Breakthrough  proves efficacy of new sample preparation method that could accelerate cancer research and development of treatments and diagnostic tests.  Reported in peer-reviewed PLOS One

San Carlos, June   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), the method  “can greatly enhance scientists’ ability to understand the underlying oncogenic impact of a variety of genomic disruptions,” 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.”

As described in the June 1, 2015 issue of the peer-reviewed journal PLOS One, 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 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 in PLOS, “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.”

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 disruptions). This means that therapeutics effective in treating one type of tumor may also be useful in treating other tumors exhibiting similar molecular changes.

“Our technology allows researchers to better understand the cellular pathways that are disrupted,” Amorese said.

NuGEN’s new technology, offered in easy-to-use reagent kits, will initially be employed by researchers and clinical oncologists seeking to group tumors by genomic signature. “Such classifications will make it possible to develop and target therapies more effectively,” Amorese said.

The new, SPET-based technology will also be used by laboratories developing diagnostic tests and by pharmaceutical companies to develop, test and predict the efficacy of specific therapeutics for individual cancer patients. All of the above will   contribute to the realization of precision medicine, Hutt said.

Amorese likened the new SPET method to “a microscope with greater power to detect fusions than has ever before been available.” Now, he said, “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.

The complete article, “An Efficient Method for identifying gene fusions by targeted RNA sequencing from fresh frozen and FFPE samples,”  is by  Jonathan A. Scolnick, Michelle Dimon, I-Ching Wang, Stephanie C. Huelga, and Douglas A. Amorese, all of NuGEN Technologies. The article is available free of charge at .


NuGEN Technologies Inc. is a rapidly-growing, privately-held company that provides  innovative products and systems used to prepare biologic samples for targeted genomic analysis.  Founded in 2000 and based in San Carlos, CA, NuGEN has long been at the cutting edge of genomic technology, with accurate, cost-effective reagent kits for even the most challenging sample types.  NuGEN products are used in more than 1000 leading life science institutes and in diagnostic and pharmaceutical  companies in 40 countries.