Franklin is data-driven by nature. On top of the evidence from publicly available data sources and the insights from the Franklin Community, the platform helps you build your own organizational genetic data repository and integrate it into future case analysis.
To access your Franklin knowledge base, simply click on the KNOWLEDGE BASE button on the top center of the platform. In this application, you can find your organization's past clinical evidence, curated by you or other users from your organization.
The knowledge base is divided into three sections:
Panels
All Franklin organizations come with some default panels, including the ACMG Secondary Findings list of genes. In addition, you can create your own custom virtual panels, which will be saved to the Knowledge Base and shared with the rest of your organization. If you'd like to know more about creating virtual panels, head over to this article.
Genes
This section presents all curated information at the gene level. This feature can help you review in detail all the available information regarding the genes that are relevant to your organization, including the ones that are part of a Virtual Panel you've created. Each tile represents a gene, and by clicking on it the Gene hub pops up, which comprises several tools:
Gene Assessment: In this tab, users can access a short summary of the gene, curated by Franklin's team of genetic experts, alongside their own organization's curated information. The platform also displays metrics for the Variant Distribution of the gene and the Gene Pathogenicity, aggregating data from renowned data sources such as ClinVar, UniProt, ClinGen, gnomAD, and the Franklin Community.
Publications: For this tab, Franklin scrapes the web for genomic literature from several well-known databases using its AI-based NLP Publication Engine. This tool provides you with processed and prioritized scientific articles that mention the gene of interest and gives you access to the abstract and link to the original publication. If you're looking to learn more about Franklin's Publication Engine, go to this article.
Associated Conditions: The final tab shows a prioritized list of conditions that are linked to the gene of interest. Franklin imports gene-disease relations from widely utilized databases such as OMIM, Monarch, GeneCC, and Orphanet. Each tile represents a condition, and by clicking on it we can access the Condition page, which displays information regarding the inheritance model, the age of onset, the possible phenotypes, and their occasionality.
Variants
Finally, in the Variants section users can review all the variants and segments previously classified by someone from their organization, alongside the interpretation text introduced during the classification process, and the condition the variant was associated with. All these variants are part of your organization's own clinical repository, and the previous classification will be highlighted by Franklin in case the variant (or a similar segment) appears again in a future case.
There are two different sections for Single Nucleotide Variants (SNV) and Structural Variants (SV), which includes CNVs and other segments from CMA analysis. Additionally, you can filter either of the variant lists by Classification, Somatic Classification, Inheritance model, Variant type, Region, and gnomAD frequency.
Importing variants:
Please note that you can use the + Add Variants button on the top right to import a file with classified variants into the platform, integrating your previous repository to your Franklin Knowledge Base, and therefore gaining insights from past cases that were not analyzed in the software.
After clicking on + Add Variants, you can download Franklin's upload template in an Xls or CSV format, fill it with the required variants and drop the file.
Still have questions? Reach out to our Support Team, they'll be happy to help!