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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 2 : False discovery rate.

False Discovery rate (FDR) was determined for the cross-resistance group and the vincristine plus asparaginase (VCR-ASP) discordant resistant group. Corresponding number of probe sets and Spearman's rank correlation P-value (a) are shown. FDR is lower and the number of gene probe sets is higher if the PCA score is based on the in vitro sensitivity data of 441 patients compared to using the PCA score based on the in vitro sensitivity data of only 129 patients.

	In vitro sensitivity of 441 patients				In vitro sensitivity of 129 patients
	Cross-resistance		VCR-ASP discordant resistance		Cross-resistance		VCR-ASP discordant resistance
a	Probe Sets	FDR [%]	Probe sets	FDR [%]	Probe Sets	FDR [%]	Probe sets	FDR [%]
0.00001	12	1.0	118	0.1	0	0	0	0
0.0001	51	2.8	229	0.6	4	23	4	16
0.001	170	8.0	496	2.9	32	40	32	40
0.01	480	20.6	1240	11.7	258	51	274	49