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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 9: Overlap in genes discriminating VCR-ASP discordant resistance and genes discriminating VCR- and ASP single-drug resistance.

Summary of the overlapping gene probe sets with corresponding gene symbol (GS), map location (ML) and ratio of expression in the unfavorable versus favorable group for VCR-ASP discordant resistance (Ratio). The ratio was calculated using the median log-transformed signal in VCR-sensitive plus ASP-resistant versus VCR-resistant plus ASP-sensitive (>1 is a gene probe set over-expressed in VCR-sensitive plus ASP-resistant ALL cells). A ratio of <1 is a gene probe set under-expressed probe sets in VCR-sensitive plus ASP-resistant ALL cells. The probe sets in overlap between VCR-ASP discordant resistance and single-drug resistance to ASP (A) and single-drug resistance to VCR (B) no overlap was found with PRD or DNR single-drug resistance. See also Supplemental Table 8D.

Probe Set ID	Gene Name	GS	ML	Ratio
203388_at	arrestin, beta 2	ARRB2	17p13	0.54
202315_s_at	breakpoint cluster region	BCR	22q11.23	1.48
212886_at	DKFZP434C171 protein	DKFZP434C171	5q33.1	1.85
200705_s_at	eukaryotic translation elongation factor 1 beta 2	EEF1B2	2q33-q34	1.52
200689_x_at	eukaryotic translation elongation factor 1 gamma	EEF1G	11q12.3	1.35
211927_x_at	eukaryotic translation elongation factor 1 gamma	EEF1G	11q12.3	1.27
210501_x_at	eukaryotic translation initiation factor 3 subunit k	eIF3k	19q13.2	1.33
200005_at	eukaryotic translation initiation factor 3, subunit 7 zeta	EIF3S7	22q13.1	1.36
221773_at	ELK3, ETS-domain protein (SRF accessory protein 2)	ELK3	12q23	0.44
211623_s_at	fibrillarin	FBL	19q13.1	1.40
220306_at	FLJ20202 protein	FLJ20202	1p12	1.84
209602_s_at	GATA binding protein 3	GATA3	10p15	8.01
209604_s_at	GATA binding protein 3	GATA3	10p15	2.74
217807_s_at	glioma tumor suppressor candidate region gene 2	GLTSCR2	19q13.3	1.42
200651_at	guanine nucleotide binding protein (G protein)	GNB2L1	5q35.3	1.42
212070_at	G protein-coupled receptor 56	GPR56	16q13	0.30
213828_x_at	H3 histone, family 3A	H3F3A	1q41	1.30
208755_x_at	H3 histone, family 3A	H3F3A	1q41	1.26
211940_x_at	H3 histone, family 3A	H3F3A	1q41	1.22
209806_at	histone 1, H2be	HIST1H2BE	6p21.3	0.58
201163_s_at	insulin-like growth factor binding protein 7	IGFBP7	4q12	1.93
201015_s_at	junction plakoglobin	JUP	17q21	0.78
200010_at	ribosomal protein L11	RPL11	1p36.1-p35	1.29
200715_x_at	ribosomal protein L13a	RPL13A	19q13.3	1.58
201217_x_at	ribosomal protein L3	RPL3	22q13	1.58
215963_x_at	ribosomal protein L3	RPL3	22q13	1.57
211666_x_at	ribosomal protein L3	RPL3	22q13	1.54
211073_x_at	ribosomal protein L3	RPL3	22q13	1.53
212039_x_at	ribosomal protein L3	RPL3	22q13	1.50
200089_s_at	ribosomal protein L4	RPL4	15q22	1.34
213080_x_at	ribosomal protein L5	RPL5	1p22.1	1.37
200034_s_at	ribosomal protein L6	RPL6	12q24.1	1.33
217740_x_at	ribosomal protein L7a	RPL7A	9q34	1.32
214167_s_at	ribosomal protein, large, P0	RPLP0	12q24.2	1.57
208692_at	ribosomal protein S3	RPS3	11q13.3-q13.5	1.28
200024_at	ribosomal protein S5	RPS5	19q13.4	1.38

B

Probe Set ID	Gene Name	GS	ML	Ratio
219471_at	chromosome 13 open reading frame 18	C13orf18	13q14.11	0.38
44790_s_at	chromosome 13 open reading frame 18	C13orf18	13q14.11	0.38
217523_at	CD44 antigen	CD44	11p13	2.33
218642_s_at	coiled-coil-helix-coiled-coil-helix domain containing 7	CHCHD7	8q11.23	0.63
218951_s_at	hypothetical protein FLJ11323	FLJ11323	xp22.33; yp11.32	0.60
212492_s_at	jumonji domain containing 2B	JMJD2B	19p13.3	0.75
212956_at	KIAA0882 protein	KIAA0882	4q31.1	0.19
221011_s_at	likely ortholog of mouse limb-bud and heart gene	LBH	2p23.3	0.68
200088_x_at	ribosomal protein L12	RPL12	9q34	1.29
200909_s_at	ribosomal protein, large P2	RPLP2	11p15.5-p15.4	1.45
200031_s_at	ribosomal protein S11	RPS11	19q13.3	1.24
213377_x_at	ribosomal protein S12	RPS12	6q23.1	1.30
200781_s_at	ribosomal protein S15a	RPS15A	16p	1.27
212438_at	putative nucleic acid binding protein RY-1	RY1	2p13.3	0.65
204849_at	transcription factor-like 5 (basic helix-loop-helix)	TCFL5	20q13.3-qter	0.15