filtration using the SV Inheritance filter, as available in other case types containing SVs.
LOHs are displayed and filterable for the proband, similar to CMA single cases. LOHs do not display family zygosity, nor do they undergo inheritance model calculation. Accordingly, when using the Inheritance filter, LOH variants will always pass. As in CMA single cases, SNV information is not available in CMA Family cases. Hence, such cases will not contain SNV-based QC metrics or biomarkers.
Configuring Hard Panels to Apply Only to SNVs
In germline workflows, a hard panel can now be configured to apply exclusively to SNVs, without extending to CNVs. This makes it possible to analyze SNVs only from the panel, as well as CNVs located outside of it. When this configuration is enabled, the assay’s hard panels will not appear in the Panels filter of the SV Variants tab. Notably, coverage calculation will not be impacted (i.e. will still be calculated for the panel’s genes). This enhancement is particularly valuable for whole exome workflows that rely on oligonucleotide probes for enhanced backbone capture. To enable this for your assay, please contact our support team.([email protected]).
Import Somatic CNV to Knowledge Base
The Knowledge Base now supports importing CNV with somatic interpretations. The CNV template is available for download as a XLSX or TSV file as before, but now supports somatic interpretations in addition to germline interpretations.
Importantly, the updated template includes the new mandatory column “Classification System”, which requires filling a single value per row - germline or somatic. Notably, in a somatic variant row, only a single condition can be filled for that row.
Moreover, it is possible to submit sub-tiered classifications, e.g. “Tier 1A”, if this option is configured for your organization generally.
For more information on importing variants and the updated template, please visit the following Franklin Help Center article.
Internal Occurrences in Variant Search
When searching for a CNV in Franklin’s Search, the CNV’s Variant Assessment tab now includes the Internal Occurrence section, as exists for a variant in a case. Internal Occurrence shows the samples in your organization that have a similar CNV, i.e. that overlaps by 50% or more with the given variant.