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Table 3 Lung cancer genomic sequencing classifier validation performance (Down, up classification). *Cancer prevalence calculation includes local benign subjects as Prevalence = \( \frac{\# Malignant}{\# Malignant+\# Benign+\# Local\ Benign} \). The local benign subjects had local label as benign but did not have an adjudicated label. NPV, PPV and % Reclassified are all functions of prevalence (estimated including local benign subjects), sensitivity and specificity (both estimated excluding local benign subjects)

From: Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts

AUC Pre-test Cancer Risk *Cancer prevalence Cancer risk re-stratification Specificity Sensitivity Post-test NPV/PPV §% Re-stratified
73.4% [68.3–78.4] Low 5% Low to Very Low 57.4% [44.8–69.3] 100% [39.8–100] 100% NPV [91.0–100] 54.5%
Intermediate 28.2% Intermediate to Low 37.3% [27.9–47.4] 90.6% [79.3–96.9] 91.0% NPV [80.8–96.0] 29.4%
Intermediate to High 94.1% [87.6–97.8] 28.3% [16.8–42.3] 65.4% PPV [43.8–82.1] 12.2%
High 73.6% High to Very High 91.2% [76.3–98.1] 34.0% [25.0–43.8] 91.5% PPV [77.9–97.0] 27.3%
  1. §% Reclassified (Low to Very Low, Intermediate to Low) = (1- Prevalence) specificity + Prevalence (1-sensitivity)
  2. §% Reclassified (Intermediate to High, High to Very High) = Prevalence sensitivity + (1-Prevalence) (1- specificity)
  3. * There are 8, 33 and 4 local benign subjects in low, intermediate and high-risk group