Gene-based outcome prediction in multiple cohorts of pediatric T-cell acute lymphoblastic leukemia: a Children's Oncology Group study

Table 4 Validation of gene-classifier models for outcome prediction across multiple T-ALL cohorts

Model	Cohort	Acc	PPV	NPV	Sens	Spec	P-value
5-GC (5 genes)	Training	82	81	83	77	86	9.4 × 10^-6
	Validation	79	100	78	22	100	0.064
	COG 9404†	75	71	76	36	93	0.025
	POG 8704†	68	83	66	29	96	0.066
	Combined	76	81	75	47	93	1.5 × 10 ^-9 (1.2 × 10 ^-4 )
Pathway NFκB (7 genes)	Training	76	71	81	77	75	4.8 × 10^-4
	Validation	-	-	-	-	-	-
	COG 9404†	77	83	76	36	97	0.009
	POG 8704†	56	44	59	24	79	1
	Combined	70	67	72	49	84	7.2 × 10 ^-5 (0.073)
Pathway Wnt/Ca²⁺/cGMP (12 genes)	Training	76	75	77	68	82	4.6 × 10^-4
	Validation	-	-	-	-	-	-
	COG 9404†	75	67	77	43	90	0.019
	POG 8704†	68	63	72	59	75	0.05
	Combined	73	69	76	58	83	8.7 × 10 ^-7 (0.0011)
Pathway Cell Adhesion (14 genes)	Training	82	84	81	73	89	8.6 × 10^-6
	Validation	-	-	-	-	-	-
	COG 9404†	75	62	81	57	83	0.012
	POG 8704†	85	87	85	76	92	1.1 × 10^-5
	Combined	81	79	82	70	88	8.2 × 10 ^-12 (4.5 × 10 ^-7 )

Cohorts represent the Training Cohort (HG-U133Plus2, n = 50), Validation Cohort (qRT-PCR, n = 34), COG 9404 (HG-U133Plus2, n = 44), and POG 8704 (HG-U133A, n = 41); Acc, Accuracy; PPV, Positive Predicted Value; NPV, Negative Predicted Value; Sens, Sensitivity; Spec, Specificity (all model performances given as % and combined using means weighted for cohort size and CCR/relapse patient composition); P-value, Fisher's Exact Test of individual or combined model performances across the four cohorts (significance with the omission of the Training Cohort given in parenthesis); † Microarray cohorts downloaded from Winter et al (2007).

ISSN: 1476-4598