Franklin’s Microarray Workflow

ThermoFisher CytoScan

Franklin for CytoScan solution complements the Chromosome Analysis Suite (ChAS) software to offer an end-to-end suite of tools that help you sharpen pre- and post-natal case analysis by combining AI technology with the richest genetic data available for all relevant copy number variants (CNVs), mosaics, and loss-of-heterozygosity (LOH) chromosomal aberrations.

Used by top laboratories worldwide

Validated detection
of CNVs and
rearrangements

Automated AMP and ACMG variant classification

Collaboration with teammates and other organizations

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Franklin has partnered with ThermoFisher to streamline all chromosomal microarray analysis (CMA) workflow, including the CytoScan 750K Array and the CytoScan HD Array, integrating each step from raw data to report. The platform uses powerful tools for interpretation, including automated segment classification, to efficiently process microarray data from the GeneChip into clinically actionable results. 

Streamline your microarray 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 to quickly access case clinical background, including phenotypic information that may impact segment analysis. You can easily create cases from lists of segments individually or in bulk, by uploading batches of AED or VCF files from the ChAS software, as well as local computer, directly through the platform’s UI. 

 Developed in collaboration with experts in cytogenetics, the ThermoFisher CytoScan 750K and HD kits provide high specificity, sensitivity, dynamic range, and resolution across the genome microarray analysis, with comprehensive coverage across RefSeq, OMIM, ClinGen, DECIPHER/DDG2P constitutional regions, and Sanger cancer genes.
- CytoScan 750K covers 750,000 markers for copy number analysis, including 200,000 SNP and 550,000 non-polymorphic probes. 
- CytoScan HD covers 2.67 million markers for copy number analysis, including 750,000 SNP and 1.9 million non-polymorphic probes. 

Segment interpretation

Franklin’s interpretation engine leverages data available in ChAS and the power of AI to help pinpoint the relevant segments for your case, taking into account updated gene curations, genotype-phenotype association given the clinical context of the case, automatically-calculated ACMG classification of each segment, and recent publications. Franklin presents annotations from more than 100 databases including prediction tools, general and specific clinical data repositories for segments, genes and diseases, with dedicated tools for complex genomic copy number variations, ClinGen curated recommendations, and more. The platform works as a one-stop shop for genetic evidence, helping users integrate all the relevant information from available sources, as well as Franklin Community data, all regularly updated and curated by our dedicated team of cytogenetics specialists. 

Clinical Knowledge Base

Franklin will also help you seamlessly create your own Knowledge Base to centralize your organization’s exclusive variant repository composed of your unique historical data, combining both CMA and NGS data in one database. Your curated information is then automatically integrated into each new case analysis, saving time and promoting consistency in the classification. This feature allows you to identify common benign polymorphisms in your patient population, detect common artifacts in your samples and benefit from past variant classifications to bootstrap your clinical analysis and increase overall diagnostic accuracy.  
Working side by side with colleagues? Franklin promotes collaboration among team members by allowing you to share relevant observations and assessments and create SOPs that work specifically for your organization.  

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.


CMA is the state-of-the-art technique used globally to detect gains, losses and other chromosomal abnormalities. This widespread technique provides fast and reliable results with clinically actionable impacts for a broad range of clinical applications. The ThermoFisher/Affymetrix CytoScan 750K and HD kits were designed to provide the most comprehensive coverage and highest performance for detecting CNVs, mosaics, and LOH aberrations in both research and clinical settings.

With Franklin, you can easily analyze and report CytoScan data for pre- and post-natal cases to reach faster and more accurate results, filled with clinically relevant insights and exceptional segment interpretation tools, while building up your own clinical repository of variants. 

Want to know more? 

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Take advantage of the unique genetic dataset and curated information that Franklin Community has to offer

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