The ALL subtypes of the 129 patients for whom gene expression was performed included 40 with the TEL-AML1 gene fusion t(12;21), 33 hyperdiploid (>50 chromosomes), six with the E2A-PBX1 gene fusion t(1;19), five with the BCR-ABL gene fusion t(9;22) and three with the MLL-AF4 gene fusion t(4;11). The remaining 40 B-lineage ALLs were negative for all five of these genetic subtypes. White blood cell count at diagnosis (WBC), age at diagnosis and sex in patients defined as cross-resistant (n=29) or cross-sensitive (n=38) by the CR-score. Patients with VCR-sensitive plus ASP-resistant ALL (VCR-S+ASP-R, n=42) or VCR-resistant ALL plus ASP-sensitive (VCR-R+ASP-S, n=34), as defined by the VCR-ASP discordant resistance phenotype. TEL-AML1 translocation and hyperdiploidy showed a trend of higher prevalence in younger children, but was not statistically significant in our population (P=0.1074, ANOVA). Sixteen of 34 (47%) ALLs that were VCR-resistant plus ASP-sensitive compared to only three of 42 (7%) that were VCR-sensitive plus ASP-resistant, had the t(12;21) translocation yielding the TEL-AML1 gene fusion (P=0.0001, Fisher's exact test). Fifteen of 34 (44%) ALLs that were VCR-resistant plus ASP-sensitive, compared to only four of 42 (10%) that were VCR-sensitive plus ASP-resistant, were hyperdiploid (P=0.001, Fisher's exact test). All 19 TEL-AML1 positive and 19 hyperdiploid ALLs grouped together in one branch in the hierarchical clustering using the 200 probe sets discriminating VCR-ASP-discordant resistance (Supplemental Figure 6A).
* Fisher's exact test