Table 1.

ROC AUC scores for predicting TMB (≥6, ≥10, and ≥20 thresholds) from FFPE RNAseq data, according to TMB-WES standards calculated with matched normal WES profiles.

Filtering method	TMB ≥ 6	TMB ≥ 10	TMB ≥ 20
TCGA (matched norm was used for WES mutation calling)
WES ∩ RNAseq variants	0.925	0.903	1
Default Mutect2 filtering	0.694	0.701	0.781
Default Mutect2 filtering + ExAC <0.000033	0.825	0.757	0.81
ML filtering using XGBoost method	0.825	0.854	0.905
TCGA (matched norm was not used for WES mutation calling)
WES ∩ RNAseq variants	0.953	0.921	1
Default Mutect2 filtering	0.573	0.64	0.726
Default Mutect2 filtering + ExAC <0.000033	0.693	0.763	0.857
ML filtering using XGBoost method	0.7	0.868	0.857
Experimental dataset (high coverage)
WES ∩ RNAseq variants	0.75	1	NA
Default Mutect2 filtering	0.812	0.857	NA
Default Mutect2 filtering + ExAC <0.000033	1	1	NA
Experimental dataset (low coverage)
WES ∩ RNAseq variants	0.719	0.748	NA
Default Mutect2 filtering	0.407	0.226	NA
Default Mutect2 filtering + ExAC <0.000033	0.622	0.674	NA
ML filtering using XGBoost method	0.53	0.613	NA

NA, Not applicable.