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).
| Cross-sensitive | Cross-resistant | P-value* | VCR-R+ASP-S | VCR-S+ASP-R | P-value* | |
| Sex | ||||||
| Female | 15 | 12 | 1.00 | 16 | 19 | 1.00 |
| Male | 23 | 17 | 18 | 23 | ||
| Age | ||||||
| <10 years | 34 | 16 | 0.002 | 27 | 28 | 0.30 |
| >10 years | 4 | 13 | 7 | 14 | ||
| WBC | ||||||
| <50/nL | 24 | 20 | 0.80 | 23 | 27 | 0.81 |
| >50/nL | 14 | 9 | 11 | 15 | ||
| ALL subtype | ||||||
| B-lineage other | 9 | 18 | 0.006 | 3 | 25 | <0.0001 |
| BCR-ABL | 2 | 1 | 0 | 5 | ||
| E2A-PBX1 | 5 | 0 | 0 | 3 | ||
| MLL-AF4 | 0 | 1 | 0 | 2 | ||
| TEL-AML1 | 11 | 6 | 16 | 3 | ||
| Hyperdiploid | 11 | 3 | 15 | 4 |
* Fisher's exact test