Supplementary Information for: Identification of genes associated with chemotherapy cross-resistance and treatment response in childhood acute lymphoblastic leukemia. Sanne Lugthart 1,2,6,8 , Meyling H. Cheok 1,2,8 , Monique L. den Boer 6 , Wenjian Yang 1,2,5 , Amy Holleman 6 , Cheng Cheng 3 , Ching-Hon Pui 1,4,5 , Mary V. Relling 1,2,5 , Gritta E. Janka-Schaub 7 , Rob Pieters 6,9 , William E. Evans 1,2,5,9 1 Hematological Malignancy Program 2 Department of Pharmaceutical Sciences 3 Department of Biostatistics 4 Department of Hematology-Oncology ,St. Jude Children's Research Hospital , Memphis , USA 5 The Pharmacogenetics of Anticancer Agents Research Group in the Pharmacogenetics Research Network, Memphis , Tennessee , USA 6 Department of Pediatric Oncology/Hematology ,Erasmus University Medical Center/Sophia Children's Hospital, ,Rotterdam , The Netherlands 7 COALL study group ,Children's University Hospital , Hamburg , Germany 8 These first authors contributed equally to this work. 9 These last authors contributed equally to this work.

Supplemental Table 8: Overlap in genes discriminating multiple-drug cross-resistance and genes discriminating PRD-, VCR-, ASP- and DNR single-drug resistance.

Summary of the overlapping gene probe sets with corresponding gene symbol (GS), map location (ML) and ratio of the median log-transformed expression signal in cross-resistant versus cross-sensitive ALL for multiple-drug cross-resistance (Ratio). A gene probe set with a ratio of >1 is over-expressed and with a ratio of <1 is under-expressed probe sets in cross-resistant ALL compared to cross-sensitive ALL. The probe sets in overlap between multiple-drug cross-resistance and single-drug resistance to PRD (A), ASP (B) and DNR (C) alone are shown, highlighted in orange and yellow are genes that are in common, no overlap was found with VCR alone. (D) Rows indicate the overlapping genes (n) for single-drug resistance PRD, VCR, ASP, DNR; and columns overlapping genes (n) and percentages for cross-resistance (CR) and VCR-ASP discordant resistance (VA). Overlap occurs in cases the total is not matching the sum of the genes. (1) shows the numbers and the percentages if the significant set of genes identified were compared and (2) shows the results if the analysis is done using the same number of genes for multiple-drug resistance versus single-drug resistance.

A