Microsatellite instability assessment of FFPE tumor samples through targeted next-generation sequencing.

Abstract

e14213 Background: Immunotherapies to treat malignancies have shown great promise, however, only a fraction of cancer patients respond to immunotherapy, making it imperative to identify biomarkers that predict response. Cancer-associated instabilities at microsatellite locations throughout the genome have been shown to be predictive of response to immunotherapy treatment. Here we determine the accuracy of determining the MSI status through targeted sequencing using Ion Torrent sequencing technology. Methods: We have identified optimal chemistry and developed a novel algorithm to assess MSI status of samples using a large number of markers on the Ion GeneStudio S5 Series sequencer. The diverse marker set includes monomers that vary in length between 10 BP and 40 BP in addition to di-and tri-nucleotide STR markers. Each sample is assigned an MSI score based on features that measure MSI response of markers in the assay. Results: We evaluated performance of the MSI markers in the context of a comprehensive targeted next generation sequencing assay with the MSI algorithm. A large set of FFPE tumor samples and MSI controls were evaluated. The resulting scores were in concordance with results from capillary electrophoresis studies. Conclusions: In summary, a next-generation sequencing based assay using multiple markers was developed to assign MSI status to FFPE tumor samples. The accuracy of the assay was validated using an orthogonal test. This allows us to use Ion Torrent sequencing technology to identify changes in complex repeat regions of the genome as part of a comprehensive genomic profiling approach.