An NGS assay for an emerging immuno-oncology biomarker

Immune checkpoint inhibitors have changed the treatment paradigm for a variety of cancers, but not all patients will respond to immunotherapies. Relevant biomarkers have shown to be as important as the therapies since they guide in our quest to help match patients with the appropriate treatment. Our multi-biomarker next-generation sequencing (NGS)-based assays have been adopted by leading cancer institutions to comprehensively profile thousands of clinical research samples. Given the complexity of the immune response and tumor biology, additional biomarkers are needed to evaluate their associations with response to immuno-oncology (I-O) therapies.  Tumor mutational burden (TMB) is an exciting biomarker in multiple disease types that may further immunotherapy research.

The Ion Torrent Oncomine Tumor Mutation Load Assay is a robust, targeted next-generation sequencing (NGS) assay providing clinical researchers with an accurate quantification of somatic mutation counts to assess TMB from limited formalin- fixed, paraffin-embedded (FFPE) samples. Our streamlined, built-in analysis solution allows you to confidently quantify somatic mutations and assess tumor mutational burden in ~2.5 days for your research studies.

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Featured webinar & video

Webinar: Determining tumor mutation load using Oncomine Tumor Mutation Load Assay

Speaker: Dr. Jose Carlos Machado, PhD, Ipatimup, Porto, Portugal

Video: How can the tumor mutation burden be a game changing immuno-oncology biomarker

Dr Wolfram Jochum, Institute of Pathology, Kantonsspital St.Gallen, Switzerland

The next immuno-oncology biomarker

Tumor mutation load may be the next immuno-oncology biomarker to be implemented in our daily routine 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 MSI status of the tumors. 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.

Prof. José Carlos Machado, PhD
Board of Directors member and Group Coordinator
Ipatimup, Porto, Portugal

A large targeted panel for tumor mutational burden assessment

A targeted NGS panel can replace exome sequencing, bringing the advantage of a robust assay designed for oncology research specimens such as FFPE tissue. The Oncomine Tumor Mutation Load Assay enables accurate measurements of somatic mutations without the need of a matched normal sample. As panels become smaller in size, the zone of uncertainty associated with estimates of TMB expands rapidly (Figure 1A). Additionally, the coefficient of variance increases rapidly when the size of targeted panels is less than 1 Mb (Figure 1B), especially at low mutation loads. The Oncomine Tumor Mutation Load Assay covers a large genomic footprint of 1.7 Mb to enable accurate mutation counts for samples with a range of tumor mutational burden.

Our streamlined solution allows you to confidently quantify somatic mutations and assess TMB with limited sample amount in ~2.5 days. Whether you are using our manual or automated library preparation, you will be able multiplex up to 8 samples per Ion 540 Chip for maximum throughput.

  • Prepare libraries from as little as 20 ng of DNA input from FFPE samples
  • Template on the Ion Chef and sequence on the Ion GeneStudio S5 Systems
  • Analyze with Ion Reporter Software for a sample to answer solution

The Ion Reporter analysis workflow has been designed to generate results using a tumor only workflow—and optimized using filters for germline variants.  A fully annoted report of the somatic mutation load and analysis of mutation signatures analysis of mutation signatures may provide meaningful insights for researching the disease etiology (Figure 2).

Figure 2.

Figure 3 below demonstrates consistent reproducibility of the Oncomine Tumor Mutation Load Assay. Multiple sample replicates were processed to measure the reproducibility of the assay. The somatic mutation counts were highly reproducible across multiple sample types, from cell line DNA to FFPE samples, from a variety of cancer types as well as normal tissue. The Oncomine Tumor Mutation Load Assay was tested in a series of retrospectively collected colorectal cancer samples that had been typed for microsatellite instability. As expected, tumor mutational burden counts in microsatellite instability high samples were significantly higher than in microsatellite stable samples.

Figure 3A. Reproducibility of the Oncomine Tumor Mutation Load Assay. Cell lines were obtained from the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research.

Figure 3B. Stratification of MSI positive and MSI negative samples with the Oncomine Tumor Mutation Load Assay. MSI status determined by orthogonal method. Data courtesy of Ipatimup.

Learn more about our multi-dimensional approach to immuno-oncology ›

Learn more about our Oncomine oncology assays for comprehensive genomic profiling ›