Table 3.

a: Predictive performance and comparison of clinical phenotypes in blood and biopsy by microarrays and RNA-seq using 5-fold cross validation.
Microarray Blood	# Genes*	Sensitivity	Specificity	PPV	NPV	AUC
cAR vs. TX	200	0.857	0.848	0.825	0.876	0.957
subAR vs. TX	100	0.652	0.792	0.742	0.712	0.954
Microarray Biopsy	# Genes*	Sensitivity	Specificity	PPV	NPV	AUC
cAR vs. TX	150	1.000	0.920	0.913	1.000	1.000
subAR vs. TX	250	0.918	0.872	0.863	0.923	0.993
RNA-seq Blood	# Genes*	Sensitivity	Specificity	PPV	NPV	AUC
cAR vs. TX	30	1.000	0.933	0.937	1.000	1.000
subAR vs. TX	250	0.867	0.933	0.928	0.875	0.962
NGS Biopsy	# Genes*	Sensitivity	Specificity	PPV	NPV	AUC
cAR vs. TX	100	0.990	0.925	0.916	0.991	0.990
subAR vs. TX	300	0.714	0.866	0.824	0.776	0.926

b: Predictive performance and comparison of clinical phenotypes in blood and biopsy by microarrays and RNA-seq using bootstrap methodology
Microarray Blood	# Genes*	Sensitivity	Specificity	PPV	NPV	AUC
cAR vs. TX	300	0.941	0.904	0.888	0.950	0.963
subAR vs. TX	20	0.714	0.861	0.833	0.756	0.817
Microarray Biopsy	# Genes*	Sensitivity	Specificity	PPV	NPV	AUC
cAR vs. TX	200	0.918	0.869	0.850	0.930	1.000
subAR vs. TX	350	0.916	0.705	0.687	0.923	0.951
RNA-seq Blood	# Genes*	Sensitivity	Specificity	PPV	NPV	AUC
cAR vs. TX	250	1.000	1.000	1.000	1.000	1.000
subAR vs. TX	150	0.937	1.000	1.000	0.909	0.877
NGS Biopsy	# Genes*	Sensitivity	Specificity	PPV	NPV	AUC
cAR vs. TX	30	0.974	0.976	0.974	0.976	0.999
subAR vs. TX	200	0.767	0.902	0.891	0.787	0.778

^*Best classifier set; AUC, area under the curve; cAR, clinical acute rejection; NPV, negative predictive value; PPV, positive predictive value; subAR, subclinical acute rejection; TX, transplant excellence.