Developing DNA Shearing Devices for Short- and Long-Read Sequencing at Hologic Diagenode

Significance of the Topic

Optimizing DNA fragment sizing is critical for epigenetic research, enabling accurate gene expression analysis under varying environmental and behavioral conditions. High-precision shearing and rigorous quality control underpin reliable next-generation sequencing (NGS) and long-read sequencing (LRS) workflows.

Objectives and Study Overview

Hologic Diagenode’s R&D team aimed to develop and validate high-performance DNA shearing devices for both short-read (150 bp–1 kb) and long-read (5 kb–100+ kb) sequencing. The goal was to enhance throughput, ensure tight fragment distributions, and integrate efficient QC processes.

Methodology and Instrumentation

The team evaluated the performance of existing and new electrophoretic systems to handle increasing sample volumes and larger DNA fragments. Key steps included:

• Shearing trials using Bioruptor and Megaruptor 3 across target fragment size ranges
• Fragment sizing and QC with Agilent Fragment Analyzer (High Sensitivity NGS and Large Fragment kits) and Femto Pulse systems
• Protocol optimization for continuous plate loading and pulsed-field capillary electrophoresis
• Automated smear analysis and data extraction via Agilent ProSize software

Instrumentation Utilized

• Agilent Femto Pulse system (Genomic DNA 165 kb kit)
• Agilent Fragment Analyzer system (HS NGS Fragment kit; Large Fragment kit)
• Hologic Diagenode Megaruptor 3 shearing device
• Bioruptor shearing device
• Agilent ProSize data analysis software

Main Results and Discussion

Switching to the Fragment Analyzer enabled continuous sample loading and flexible run ordering, significantly improving throughput and reducing hands-on time. The Femto Pulse system extended accurate sizing up to 165 kb, delivering tight fragment distributions essential for LRS. Automated ProSize analysis accelerated data processing, allowing the team to analyze hundreds of samples in hours and focus on data interpretation.

Benefits and Practical Applications

Key advantages of the optimized workflow include:

• Seamless scaling from short to ultra-high molecular weight DNA
• Enhanced laboratory productivity through high-throughput electrophoretic analysis
• Flexible run management and robust QC supporting device development
• Quantitative fragment sizing facilitating epigenetic biomarker discovery and NGS library profiling

Future Trends and Opportunities

Hologic Diagenode plans to expand its solutions to methylation biomarker assays and further refine long-read sequencing protocols. Anticipated advances in instrument sensitivity and throughput will support emerging epigenomic studies and clinical research demands.

Conclusion

Implementing Agilent’s advanced Fragment Analyzer and Femto Pulse platforms has empowered Hologic Diagenode to achieve precise DNA shearing across a broad size range, substantially improving efficiency and data quality in both short- and long-read sequencing workflows. These enhancements accelerate epigenetics research and drive biomarker discovery.