Assistance Publique – Hôpitaux de Marseille (APHM), one of France’s premier university hospital networks, has embarked on a groundbreaking journey in genetic diagnostics. In collaboration with SeqOne, APHM has automated its exome sequencing process, setting a new standard in precision medicine. This case study explores how this partnership is transforming patient care through cutting-edge technology and innovative workflows.
The Challenge: Meeting Growing Demands in Rare Disease Diagnostics
With over 3 million patients affected by rare genetic diseases in France alone (Amselem et al., 2021), the demand for fast, accurate genetic testing has never been higher. APHM, serving the vast Provence-Alpes-Côte d’Azur region, faced the challenge of scaling up its diagnostic capabilities while maintaining the highest standards of accuracy.
The Solution: Automation and AI-Powered Analysis
In 2023, APHM implemented an automated exome sequencing workflow, leveraging:
- Agilent Magnis NGS Prep System for automated Agilent SureSelect Human All Exon V8 library generation
- Illumina NovaSeq technology for high-throughput sequencing
- Illumina DRAGEN Suite for rapid secondary analysis
- SeqOne’s AI-powered Cloud Analysis platform for tertiary analysis
This integrated approach created a seamless “dry lab automation” process, where VCF files are seamlessly fed into SeqOne’s platform for advanced variant annotation and AI-based prioritization.
The Results: Transformative Improvements in Efficiency and Accuracy
Since launching in January 2024, the new workflow has yielded highly promising results:
- Significant reduction in analysis time per sample
- Increased throughput to 1,500 – 2,000 samples annually
- Higher diagnostic yield
- Successful transfer of all high-throughput sequencing activity to the new strategy
Professor Martin Krahn, Director of the Molecular Genetics Laboratory at APHM, comments: “The automation of exome sequencing marks a pivotal moment for our laboratory. With SeqOne’s support, we’ve dramatically increased our sample analysis capacity and precision, significantly improving our ability to diagnose rare genetic diseases.”
Beyond Technology: A Collaborative Partnership
The APHM-SeqOne collaboration extends beyond implementation, fostering continuous improvement through:
- Regular feedback loops between APHM experts and SeqOne developers
- Customization of the platform based on real-world clinical needs
- Joint exploration of new applications & collaborative research projects
Looking Ahead: A Model for the Future
This success story serves as a blueprint for other molecular labs, demonstrating how integrating best-of-breed technologies can significantly improve turnaround times and workflow efficiency.
Martin Dubuc, CEO of SeqOne, envisions the broader impact: “Our partnership with APHM exemplifies how automation and advanced analytics can transform genetic diagnostics. We’re not just optimizing workflows; we’re paving the way for more accessible and impactful precision medicine at population scale.”
Key Takeaways
- Automated exome sequencing workflow increases efficiency and diagnostic yield
- AI-powered analysis enhances variant interpretation accuracy
- Collaboration between clinical experts and technology providers drives continuous improvement
- Scalable solution applicable to various genetic testing domains
- Potential to significantly impact patient care through faster, more accurate diagnoses
By embracing digital innovation and strategic partnerships, APHM and SeqOne are setting new standards in genetic diagnostics, promising a future where rare disease patients receive faster, more accurate diagnoses and personalized care.
About SeqOne
SeqOne is a leading European provider of AI-powered software for next-generation sequencing (NGS) data analysis in oncology and rare diseases. Its cloud-based platform transforms complex genomic data into fast, precise, and actionable insights, supporting molecular labs in delivering life-saving diagnoses and treatments. The SeqOne Platform is a CE-IVD Class C certified under IVDR in vitro diagnostic medical device. Driven by the vision of personalized medicine for every patient, everywhere, SeqOne is scaling the future of genomic medicine—one lab at a time.
For more information, visit seqone.com.
