Table 3.

Gene-expression signatures.

Event	Genes	Data	AUC	Sens	Spec
TCMR	All genes	Training data	0.96 (0.92–1.00)	0·85	0·89
		Cross-validation	0.80 (0.75–0.83)	0.67 (0.59–0.70)	0.81 (0.71–0.88)
TCMR	IFNG, IP-10, ITGA4, MARCH8, RORc,	Training data	0.95 (0.91–1.00)	0.85	0.93
	SEMA7A, WDR40A	Cross-validation	0.84 (0.77–0.88)	0.67 (0.59–0.74)	0.85 (0.75–0.89)
BKVN	All genes	Training data	0.93 (0.85–1.00)	0.71	0.93
		Cross-validation	0.68 (0.64–0.73)	0 (0–0.25)	0.91 (0.85–0.94)
BKVN	IL-15, IL1R2, MARCH8, PDCD1,	Training data	0.95 (0.90–1.00)	0.71	0.91
	TGFB, WDR40A	Cross-validation	0.73 (0.66–0.80)	0.43 (0·29–0.57)	0.89 (0.83–0.91)

Signature-development (training) data comprised the following groups of patients defined according to the criteria in Table 1: Rejectors (n = 27) with T-cell mediated rejection providing a single sample per patient, collected between zero and nine days (median three days) prior to the date of the diagnostic biopsy; Stable (n = 27) patients providing a summary (median) of the predicted probabilities for all samples from a given patient (10 to 20 samples per patient, median 12, total 335 samples); BKVN (n = 7) patients with biopsy-proven BK-virus nephropathy providing a single sample per patient collected within seven days before or after a diagnostic biopsy (median zero days); Gene-expression signatures resulted from gene selection based on penalised logistic regression with elastic net penalty (Supplementary Fig. S5 and Fig. S11); AUC – area under the receiver operating characteristics (ROC) curve with 95% DeLong confidence interval; Sens – sensitivity; Spec – specificity; Cut-offs for Sens and Spec– probability of TCMR 0·5, probability of BKVN 0·2; Cross-validation – summary of model performance measures based on the predicted probabilities for unseen data obtained in each of 50 repeats of seven-fold cross-validation cycles – median (2.5^th – 97.5^th centile).

Highlighted in bold the most relevant AUC.