A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

Table 2 Performance of gene expression algorithms in predicting microsatellite instability

	COAD	STAD	UCEC
TPR
MMR Loss score	0.9 (0.76–0.96)	0.92 (0.82–0.96)	0.94 (0.86–0.98)
Hypermutation Predictor score	0.74 (0.59–0.85)	0.8 (0.68–0.88)	0.94 (0.86–0.98)
MSI Predictor score	0.9 (0.76–0.96)	0.9 (0.8–0.95)	0.93 (0.84–0.97)
FPR
MMR loss score	0.26 (0.2–0.32)	0.3 (0.24–0.36)	0.36 (0.3–0.43)
Hypermutation Predictor score	0.17 (0.12–0.23)	0.23 (0.18–0.29)	0.37 (0.31–0.43)
MSI Predictor score	0.21 (0.16–0.28)	0.25 (0.19–0.31)	0.3 (0.24–0.36)

Note: A p-value threshold of 0.01 was used for all gene expression algorithms. True positive rate (TPR) is the proportion of high-level microsatellite instability (MSI-H) cases detected by each algorithm. False positive rate (FPR) is the proportion of non-hypermutated cases falsely called hypermutated by the gene expression algorithms. Numbers in parentheses give 95% confidence intervals calculated by the Wilson method. COAD colon adenocarcinoma, STAD stomach adenocarcinoma, UCEC uterine corpus endometrial carcinoma