Next-Generation Sequencing Cancer Research Assays from Thermo Fisher Scientific

New Oncomine products enable immune response analysis of the tumor microenvironment, interrogation of BRCA 1-2 genes, and liquid biopsy research using cell-free DNA from breast and colon cancer samples.

Thermo Fisher Scientific has announced four new additions to its portfolio of multi-biomarker targeted assays for cancer research, including the Oncomine Immune Response Research Assay, which is designed to interrogate the tumor microenvironment and enable identification of predictive biomarkers for immunotherapy clinical research trials. The very low sample input gene expression assay for Ion Torrent next-generation sequencing (NGS) platforms targets low expressing transcripts derived from FFPE samples. This solution, plus other new Oncomine-based assays for cancer research, is being highlighted this week at the 2016 Association of Molecular Pathology (AMP) meeting Nov. 10-12.

Development of new drugs that help activate the body’s natural defense system against cancer is an exciting new research area being pursued by pharmaceutical companies. The promising work is being driven by poor survival rates for certain cancer types and the limited number of therapy options available due to drug resistance. Studies have shown that a combination of genomically targeted compounds and immune therapies can extend survival rates, but a lack of effective tools to accurately measure expression of key genes slows the pace of discovery.

“Low-expressing genes play a critical role in regulating the immune system,” said Carl Morrison, M.D., DVM, founder, president and chief scientific officer of OmniSeq LLC, a subsidiary of Roswell Park Cancer Institute. “While there are hundreds of immune therapy trials underway, many do not incorporate key biomarkers necessary for successfully stratifying tumor samples. NGS-based solutions like the Oncomine Immune Research Assay can help elucidate expression of these relevant variants more effectively.”

Using the power of targeted NGS, the Oncomine Immune Response Research Assay is a 395-gene panel that is specifically designed to identify expression of key genes in the immune system pathway using just 10ng of FFPE RNA. Mutliplexing four, eight, or 32 samples per run enables cost-effective experiments on a sample-to-data solution using the automated Ion Chef and Ion S5 systems.

In development and validation studies, the Oncomine Immune Response Research Assay demonstrated more than 20-fold improvement in detection over transcriptome analysis, high reproducibility for detecting low expression cytokine-encoding genes, and high sensitivity and specificity for detecting differential expression as low as two-fold. More information on this assay will be shared by Jeffrey M. Conroy, senior vice president of Technology Development at OmniSeq LLC, who will lead a presentation on immune cancer profiling during a Thermo Fisher workshop today from 1-1:50 pm EST.

All new Oncomine assays are part of an end-to-end workflow that includes targeted sequencing on Ion Torrent sequencers, including the Ion PGM, and Ion S5 and Ion S5 XL systems, as well as optimized bioinformatics.

The Oncomine BRCA Research Assay is optimized for comprehensive analysis of the BRCA 1 and 2 genes for both somatic and germline mutations from FFPE tissue. It is based on Ion AmpliSeq technology and provides 100 percent coverage, including flanking intronic sequences (average of 64 bases in either direction), via sequencing on the Ion Torrent platform. The assay’s performance on challenging FFPE tissue has been evaluated by 22 laboratories and is described in a poster presented this year at the annual European Conference of Pathology (ECP).

Available in the coming weeks, the Oncomine Breast cfDNA Assay and the Oncomine Colon cfDNA Assay are multi-biomarker next-generation sequencing (NGS) research assays that enable detection of primary driver and resistance mutations from cell-free DNA down to a level of 0.1 percent. The research assays—developed with the OncoNetwork Consortia—are part of a comprehensive workflow that achieves high sensitivity and specificity for SNV hotspots and indels with the help of an optimized variant caller. Enabling results in less than two days with Ion Chef System automation and Ion S5 System sequencing, the assays add to a comprehensive set of Thermo Fisher liquid biopsy research applications.

“As researchers broaden their efforts to push discovery in promising areas of cancer research, we also are driven to enable their work through development of sophisticated analysis tools,” said Joydeep Goswami, president of clinical sequencing for Thermo Fisher Scientific. “We are happy to be able to extend our multibiomarker Oncomine research assays to the areas of Immune response and liquid biopsy and privileged to see rapid adoption by customers who are leveraging this technology for applications ranging from basic research, drug development and clinical trial placement.”