SAN CARLOS, Calif.—Scientists at NuGEN Technologies Inc. have simultaneously surveyed the 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—based on NuGEN’s Single Primer Enrichment Technology (SPET), which allows the simultaneous interrogation of multiple, specific genes for RNA sequencing—is said to significantly simplify fusion detection when compared with standard RNA sequencing approaches.
The method “can greatly enhance scientists’ ability to understand the underlying oncogenic impact of a variety of genomic disruptions,” according to Elizabeth Hutt, NuGEN’s CEO. “Applications based on this exciting new technology promise to speed up cancer research and lead to more effective diagnoses and treatments.”
As described in the June 1, 2015, issue of the peer-reviewed journal PLOS ONE, in a paper titled “An efficient method for identifying gene fusions by targeted RNA sequencing from fresh frozen and FFPE samples,” 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 disruption of regulatory mechanisms. 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’s 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.”
Reportedly, the assay is fully customizable to target any gene or set of genes in any genome; it will be the foundation for a suite of sample preparation products provided by NuGEN. Offered in easy-to-use reagent kits, the new method will initially be employed to discover the role of gene fusions in many more types of cancer. It will ultimately be used in molecular diagnostic products to guide treatment.