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Supplementary Information

Gene-expression patterns in drug resistant acute lymphoblastic leukemia cells and response to treatment.

Supplemental Table 6 : Gene expression scores for the intermediate sensitivity group, using genes selected to discriminate resistant and sensitive B-lineage ALL.

We randomly split the resistant and sensitive patients into 2/3 training set and 1/3 test set. Additionally, all patients with an intermediate drug sensitivity phenotype were included in the test set. In each random split, probe sets were reselected based on the training set. A patient in the test set was assigned a score of 1 if classified by the model as sensitive and 2 if resistant; no score was assigned to patients in the training set. The above was repeated 1000 times to compute a gene expression score for each patient as the average of scores assigned to the patient. Median gene expression scores of resistant (R), sensitive (S) and intermediate (I) samples as well as the range in parentheses are presented based on 50 and 100 probe sets. The P-values are given for each pair-wise comparison, using Wilcoxon rank sum test. Patients with intermediate drug sensitivity had median scores that were between the median gene expression score of the drug sensitive and drug resistant groups for all four antileukemic agents. For asparaginase and prednisolone, the gene expression scores of the intermediate group were significantly different from both the sensitive group and the resistant group (P<0.05, Wilcoxon rank sum test). For daunorubicin and vincristine, the intermediate group was significantly different from the sensitive group, but not from the resistant group.

  N

Score
Resistant (R)

Score
Intermediate (I)

Score
Sensitive (S)

P-value
R vs. S

P-value
R vs. I

P-value
I vs. S

PRED 50

1.28 (1.01-1.96)

1.04 (1-1.88)

1.02 (1-1.65)

<0.001

0.002

0.044

  100

1.29 (1-1.99)

1.01 (1-1.92)

1.01 (1-1.72)

<0.001

0.001

0.035

VCR 50

1.28 (1.01-1.88)

1.29 (1.01-1.61)

1.11 (1.01-1.9)

0.006

0.659

0.002

  100

1.26 (1-1.93)

1.24 (1-1.68)

1.08 (1-1.94)

0.002

0.518

0.002

ASP 50

1.53 (1.03-1.91)

1.31 (1.02-1.88)

1.14 (1.01-1.97)

<0.001

0.013

0.004

  100

1.51 (1.02-1.91)

1.31 (1-1.92)

1.1 (1-1.98)

<0.001

0.024

0.008

DNR 50

1.16 (1-1.5)

1.11 (1-1.71)

1.04 (1-1.6)

0.021

0.404

0.09

  100

1.15 (1-1.47)

1.07 (1-1.81)

1.01 (1-1.56)

0.019

0.583

0.045

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