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Table 3 Performance of gene expression algorithms and microsatellite instability in predicting hypermutation

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

  COAD STAD UCEC
TPR
 MMR Loss score 0.77 (0.62–0.87) 0.8 (0.69–0.88) 0.73 (0.63–0.81)
 Hypermutation Predictor score 0.65 (0.5–0.78) 0.74 (0.63–0.83) 0.83 (0.74–0.9)
 MSI Predictor score 0.79 (0.65–0.89) 0.79 (0.67–0.87) 0.74 (0.65–0.82)
 MSI status 0.86 (0.73–0.93) 0.88 (0.78–0.94) 0.74 (0.65–0.82)
FPR
 MMR loss score 0.1 (0.06–0.15) 0.11 (0.07–0.16) 0.13 (0.08–0.19)
 Hypermutation Predictor score 0.02 (0.01–0.05) 0.04 (0.02–0.08) 0.12 (0.08–0.18)
 MSI Predictor score 0.04 (0.02–0.08) 0.03 (0.02–0.07) 0.03 (0.01–0.07)
 MSI status 0.01 (0–0.04) 0 (0–0.03) 0.01 (0–0.05)
  1. Note: A p-value threshold of 0.01 was used for all gene expression algorithms. True positive rate (TPR) is the proportion of hypermutated cases detected by algorithm scores below a p-value threshold of 0.01 or by a high-level microsatellite instability (MSI-H) call. False positive rate (FPR) is the proportion of non-hypermutated cases falsely called hypermutated by gene expression algorithms of MSI-H calls. Numbers in parentheses give 95% confidence intervals calculated by the Wilson method. COAD = colon adenocarcinoma; STAD = stomach adenocarcinoma; UCEC = uterine corpus endometrial carcinoma