Oncomine Tumor Mutation Load Assay

The Ion Reporter analysis workflow has been designed to generate results with a tumor-only workflow. Using the Oncomine Variant Annotator Plugin, driver variants are separated from passenger mutations, allowing the user to focus on the relevant few specific to targeted therapies.  A simple TMB readout (Mutations/Mb) is provided in addition to a detailed analysis of mutation signatures, providing meaningful insights for researching the disease etiology (Figure 1).

Figure 1.

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 2A). Additionally, the coefficient of variance increases rapidly when the size of targeted panels is less than 1 Mb (Figure 2B), especially at low mutation loads. The Oncomine Tumor Mutation Load Assay covers a large genomic footprint of 1.7 Mb, encompassing 1.2 Mb of exonic sequence, to enable accurate mutation counts for samples with a range of tumor mutational burden.

High reproducbility
TMB was measured by running the assay on eight pairs of replicates. The TMB values were highly correlated (Pearson’s R = 0.99) and demonstrated reproducibility across multiple cancer types and sample types, from cell line DNA to FFPE samples (Figure 3A).  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, high microsatellite instability samples had significantly higher TMB values than microsatellite stable samples.