Detecting Microsatellite Instability in Endometrial, Colon, and Stomach Cancers Using Targeted NGS

SIMPLE SUMMARY: Among the genomic biomarkers, high microsatellite instability (MSI-H) has received FDA approval for selecting patients for immunotherapy with checkpoint inhibitors. In this regard, methods for accurate testing of MSI-H for a wide range of tumors are required. In this study, we developed an MSI testing method based on NGS of 81 microsatellite repeats and assessed its accuracy in 294 tumors from three cancer types. The method achieved the accuracy of classification of MSI-H and MSS tumors with AUC 0.99. The method can be integrated into the procedure of genomic profiling of tumors in standard clinic practice. Due to the use of a relatively large number of microsatellite markers, the method provides a quantitative assessment of MSI status and can be used in studies of the significance of MSI load as a prognostic marker of treatment outcome. ABSTRACT: Purpose: To develop a method for testing the MSI based on targeted NGS. Methods: Based on the results of previous studies, 81 microsatellite loci with high variability in MSI-H tumors were selected, and a method for calculating the MSI score was developed. Using the MSI score, we defined the MSI status in endometral (162), colon (153), and stomach (190) cancers. Accuracy of the MSI scores was evaluated by comparison with MMR immunohistochemistry for 137 endometrium (63 dMMR and 74 pMMR), 76 colon (29 dMMR and 47 pMMR), and 81 stomach (8 dMMR and 73 pMMR) cancers. Results: Classification of MSS and MSI-H tumors was performed with AUC (0.99), sensitivity (92%), and specificity (98%) for all tumors without division into types. The accuracy of MSI testing in endometrial cancer was lower than for stomach and colon cancer (0.98, 87%, and 100%, respectively). The use of 27 loci only, the most informative for endometrial cancer, increased the overall accuracy (1.00, 99%, and 99%). Comparison of MSI score values in 505 tumors showed that MSI score is significantly higher in colon (p < 10(−5)) and stomach (p = 0.008) cancer compared with endometrial cancer. Conclusion: The MSI score accurately determines MSI status for endometrial, colon, and stomach cancers and can be used to quantify the degree of MSI.