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Supplementary Information

Treatment Specific Changes in Gene Expression Discriminate in vivo Drug Response
in Human Leukemia Cells

A. Patient Characteristics and Bone Marrow Sampling Times

Figure 1: Treatment regimen and bone marrow sampling times



Figure 1: Treatment regimen and bone marrow sampling times.

Bone marrow samples from children with acute lymphoblastic leukemia (ALL) were obtained at diagnosis (BM Pre-TX) and one day post-treatment (BM Post-TX) with mercaptopurine (MP) or high-dose methotrexate (HDMTX) given alone, or mercaptopurine in combination with either low-dose MTX (LDMTX+MP) or high-dose MTX (HDMTX+MP).

Table 1: Patient characteristics.

(a) The study included 60 pediatric patients with newly diagnosed ALL randomized to one of four initial treatments (“training set”). (b) Additionally, 17 new patients from the current protocol were included as an independent “test set”.

(a) treatment n (n=60) age at diagnosis
(median in years)
sex race lineage DNA ploidy molecular translocations
MP 12 6.8 male: 7
female: 5
white: 10
black: 2
other: 0
B: 8
T: 4
hyperdiploid: 1
other: 11
MLL: 1
E2A-PBX: 0
TEL-AML: 1
BCR-ABL: 0
ND2: 10
HDMTX 22 6 male: 14
female: 8
white: 19
black: 1
other: 2
B: 19
T: 3
hyperdiploid: 4
other: 18
MLL: 0
E2A-PBX: 2
TEL-AML: 9
BCR-ABL: 0
ND2: 11
HDMTX+MP 10 5 male: 5
female: 5
white: 8
black: 1
other: 1
B: 8
T: 2
hyperdiploid: 0
other: 10
MLL: 2
E2A-PBX: 1
TEL-AML: 3
BCR-ABL: 0
ND2:4
LDMTX+MP 16 6.1 male: 13
female: 3
white: 12
black: 1
other: 3
B: 13
T: 3
hyperdiploid: 2
other: 14
MLL: 0
E2A-PBX: 0
TEL-AML: 4
BCR-ABL: 0
ND2: 12
P value1   P=0.726 P=0.390 P=0.665 P=0.552 P=0.643 P=0.120


(b) treatment n (n=17) age at diagnosis
(median in years)
sex race lineage DNA ploidy molecular translocations
HDMTX 17 5 male: 11
female: 6
white: 8
black: 5
other: 4
B: 13
T: 4
hyperdiploid: 8
other: 9
MLL: 0
E2A-PBX: 0
TEL-AML: 2
BCR-ABL: 1
ND2: 14

1P value determined by Fisher’s exact test except Age by Wilcoxon’s rank sum test. 2ND=none detected