Scientists at NuGEN Technologies, Inc. have simultaneously surveyed RNA of more than 400 targeted genes in a single assay, using next generation sequencing (NGS) to detect fusions known to be key drivers of tumor growth in several cancer types. The scientists, who employed an innovative method of targeted sequence library preparation, also discovered low-frequency fusions that had not previously been reported.
The new method, which allows the simultaneous interrogation of multiple, specific genes for RNA sequencing, significantly simplifies fusion detection when compared with standard RNA sequencing approaches.
Based on NuGEN’s Single Primer Enrichment Technology (SPET), “This method can greatly enhance scientists’ ability to understand the underlying oncogenic impact on gene regulation,” according to Elizabeth Hutt, the NuGEN CEO. “Applications based on this exciting new technology promise to speed up cancer research and lead to more effective diagnoses and treatments, contributing to the realization of precision medicine.”
The scientists used the new method to prepare cancerous and normal tissue samples for targeted RNA sequencing. The goal was to detect the presence of genes that had joined together or “fused”—resulting in changes in gene regulation. Through NGS, the scientists were able to identify multiple known and previously unreported fusions from fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue. By targeting specific RNAs for sequencing, the scientists report, they were able to reduce the number of sequencing reads and increase the sensitivity of gene fusion detection, when compared with standard RNA-Seq methods.
“Traditional methods require a much larger number of sequencing reads in order to detect fusion events in a background of some 20,000 transcripts,” said Douglas Amorese, NuGEN Vice President of Research and Development. “Other focused methods cannot survey the entire repertoire of previously recognized fusions; they are limited to detection of small numbers of potential events.”
Additionally, the scientists write, “The SPET-based assay is easy to use, has low RNA input requirements and can be used with RNA from formalin-fixed, paraffin-embedded (FFPE) tissue, which is important for clinically relevant samples. The assay is fully customizable to target any gene or set of genes in any genome.”
Dr. Bastiaan Tops, of the Radboud University Medical Center in the Netherlands, reported recently at a major human genetics conference that his team used a NuGEN custom gene fusion panel to analyze specific gene-rearrangements in sarcomas —and discovered two previously unknown fusions. The team, based in the Laboratory of Tumor Genetics in the University’s pathology department, plans to look for those fusions in additional sarcoma samples. “Our eventual goal is to utilize such gene fusion panels in molecular diagnostic tests for sarcomas,” Tops said.
The new technology is one in a suite of sample preparation products NuGEN continues to develop in light of new scientific understanding about the shared molecular mechanisms underlying cancers originating in different tissues, according to Amorese. While a tumor might appear to originate in a specific organ, the molecular mechanism or change involved may also play a role in cancers originating elsewhere. (For example, certain breast and ovarian cancers exhibit similar genetic changes). This means that therapeutics effective in treating one type of tumor may also be useful in treating other tumors exhibiting similar molecular changes.
Offered in easy-to-use reagent kits, the new method will be used initially by researchers and clinical oncologists to discover the role of gene fusions in many more types of cancer and ultimately be used in molecular diagnostic products to guide treatment. It will also be used by pharmaceutical companies to develop, test and predict the efficacy of specific therapeutics for individual cancer patients.
Amorese likened the new SPET method to “a microscope with greater power to detect fusions than has ever before been available. Now you can look for potential fusion events among hundreds of genes known to be associated with tumors just as easily as you can look at a single gene. Tests that narrowly focus on small subsets of potential fusions can be misleading and fail to take advantage of the power of next gen sequencing. Those tests are just scratching the surface as it relates to understanding what is happening in the cell,” Amorese said.