Product News: Thermo Fisher Scientific Expands Oncomine Portfolio for Liquid Biopsy and Immuno-Oncology Clinical Research

New pan-cancer cell-free total nucleic acid (cfTNA) assay and FFPE-based tumor mutation load analysis assay

09 Jan 2018

Thermo Fisher Scientific has expanded its Oncomine portfolio with new assays for liquid biopsy and immuno-oncology to complement its comprehensive solutions for clinical research. The company also announced its next generation Ion AmpliSeq HD technology, which now adds highly customizable design capabilities to solid tumor and cell-free DNA panels. These innovations extend Thermo Fisher’s commitment to help researchers bring new cancer diagnostics to clinic. 

Pan-Cancer Cell-Free Total Nucleic Acid Assay Delivers Fastest Liquid Biopsy Solution 
The Ion Torrent Oncomine Pan-Cancer Cell-Free Assay enables reproducible detection and analysis of tumor DNA and RNA across all major classes of somatic mutations (SNVs, indels, CNVs and fusions) from a single vial of blood with as little as 1ng of nucleic acid input within two days. Targeting more than 50 genes across multiple cancer types, including lung, colorectal, breast, pancreatic, thyroid and others, the cell-free total nucleic acid (cfTNA) assay is the broadest developed by Thermo Fisher for liquid biopsy clinical research applications. 
“The new Oncomine Pan-Cancer Cell-Free Assay addresses our unmet need to sequence samples for multiple tumor entities in a single run,” said Luca Quagliata, M.D., senior director of contract R&D at University Hospital Basel, Switzerland. “We evaluated this new product and obtained solid results. We now look forward to adding the Oncomine Pan-Cancer Assay into our portfolio.” 
Analysis of tumor DNA and RNA from blood has rapidly become a non-invasive alternative to sequencing tissue samples. It also holds promise as a method to accelerate targeted clinical trials, targeted therapy selection, disease monitoring and drug resistance. In addition to the new pan-cancer product, the Oncomine liquid biopsy portfolio for clinical research includes five single-indication-focused assays with the same rapid sample-to-answer workflow on a single platform. 

Tumor Mutation Load Assay Joins Growing Immuno-Oncology Portfolio 
Immuno-oncology clinical research has shown that the level of mutational burden is directly linked to therapeutic response in immunotherapies. The Ion Torrent Oncomine Tumor Mutation Load Assay is based on a carefully selected set of 409 genes that can be sequenced using as little as 20 nanograms of formalin-fixed paraffin-embedded (FFPE) DNA.  
The assay is designed to improve potential selection strategies for immune therapy clinical trials. It follows the recent introduction of  Ion AmpliSeq Immune Repertoire Assay Plus, TCR beta, which helps identify population subsets predisposed to immune-mediated adverse events, and the Oncomine Immune Response Research Assay, which characterizes gene expression in tumor microenvironment for immune response pathways. Together these comprise a complete suite of solutions for immunooncology clinical research. 
“We used the Oncomine Tumor Mutation Load Assay on a retrospective colon cancer cohort, and were able to separate high and low mutation load samples with results correlating well with the microsatellite instability status of the tumors,” said Professor Jose Carlos Machado, Ph.D., group coordinator for the Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP) in Porto, Portugal. “The assay yielded rapid and robust results with its streamlined informatics. Together with other Oncomine assays, we truly have a comprehensive solution for tumor samples.” 
Both new assays integrate with Ion Torrent sample preparation, targeted sequencing and downstream bioinformatics and reporting tools, such as the Oncomine Knowledgebase Reporter – one of the largest curated sets of evidence in oncology research. The entire solution is the industry’s most-complete, endto-end workflow based on a single platform. When combined with the newly launched Ion GeneStudio S5 Series instruments, the entire offering provides clinical researchers a set of comprehensive, costeffective and rapid sample-to-answer tools they can implement in their own lab.  

Ion AmpliSeq HD Technology Improves Accuracy and Design Flexibility for cfDNA and FFPE Assays 
Ion AmpliSeq HD technology is a new, highly customizable, next-generation core chemistry that can achieve increased detection sensitivity down to ≤0.1 percent mutant allele fractions in blood samples. A proprietary primer design process will help expand the scope of fixed panels and enable clinical researchers to, for the first time, create custom-design cell-free DNA (cfDNA) panels with maximum flexibility. The technology will be equally applicable to FFPE samples and will extend the benefits of heightened sensitivity beyond what is currently available.   
In both blood and solid tumor applications, the heightened performance achieved with Ion AmpliSeq HD technology offers several distinct benefits in addition to ultra-high sensitivity, including workflow improvements that reduce library preparation time to less than three hours. When available second quarter of 2018, the new chemistry will serve as a foundational solution—alongside Ion AmpliSeq technology—to power gene panels currently in development. 
“We are delivering best-in-class tools designed to enable further advancements in precision oncology,” said Joydeep Goswami, president of Clinical Next-Generation Sequencing and Oncology at Thermo Fisher. “The latest Oncomine assays, in combination with Ion AmpliSeq HD technology, help strengthen Thermo Fisher’s leadership in providing clinical and research oncology solutions.”