FFPE Sample Prep Advancements To Transform Solid Tumor Treatment

a PerkinElmer Company 1 Precision Diagnostics Advances Treatment of Solid Tumors: Omniseq/Labcorp Integrates Covaris Technology to Automate FFPE Sample Prep for CGIP In a recent webinar, Jeffrey Conroy, Head of Science at OmniSeq and Executive Director at LabCorp, and Eugenio Daviso, Ph.D, Vice President of Solutions at Covaris, highlighted the significant role of Comprehensive Genomic and Immune Profiling (CGIP) in enhancing decision-making for cancer treatments. They presented Covaris’ truXTRAC® FFPE SMART Solutions, a scalable, automation-friendly workflow solution for active deparaffinization, extraction, and purification of DNA and RNA from FFPE samples. By employing Adaptive Focused Acoustics® (AFA®) Technology in an automated workflow, this method ensures high quality and yield of total nucleic acids from the same FFPE sample while providing reliable data and flexibility in throughput and batch size. Eugenio Daviso, Ph.D. VP Solutions, Covaris Jeffrey Conroy Head of Science, OmniSeq Inc. Executive Director, LabCorp Introduction Recent advances in multiomics approaches have provided a more comprehensive view of tumors, accelerating the development of precision medicine. However, incorporating such complex workflows into diagnostic laboratories remains challenging. Comprehensive Genomic and Immune Profiling (CGIP) is the standard of care for cancer that allows molecular pathology laboratories to consolidate individual biomarkers into a nextgeneration sequencing (NGS) assay.1 Yet, the use of formalinfixed paraffin-embedded (FFPE) methods for preserving human tissue specimens introduce obstacles—including the need to remove paraffin and deal with degraded or crosslinked nucleic acids. The workflows to isolate DNA and RNA are complex and time-consuming, involving toxic chemicals and requiring high sample input. In addition, as the demand for actionable results from FFPE tissues continues to grow, clinical laboratories are tasked to process more samples in less time as patients and their caregivers wait for results. Thus, better solutions for nucleic acid isolation from FFPE samples are urgently needed.1 Working together, OmniSeq/LabCorp and Covaris developed an innovative workflow that provides both high quality and yield of DNA and RNA from the same FFPE sample while ensuring reliable, reproducible data along with flexibility in throughput and batch size. Automating Sample Prep for CGIP with Covaris truXTRAC FFPE SMART Solutions Extraction of DNA and RNA from FFPE samples can be challenging, time consuming, and labor-intensive. Traditional methods of extraction require toxic chemicals, often resulting in degraded and fragmented nucleic acids. This underscores the need for greater yield with minimal tissue input, simplified and automated workflows, as well as suitable vessel design for better tracking and access. The ultimate goal is to achieve actionable outcomes, whether that is to identify an effective treatment or to qualify a patient for clinical trials. The workflow developed by OmniSeq/LabCorp and Covaris is a fully automated system for evaluating FFPE samples, designed to overcome these challenges. Covaris truXTRAC FFPE SMART Solutions with R230 Focused-ultrasonicator enable assays.1 This solution offers a scalable, automation-friendly workflow for active deparaffinization, extraction, and purification of highquality DNA and RNA from FFPE samples. a PerkinElmer Company 2 By utilizing the power of focused ultrasonication with Adaptive Focused Acoustics (AFA) Technology, this workflow provides both high quality and yield of DNA and RNA from the same FFPE sample while ensuring reliable, reproducible data along with flexibility in throughput and batch size. With no toxic organic solvents or harmful chemicals, the workflow easily integrates with most liquid handling systems. In addition, this workflow was shown to save time, reduce costs, and offer flexibility in terms of hands-on time. The accuracy and precision of NGS outcomes was prioritized, aiming to improve the efficiency and reliability of genomic profiling (Figure 1). Figure 1. Innovative workflow using Covaris AFA Technology resulted in repeatable, reproducible results regardless of sample type. Case Study: Examining the Efficiency of Protein Extraction Using the R230 Focused-ultrasonicator The workflow tests multiple biomarkers from small volume specimens and generates a single report of detected variances and associated therapies, aiding in treatment decisions and clinical trial selection. It also simultaneously evaluates both genomic and immune profiles from a single sample and reports alterations at various levels, including single nucleotide variants, copy number variation, gene rearrangements, splice variance, TMB, MSI, and regions of loss. Revolutionizing Cancer Diagnostics with Broad Access and Rapid Results In a study using this workflow, patients from 44 states were tested, showcasing the broad access provided by the LabCorp distribution network. Genomic alteration viewpoint showed single nucleotide variants and copy number variance as the most prevalent alteration types detected. When focusing on alterations matchable to targeted and/or immunotherapy guidelines or associated with clinical trials, it was found that 1.6–95% of patients had a positive biomarker across any single class of alteration type. Nearly all MSI and TMV high patients matched to an approved therapy, while a high percentage of patients without tier one alterations had alterations that matched inclusion criteria for at least one trial. Overall, the number of patients not matching either category was minimal, highlighting the potential of tumor profiling in personalized cancer treatment and clinical trial matching. The test detected tier one alterations in almost 85% of lung cancer patients. This is significant given the high number of biomarkers associated with personalized therapies and their prevalence. Over 50% of patients were PD-1 positive above a 1% TPS cutoff for 22C3, and a similar percentage tested positive for either an EGFR or KRASS mutation. These findings emphasize the importance of simultaneous testing of all relevant biomarkers. The study also highlighted the need to match patients with appropriate therapies based on up-to-date guidelines and biomarkers. For newly diagnosed stage IV non-small cell lung cancer (NSCLC) patients, timely identification of actionable a PerkinElmer Company mutations significantly improved outcomes. Other cancers, including cervical, melanoma, head and neck, bladder, thyroid, and stomach, showed therapy associations in nearly 50% of cases or higher, driven by high PDL-1 positivity rates and specific mutations. Conclusion Adopting Covaris’ truXTRAC FFPE SMART Solutions helped OmniSeq/LabCorp facilitate the extraction of high-quality DNA and RNA from FFPE samples. Utilizing focused ultrasonication to break down the paraffin and extract the nucleic acids eliminates the need for toxic solvents or harsh chemicals. This innovative workflow is scalable and automation-friendly, saving time while delivering reliable results, no matter how many samples need to be processed. This work by OmniSeq/LabCorp and Covaris is helping to bring the industry closer to realizing the full potential of precision medicine in cancer care, making it accessible to all patients. Reference 1. Poster: Total Nucleic Acids (tNA) Extraction from FFPE Samples Using Adaptive Focused Acoustics (AFA) Technology for Comprehensive Genomic Profiling. Presented at ABRF 2023. Curious how Covaris’ truXTRAC FFPE SMART Solutions can streamline extraction of high-quality DNA and RNA from your FFPE samples? Contact us at www.covaris.com/contact To view the recorded webinar, please visit https://ln.run/m_nbO US: +1 781.932.3959 customerservice@covaris.com EU: +44 (0)845 872 0100 emeacustomerservice@covaris.com APAC: +86 137 6427 6714 APACcustomerservice@covaris.com Applications applicationsupport@covaris.com Service and Support techsupport@covaris.com www.covaris.com | 2024© Covaris, LLC M020178_RevA_Apr2024 Information subject to change without notice. For research use only. Not for use in diagnostic procedures. a PerkinElmer Company