Automating Diagnostic Workflows for Whole Exome and Whole Genome Sequencing

In a recent webinar, Tom Hofste, Head of Core Facility, Human Genetics Department, Radboud University Medical Center, Nijmegen, and Madan Ambavaram, Ph.D., Sr. Applications Scientist, Covaris, discussed the implementation of an automated diagnostic workflow for whole exome sequencing (WES) and whole genome sequencing (WGS). This blog explores how integrating Covaris technology with the Hamilton Microlab® STAR™ Liquid Handling platform enabled higher throughput, minimized errors, and improved processing of diverse sample types while maintaining fast turnaround times.

Introduction

Since 2017, the Genome Diagnostics Lab at Radboud UMC has been a leader in rapid whole exome sequencing, delivering results with an impressive 15-day turnaround time from sample collection to report. However, as the demand for sequencing services grew, it became clear that the lab’s existing manual workflows could no longer keep up. Rising sample volumes created a need for higher processing capacity, while the variability in patient DNA samples—differing in concentration, volume, and buffer composition—added complexity to the workflow. These challenges not only slowed down efficiency but also increased the risk of inconsistencies and errors in results.

Automated Workflow for Whole Exome Sequencing (WES)

Recognizing the need to scale, Radboud UMC adopted automation to streamline its workflows. By integrating the Covaris R230 Focused-ultrasonicator with Hamilton’s Microlab STAR platform, the lab successfully transitioned to automated workflows for both WES and WGS. This highly efficient workflow enabled them to maintain fast turnaround times while increasing sample throughput and ensuring reliable, high-quality results.

The automated WES workflow was built upon the Twist Bioscience protocol, leveraging the combined capabilities of the Covaris R230 and Hamilton technologies. This integration enabled high-throughput processing of various sample types, including challenging inputs such as FFPE tissue.

The workflow began with DNA extraction, normalization, and quality control. Advanced mechanical shearing with Covaris’ Adaptive Focused Acoustics® (AFA®) technology on the R230 provided precise DNA fragmentation, optimized for WES workflows. The Hamilton Microlab STAR platform further streamlined the process, automating library preparation to reduce hands-on time and ensure reproducibility.

Key benefits included:

• Increased Capacity: The lab scaled up to process over 10,000 exomes annually.
• Standardized Sample Preparation: Mechanical shearing with AFA ensured consistent fragmentation regardless of sample input.
• Reduced Errors: End-to-end sample tracking eliminated many risks associated with manual handling.

Expanding to Whole Genome Sequencing

Building upon the success of the automated WES workflow, Radboud UMC implemented a cost-effective and scalable WGS workflow. This process introduced PCR-free library preparation for certain applications, which reduced amplification biases and improved coverage uniformity.

The WGS workflow demonstrated its adaptability by accommodating a wide range of sample types, including EDTA blood and FFPE tissues. Covaris’ AFA technology played a key role, reducing duplicate reads. These advancements allowed the lab to successfully process 5,000 genomes in 2024, with plans to expand capacity even further. While initial testing focused on EDTA blood samples, ongoing efforts aim to extend compatibility to other sample types, broadening the workflow’s utility.

Addressing Sample Variability with Covaris Technology

One of the biggest challenges in sequencing workflows is the variability in sample quality. Enzymatic fragmentation methods often struggled with inconsistent sample inputs, leading to unreliable results. Covaris technology offered a robust solution through its AFA technology, which provided uniform fragment sizes across diverse sample types, even under challenging conditions.

By minimizing the impact of input variability, Covaris’ mechanical shearing technology improved workflow success rates. Additionally, its seamless integration with the Hamilton platform ensured that the automation process was both efficient and reliable, addressing a critical need for streamlined, high-throughput workflows.

Key Benefits of the Automated WES workflow

The integration of Covaris and Hamilton technologies brought significant advantages to Radboud UMC’s diagnostic workflows:

• Efficiency at Scale: Automated systems handled large volumes of samples with consistent results.
• Faster Turnaround: Reduced hands-on time allowed the lab to maintain its 15-day turnaround time for WES.
• Cost-Effectiveness: Optimized workflows reduced reagent usage and minimized the need for re-sequencing.
• Improved Quality Control: Automated QC processes ensured accurate tracking and reproducible results.

Case Studies Highlighting Impact

The success of Covaris technology in Radboud UMC’s workflows reflects broader industry trends, with several real-world examples highlighting its impact:

• Quest Diagnostics faced challenges using enzymatic fragmentation in their WES workflows, leading to inconsistent results and poor fragment size distributions across clinical samples. Transitioning to Covaris mechanical shearing resolved these issues, enabling tighter, more uniform fragment sizes and improving sequencing quality while reducing costs. [1]
• The “All of Us” Research Program, a longitudinal cohort study involving one million participants, relied on Covaris technology to generate whole genome sequences from diverse samples. The use of Covaris shearing technology facilitated high-quality libraries and ensured reproducibility across a massive volume of samples, uncovering over a billion genetic variants, including 275 million previously unreported ones. [2][3]
• Discovery Life Sciences leveraged Covaris technology to improve WES workflows for low-input samples such as FFPE tissues. Mechanical shearing provided consistent results even with inputs as low as 10 nanograms, reducing discordance rates from 15% to under 2%. This transition standardized workflows and improved success rates across varying sample qualities. [4]

Future Innovations

Radboud UMC remains committed to advancing genomic diagnostics. The lab is actively working to expand the range of input types compatible with its WGS workflows and is exploring long-read sequencing technologies to gain deeper genomic insights. Additionally, efforts are underway to scale optical genome mapping, with sample volumes expected to double by 2025.

These initiatives reflect the lab’s dedication to staying at the cutting edge of genomic research and diagnostics, continually advancing its capabilities to meet evolving clinical and research needs.

Conclusion

Radboud UMC’s automated workflows for WES and WGS exemplify how cutting-edge technology can transform genomic diagnostics. The integration of Covaris and Hamilton systems not only increased throughput but also maintained the high standards required for clinical applications. These advancements position the lab to continue delivering rapid, reliable results as the demand for sequencing grows.

To learn more about Covaris solutions for NGS workflows, contact us today!

References:

1. Quest Diagnostics with Covaris launches automated NGS platform, optimizing workflows to maximize lab economics | Covaris
2. All of Us Research Program | Covaris
3. Genomic data in the All of Us Research Program https://www.nature.com/articles/s41586-023-06957-x
4. Improving Whole Exome Sequencing Library Prep from Low Input and Degraded FFPE Samples Using Covaris AFA Technology | Covaris