Asuragen NGS System Streamlines Detection of NSCLC-associated DNA Mutations, Gene Fusions, and RNA Expression Targets in Single Workflow
The targeted NGS panel enables the detection of 135 RNA and 55 DNA variants associated with non-small cell lung cancer
Austin, Texas — 06/04/2019 — Asuragen, Inc., a molecular diagnostics company delivering easy-to-use products for complex testing in genetics and oncology, today announced publication of a study demonstrating a single next-generation sequencing (NGS) workflow for the sensitive and accurate detection of DNA and RNA variants associated with non-small cell lung cancer (NSCLC) in the journal Translational Oncology (https://doi.org/10.1016/j.tranon.2019.02.012). The article, titled “An Integrated Next-Generation Sequencing System for Analyzing DNA Mutations, Gene Fusions, and RNA Expression in Lung Cancer,” describes the targeted analysis of 190 loci from low-input and low-quality NSCLC specimens using a rapid and standardized NGS procedure that is compatible with existing laboratory instrumentation.
Lung cancer is the leading cause of cancer-related death worldwide and NSCLC accounts for approximately 85% of all lung cancer cases. A number of targeted therapies for DNA and RNA variants in NSCLC are now available, but their timely detection is complicated by segregated NGS methods for DNA versus RNA and by limitations in biopsy tissue and nucleic acid quality to support split workflows. To address these challenges, the publication describes a unified DNA/RNA NGS assay that covers hotspot mutations in 20 genes, including EGFR, KRAS, BRAF, and PIK3CA, as well as 107 RNA fusion variants recurrent in NSCLC, such as ALK, RET, ROS1, and NTRK1, and MET exon 14 skipping events. RNA quantification also includes 23 transcripts with prognostic and theranostic value, such as PD-L1, PD-L2, INFG, and CTLA4 that are important in assessing T-cell-inflamed phenotypes and the impact of immune checkpoint inhibitor therapies. Analysis is achieved using proprietary software to automate variant calls from total nucleic acid, resulting in quantification of SNVs, INDELs, CNVs, fusions, splice variants, and expression targets – all within a single, harmonized NGS run. By querying functional input copies, sequence quality, sample-specific error rates, local sequence complexity, and coverage depth, the software is an essential component of the overall system and helps ensure robust and accurate results.
In the study, over 200 formalin-fixed, paraffin-embedded (FFPE) surgical resections and core needle biopsies provided by collaborators at MD Anderson Cancer Center were tested. The results were consistent with variant prevalence established by large, international consortia such as TCGA, demonstrating mutual exclusivity between driver events and distinct molecular subtypes for adenocarcinoma and squamous cell carcinoma. Sequence variants in fine needle aspirate (FNA) smears from BATTLE-2 clinical trial subjects were in 97% agreement with matched FFPE specimens tested by the FoundationOne® NGS Assay, even though the FNA biopsies had substantially fewer cells available for analysis.
“Our study with Asuragen demonstrates the continued evolution of NGS methods to reliably quantify different types of cancer-associated variants across both DNA and RNA that are relevant to precision medicine,” commented Ignacio I. Wistuba, MD, professor and chair, Department of Translational Molecular Pathology at The University of Texas MD Anderson Cancer Center. “This integrated and rapid approach may help clinicians and laboratories maximize the actionable information they can recover from small patient biopsies, and accelerate turnaround times for results and decision-making.”
This study was funded in part by a Cancer Prevention and Research Institute of Texas (CPRIT) Product Development Research grant.
Asuragen is a molecular diagnostic product company changing the way patients are treated in genetics and oncology. Asuragen’s diagnostic systems, composed of proprietary chemistry and software, deliver powerful answers using broadly installed instrument platforms. They are simple to adopt and expand the ability to serve patients. Asuragen is a product foundry rapidly and efficiently addressing current and emerging clinical needs, including cancer diagnosis and monitoring, reproductive health and aging, serving laboratories across a patient’s lifespan with its best in class diagnostic tests. For more information, visit www.asuragen.com.
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