Adaptive Focused Acoustics® Enables Cost-Efficient, Automation-Friendly Workflows for Nucleic Acid Recovery

As laboratories embrace increasingly complex genomics technologies, the need is evident for streamlined, cost-effective, and scalable extraction methods to support the pace and depth of modern genomic studies. Laboratorians not yet familiar with Adaptive Focused Acoustics (AFA) may want to explore its potential to improve the quality of DNA and RNA extraction from even challenging samples like FFPE. In a recent study, Labcorp (Omniseq) saw a 300 percent increase in the quality of recovered genetic material after it applied Covaris’ latest AFA-based protocol on an Assay-Ready Workstation to its sample preparation workflows.

Clinical lab work hinges on nucleic acid extraction
DNA and RNA extraction from biological samples plays a pivotal role in advancing scientific research and clinical diagnostics. Nucleic acid extraction serves as the critical first step in a multitude of downstream analyses, including sequencing, PCR, and gene expression profiling. With the surge in genomics-driven investigations across fields including oncology, infectious diseases, and personalized medicine, the demand for reliable, high-quality nucleic acid extraction methods has escalated. Researchers and clinicians rely on these extracted nucleic acids to uncover genetic variations, identify disease markers, and elucidate molecular mechanisms underlying biological processes.

The complications of FFPE nucleic acid extraction
Despite the growing importance of nucleic acid extraction, challenges persist, particularly with formalin-fixed paraffin-embedded (FFPE) samples commonly used in pathology and archival research. FFPE tissues are encased in paraffin wax for preservation and can later be mounted on glass slides for analysis or processed as scrolls in tubes. Working with FFPE is complex due to tedious, labor-intensive workflows, and lack of flexibility of current kits, which often require toxic chemicals and have limited automation capabilities.

FFPE tissues pose other unique hurdles for DNA and RNA extraction due to the cross-linking and degradation caused by formalin fixation, which can compromise the quality and yield of extracted nucleic acids. The cross-linking of nucleic acids with proteins and other cellular components during fixation can impede the release of intact DNA and RNA molecules. RNA degradation over time in FFPE samples also presents a substantial obstacle, limiting the usability of these archival materials for genomic analyses. Consequently, traditional extraction methods often yield suboptimal results with FFPE samples, leading to incomplete recovery of genetic material and hindering the full potential of genomic investigations utilizing these valuable clinical specimens.

Adaptive Focused Acoustics
Adaptive Focused Acoustics technology, introduced in the early 2000s, has achieved prominence in genomics and is best known for its ability to efficiently and reliably shear DNA for NGS. Eugenio Daviso, PhD, Vice President of Solutions at Covaris, LLC, highlights that AFA technology has many benefits beyond shearing, and applying AFA technology to extract DNA or RNA from FFPE tissues improves the yield, quality, and reproducibility of nucleic acid extraction, compared to traditional methods for these samples.

As explained by Daviso, AFA disrupts tissue structures and efficiently releases nucleic acids from paraffin wax without introducing chemical contaminants or compromising sample integrity. The ability to control the temperature and the focus of the acoustic energy without direct contact enables complete emulsification of the FFPE sample, preventing sample loss or potential contamination and lending critical benefits for labs handling precious samples.

AFA systems offer varying batch sizes and throughput options to accommodate different workloads in laboratories, notes Daviso. This flexibility is complemented by AFA technology's capability to integrate with automated workstations, reducing manual labor and minimizing human error. Together with an automated workflow, AFA can be used for active, organic solvent-free removal of paraffin from FFPE tissues, while ensuring higher quality end products by avoiding nucleic acid degradation resulting from fragmented transcripts.

The synergy of AFA with an automated workstation

The results of using AFA with automation are worth noting. Daviso reports that Labcorp (Omniseq) implemented Covaris’ AFA-enabled truXTRAC® FFPE SMART Solutions on an automated platform into their sample preparation workflow and reported a threefold increase in the quality of recovered genetic material with no reduction in quantity. This drastic improvement underscores the critical impact of optimized workflows. Integrating innovative technology can open new doors for research and diagnostic capabilities in clinical labs.

AFA with automation presents an exciting future for oncology
Daviso highlights that this advancement of AFA with automated workflows represents a considerable step forward, particularly in oncology, amidst the expanding field of genomics. The next major development in cancer research and diagnostics may involve analyzing tumor genomic profiling and RNA in pathology samples to identify crucial biomarkers, made possible by these workflow improvements. Implementing this novel workflow not only enhances genetic product quality and yield but also reduces turnaround times, compared to traditional extraction methods.

Using AFA with automation allows researchers to thoroughly explore biopsied and preserved tissue areas and generate high-quality genomics-ready genetic material. By reducing manual labor, this approach minimizes the risk of overlooking important features or genomic variations. Several different commercial devices are available that can be customized to specific needs, accommodating different sample sizes and formats while handling diverse throughputs.

In 2023, AFA technology was used to process nearly 60,000 FFPE samples, primarily in clinical trials, Daviso notes. This continually growing figure underscores the impact of the new comprehensive genomic profiling platform using commercially available truXTRAC FFPE SMART Solutions and an automated workstation.

“There are many environmental and other factors that contribute to cancer that we haven’t yet found or delineated. Using genome and transcriptome information from extracted products will open up the multi-omics of oncology, yielding new diagnostic and treatment possibilities. Being able to detect novel biomarkers in the NGS landscape means certain drug and clinical trial involvement can be proven in a whole new way. If the economics of this new pipeline helps the field grow and prosper, then we will be even closer to winning the fight against cancer once and for all,” said Daviso.