High-Throughput Genomic Profiling of Solid Tumor FFPE Specimens with Fully Automated Extraction—How a New Platform is Changing Clinical Testing and Cancer Research

Labcorp, Covaris, and Hamilton came together at AMP2024 to showcase a fully automated, high-throughput solution for extracting DNA and RNA from formalin-fixed paraffin-embedded (FFPE) solid tumor samples. The Hamilton Sonication STAR, enabled by Covaris truXTRAC® FFPE SMART Solutions, improves sequencing outcomes by minimizing quantity not sufficient (QNS) failures and increasing the proportion of fully reported tumor profiles by up to 16%. It provides higher-quality nucleic acids, reduces the need for re-extractions, and streamlines the workflow with a hands-off approach, enabling cost savings and more precise results for comprehensive genomic profiling (CGP).

Introduction

Modern precision oncology relies heavily on comprehensive genomic data, yet a significant bottleneck remains: formalin-fixed paraffin-embedded (FFPE) tissue. Although FFPE preservation is a long-standing technique, extracting high-quality nucleic acids from these samples continues to be a challenging task for researchers and clinicians alike. That’s why Labcorp, Covaris, and Hamilton joined forces to develop the Sonication STAR (Figure 1), a fully automated extraction platform that simplifies FFPE workflows and raises the standard for comprehensive genomic profiling (CGP).

Figure 1. Sonication STAR – a highly differentiated solution

FFPE has been a reliable method for long-term tissue storage for over a century, but the same crosslinking that stabilizes samples can compromise the integrity of DNA and RNA (Figure 2). As testing moves beyond single-gene analyses to expansive gene panels, immune biomarkers, and fusion detection, the margin for error narrows. Even a single low-yield extraction can compromise an entire patient report, leading to re-extractions, additional costs, and potentially delayed treatment decisions. This challenge becomes even more pronounced with smaller biopsy samples, such as fine-needle aspirates, where the available tissue is already limited. A robust, reproducible, and high-throughput FFPE workflow has therefore never been more urgent, particularly for sophisticated assays like Labcorp’s OmniSeq® INSIGHT, which examines hundreds of genomic and immune-related targets.

Figure 2. FFPE Sample Processing

Overcoming Obstacles of FFPE with Combined Experience

Addressing these FFPE challenges to obtain high-quality results required combining three specialized areas of expertise:

• Labcorp’s Clinical and Research Bioinformatics
  • Labcorp’s flagship OmniSeq® INSIGHT test goes beyond standard genomic analysis, integrating immune profiling and HLA haplotyping. Deep clinical experience ensures the extracted nucleic acids meet stringent standards suitable for regulatory-compliant reporting.
• Covaris’ Adaptive Focused Acoustics® (AFA®) Technology
  • Covaris’ advanced acoustic technology, combined with SMART chemistry, enables the deparaffinization and lysis of FFPE samples using precisely controlled ultrasonic energy—eliminating the need for toxic solvents. Additionally, the specialized SMART FFPE chemistry helps reverse formalin crosslinks while preserving nucleic acid integrity.
• Hamilton’s Liquid-Handling Robotics
  • Hamilton’s automated platforms specialize in reproducible, high-throughput pipetting and closed-environment sample tracking. By housing Covaris’ R230 Focused-ultrasonicator directly on the deck, the Sonication STAR eliminates manual transfers, reduces contamination risk, and streamlines the overall workflow.

How the Sonication STAR Works

What distinguishes the Sonication STAR from other automated systems is its fully integrated approach. From deparaffinization to final elution of DNA and RNA, every step occurs within a single, enclosed platform. Here is a quick tour of the process:

1. Automated Loading and Deparaffinization
   FFPE scrolls or slides are placed into Covaris consumables and are deparaffinized without the need for toxic solvents like xylene. This gentle process helps protect nucleic acids from the outset.
2. Precise Lysis and Crosslink Reversal
   Covaris’ optimized buffer chemistry works in tandem with acoustic energy to thoroughly lyse tissue and begin reversing formalin-induced crosslinks. The result is higher-quality DNA and RNA, both in yield and integrity.
3. Simultaneous DNA/RNA Extraction
   The Sonication STAR then separates the lysate for parallel DNA and RNA extraction, using proprietary bead-based protocols. Because the workflow is fully automated, human intervention is reduced to just a few simple touchpoints.
4. Integrated Tracking for Flexible Throughput
   With batch sizes ranging from 8 to 96 samples (in increments of 8), labs can easily adapt to different sequencing plate formats or handle smaller cohorts when needed. The system accommodates up to 72 samples for certain high-throughput library prep kits, further enhancing its versatility.

From Validation to Real-World Gains

During extensive verification at Labcorp’s Buffalo, NY, facility, researchers saw immediate improvements in extraction metrics (Figure 3):

• Yield Increases
  DNA and RNA yields from FFPE tissues rose by factors of two to five, particularly for challenging low-input samples. This reduction in “quantity not sufficient” (QNS) rates translates directly into more completed assays on the first attempt.
• Higher QC Pass Rates
  OmniSeq® INSIGHT analysis revealed a significant increase in the number of samples meeting key sequencing quality thresholds—rising from an average of 89% before automation to over 95% with the Sonication STAR. This improvement also led to an estimated 3% reduction in flow cell costs. The enhanced performance proved particularly valuable for assays that depend on intact RNA, such as gene fusion detection.
• Fewer Re-Extractions and Delays
  With a more consistent, reproducible approach, the team saw fewer rejected samples and less need to consume precious biopsy material in repeated extraction processes. This efficiency eases financial and time pressures on both the lab and the patient.
• Scalability
  Tests confirmed that the new workflow maintains linear performance across a wide range of input amounts, ensuring predictable yields for both small needle aspirates and larger tissue blocks.

Figure 3. Real-World Impact on the Workflow

Reinforcing Patient-Centered Oncology

While the technology behind these advancements is remarkable, clinicians and patients are the ones who benefit most. High-yield, high-integrity nucleic acids lay the groundwork for identifying critical oncogenic mutations, immune activation markers, and novel therapeutic targets. By providing these insights quickly and reliably, oncologists can deliver more targeted treatment options to their patients.

Just as crucial, fewer failed tests and minimal rework mean patients avoid repeated testing or delays—an important factor when access to potentially life-saving therapies is on the line. In today’s precision medicine landscape, every extra day matters.

Conclusion

As the cancer biomarker field grows—from next-generation sequencing to immuno-oncology markers, and beyond—workflows that blend automation with robust chemistries are quickly becoming the new standard. The Sonication STAR proves that FFPE extraction doesn’t have to be a bottleneck. With flexible throughput, minimal manual handling, and consistent performance across tumor types, this platform has set the stage for more widespread adoption of comprehensive genomic profiling in the clinical laboratory.

Interested in learning more about Covaris workflows for protein sample preparation? Contact us today!