St. Jude Research/Supplemental Data/ALL2

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Meyling H. Cheok, Wenjian Yang, Ching Hon Pui, James R. Downing, CHeng Cheng, Clayton W. Naeve, Mary V. Relling, William E. Evans

SUPPLEMENTARY CONTENTS

Sections

A. Patient characteristics and bone marrow sampling times

B. Clustering of patients based on gene expression patterns

C. Selection of discriminating genes

D. Common gene expression changes after all treatments

E. RNA source, RNA quality and array reproducibility

F. TaqMan real-time RT-PCR (RT-PCR

Individual Figures

Fig. 1: Treatment regimen and bone marrow sampling times

Fig. 2: "Unsupervised” hierarchical clustering and principal component analysis (PCA)

Fig. 3: Discriminating genes by different gene selection methods

Fig. 4: Hierarchical clustering of changes in expression for selected genes

Fig. 5: Treatment-induced changes in percentage of ALL cells in S-phase

Fig. 6: Commonly regulated genes after all four initial treatments

Fig. 7: Concordance between replicate gene expression experiments

Fig. 8: Real-time (TaqMan) RT-PCR vs. Affymetrix GeneChip®

Fig. 9: Fold-change RT-PCR versus Affymetrix GeneChip®

Fig. 10: Leave-one-out cross-validation of treatment classification

Individual Tables

Table 1: Patient characteristics

Table 2: Discriminating genes by fold-change and post-treatment expression

Table 3: Discriminating genes by one-versus-all distinction calculation

Table 4(a) & (b): Changes in gene expression after single agent chemotherapy versus the same agents in combination

Table 5(a) & (b): Human leukemia cell lines differ from primary ALL cells

Table 6: Primers and probes used for real-time (TaqMan) RT-PCR

Table 7: Genes discriminating each treatment from all others