Inter-Platform comparability of microarrays in acute lymphoblastic leukemia

BMC Genomics

Table 2 Prediction accuracies for ALL subclasses as determined by the different microarray platforms.

ALL Subclass	Microarray Platform	# of Samples in the Dataset	# of Samples Representing the Predictor Subclass	# of Genes in Predictor (out of 40)¹	Accuracy (%)²	Sensitivity (%)³	Specificity (%)⁴
Hyperdiploid	Affymetrix U95Av2	43^a	5	40	97	80	100
Hyperdiploid	Affymetrix U133A	16^b	7	38	94	86	100
T-ALL	Affymetrix U133A	16^b	9	35	100	100	100
T-ALL	Affymetrix HuGene FL	41^c	8	13	100	100	100
T-ALL	Affymetrix Hu6800	20^d	10	30	95	100	90
T-ALL	cDNA	52^e	7	5	98	86	100
T-ALL	cDNA	9^f	3	29	100	100	100
TEL-AML1	Affymetrix U95Av2	43^a	9	40	91	67	97
TEL-AML1	Affymetrix HuGene FL	23^g	14	30	86	79	100
*TEL-AML1*	cDNA	52^e	12	10	87	83	88
MLL-AF4	Affymetrix U95Av2	43^a	20	40	100	100	100
*MLL-AF4*	cDNA	52^e	2	7	98	50	100
*E2A-PBX1*	Affymetrix HuGene FL	23^c	2	26	96	50	100

¹ With a few exceptions, the majority of the gene lists published by Yeoh et al (2002) contain 40 genes.
² The ability of the predictor to correctly classify the blinded test set into the correct subgroup
³ (# of positive samples predicted correctly)/(total #of true positives)
⁴ (# of negative samples predicted correctly)/(total #of true negatives)
^a Armstrong et al. (2002) Nat. Genet. 30(1), 41–7.
^b Mitchell et al. (2003) Unpublished data.
^c Golub et al. (1999) Science 286, 531–7.
^d Ramaswamy et al. (2001) PNAS 98(26), 15149–54.
^e Moos et al. (2002) Clin Cancer Res. 8, 3118–3130.
^f Catchpoole et al. Unpublished data.
^g Stephan et al. (2000) Unpublished data.

ISSN: 1471-2164