Franklin’s Germline Workflow

Whole Exome

Franklin for WES solution is an end-to-end suite of tools that help you
sharpen single and family case analysis by combining AI technology with
the richest genetic data available for SNPs, CNVs, ROHs, and even mitochondrial variants.

Used by top laboratories worldwide

SNP and CNV
variant calling

Automated AMP and ACMG variant classification

Collaboration with teammates and other organizations

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Franklin has been optimized for all Whole Exome Sequencing (WES) workflows, supporting each bioinformatic step from raw
data to reporting. The platform uses powerful tools for variant calling and interpretation to efficiently process the vast amount of sequencing data from the protein-coding regions of the genome into clinically actionable results.

Streamline your exome case analysis from FASTQ to Report
using Franklin features such as:

Automated case creation

Franklin allows for efficient integration with LIMS, EMR, and your own organization’s information system through an API, and also provides various ways to seamlessly import your data in bulk. You can easily upload batches of all raw data file formats from the BaseSpace App, as well as Amazon servers, other cloud-based sources, or your local computer directly through the platform’s UI. Create not only single cases but also duos, trios, and any family pedigree using Franklin’s user-friendly interface.

Variant detection

Franklin has developed a dedicated and optimized variant
detection pipeline for WES workflows, which is able to pick up small and large germline variants, as well as mitochondrial variants. Franklin uses its own bioinformatic pipeline to identify SNPs and small insertions/deletions, combining different tools and drawing on the most fitting algorithm for each step of the detection process. For CNV detection, Rainbow, Franklin’s own proprietary algorithm, uses machine learning to identify structural variants with up to one exon resolution and high confidence levels. The CNV calling model keeps retraining with new batches of samples, getting better over time.

TSO 500 allows you to analyze multiple variant types and key biomarkers in 500+ cancer-relevant genes across DNA and RNA in a single assay. For DNA, the analysis covers 523 genes (1.94 Mbp) and detects SNVs, indels, CNVs, tumor mutational burden (TMB), and microsatellite instability (MSI). If using the DNA + RNA bundle, you can also identify known and novel fusions (in 55 genes) and some splice variants (in 3 genes).

Variant interpretation

Franklin’s classification and prioritization engine leverages the
power of AI to help pinpoint the relevant variants for your case,
taking into molecular effect, phenotypic information, and recent
publications. Franklin presents information from more than 100
databases with prediction tools, general and specific population
frequencies, genes and diseases, and automatically classifies
variants according to the latest ACMG guidelines. The platform
works as a one-stop shop for genetic evidence, helping users
visualize all the relevant information from available sources, as
well as Franklin Community data, all curated by our dedicated
team of genetics specialists.
Use Franklin’s powerful filtering to narrow down the WES files
from thousands of mutations to a shortlist of clinically relevant,
potentially causal variants. This comprehensive tool allows
filtering by customized virtual panels, ACMG classification,
population frequencies, ClinVar submissions, phenotypes,
genomic region and molecular effect, inheritance model and
zygosity, and more.

Community Knowledge Base

Franklin will also help you seamlessly create your own
Knowledge Base to centralize your organization’s exclusive
panel, gene and variant repository composed of your unique
historical data. Working side by side with colleagues? Franklin promotes collaboration among team members by allowing you to leave comments, share relevant information and create SOPs that work specifically for your organization.
The Franklin Community comprises more than 20,000 genetic experts from around the globe, curating their real-world evidence into the platform. All users can benefit from frequency metrics, shared publications, and even variant classifications to bootstrap their clinical analysis and increase overall diagnostic accuracy.

Reporting

Franklin’s Report Studio helps you generate completely
customizable clinical reports without any added work. After
completing the case review, users can issue and even sign off a
report that includes all relevant variants as well as their
interpretation and clinical evidence with the click of a button.
Customize a template that fits your needs, assign different roles
to members of your team, and save lots of time and effort while
ending up with a tailor-made report structure thoroughly
designed for your organization’s specific workflow.

While only covering less than 2% of the WES, can account for ~85% of known disease-related
variants, making this method a time- and cost-effective alternative to whole-genome sequencing.
These assays are becoming increasingly popular since they allow labs to unify wet lab workflows
and simplify the experimental procedures for different genetic conditions, instead of having
dedicated panels for each specific disease group, while achieving high coverage of coding
regions.
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However, the amount of data resulting from such a thorough test can still be overwhelmingly
complex and translate into time-consuming dry lab processing. Whether you are conducting
these assays for clinical or research purposes, with Franklin, you can easily analyze WES single
and family cases to reach faster and more accurate results.