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Supplementary Information

Identification of genes associated with chemotherapy cross-resistance and treatment response in childhood acute lymphoblastic leukemia.

Supplemental Table 5 : Genes discriminating VCR-ASP discordant resistance in pediatric B-lineage ALL.

Summary of the 200 gene probe sets discriminating VCR-ASP discordant resistance (139 genes, 13 cDNA clones) with corresponding Probe Set ID, gene name, gene symbol (GS), map location (ML) and ratio of expression in the unfavorable versus favorable group for VCR-ASP discordant resistance (Ratio). The ratio of expression calculated by the median log-transformed signal in VCR-sensitive plus ASP-resistant versus VCR-resistant plus ASP-sensitive (>1 is over-expressed in VCR-sensitive plus ASP-resistant ALL). A ratio of <1 represents an under-expressed probe sets in VCR-sensitive plus ASP-resistance patients. The 64 under-expressed probe sets in VCR-sensitive plus ASP-resistant samples had a median expression ratio of 0.55, and the 136 over-expressed probe sets had a median expression ratio of 1.32.

Probe Set ID Gene Name GS ML Ratio
207645_s_at chromodomain helicase DNA binding protein 1-like CHD1L 1q12 2.08
200772_x_at prothymosin, alpha (gene sequence 28) PTMA 2q35-q36 1.37
211921_x_at prothymosin, alpha (gene sequence 28) PTMA 2q35-q36 1.37
214097_at ribosomal protein S21 RPS21 20q13.3 1.42
211940_x_at H3 histone, family 3A H3F3A 1q41 1.22
208755_x_at H3 histone, family 3A H3F3A 1q41 1.26
213828_x_at H3 histone, family 3A H3F3A 1q41 1.30
211445_x_at FKSG17 FKSG17 8q22.3 1.37
200094_s_at eukaryotic translation elongation factor 2 EEF2 19pter-q12 1.30
204102_s_at eukaryotic translation elongation factor 2 EEF2 19pter-q12 1.25
211937_at eukaryotic translation initiation factor 4B EIF4B 12q13.13 1.50
201892_s_at

IMP (inosine monophosphate) dehydrogenase 2

IMPDH2 3p21.2 1.81
210501_x_at eukaryotic translation initiation factor 3 subunit k eIF3k 19q13.2 1.33
221494_x_at eukaryotic translation initiation factor 3 subunit k eIF3k 19q13.2 1.35
211623_s_at fibrillarin FBL 19q13.1 1.40
201216_at chromosome 12 open reading frame 8 C12orf8 12q24.13 1.59
213356_x_at heterogeneous nuclear ribonucleoprotein A1 HNRPA1 12q13.1 1.29
200016_x_at heterogeneous nuclear ribonucleoprotein A1 HNRPA1 12q13.1 1.29
200029_at ribosomal protein L19 RPL19 17q11.2-q12 1.27
200081_s_at CDNA clone IMAGE:6301163 unknown4 4q21.3 1.28
200651_at guanine nucleotide binding protein (G protein) GNB2L1 5q35.3 1.42
200936_at ribosomal protein L8 RPL8 8q24.3 1.35
213414_s_at ribosomal protein S19 RPS19 19q13.2 1.23
200010_at ribosomal protein L11 RPL11 1p36.1-p35 1.29
213080_x_at ribosomal protein L5 RPL5 1p22.1 1.37
200858_s_at ribosomal protein S8 RPS8 1p34.1-p32 1.25
200034_s_at ribosomal protein L6 RPL6 12q24.1 1.33
208635_x_at nascent-polypeptide-assoc. complex alpha polypeptide NACA 12q23-q24.1 1.42
200735_x_at nascent-polypeptide-assoc. complex alpha polypeptide NACA 12q23-q24.1 1.29
211939_x_at basic transcription factor 3 BTF3 5q13.3 1.30
208517_x_at basic transcription factor 3 BTF3 5q13.3 1.38
200005_at eukaryotic translation initiation factor 3, subunit 7 zeta EIF3S7 22q13.1 1.36
200036_s_at ribosomal protein L10a RPL10A 6p21.3-p21.2 1.32
212042_x_at ribosomal protein L7 RPL7 8q13.3 1.34
200717_x_at ribosomal protein L7 RPL7 8q13.3 1.26
217740_x_at ribosomal protein L7a RPL7A 9q34 1.32
200088_x_at ribosomal protein L12 RPL12 9q34 1.29
200809_x_at ribosomal protein L12 RPL12 9q34 1.22
214271_x_at ribosomal protein L12 RPL12 9q34 1.32
200715_x_at ribosomal protein L13a RPL13A 19q13.3 1.58
201592_at eukaryotic translation initiation factor 3, subunit 3 gamma EIF3S3 8q24.11 1.53
200024_at ribosomal protein S5 RPS5 19q13.4 1.38
214167_s_at ribosomal protein, large, P0 RPLP0 12q24.2 1.57
211972_x_at ribosomal protein, large, P0 RPLP0 12q24.2 1.35
211720_x_at ribosomal protein, large, P0 RPLP0 12q24.2 1.40
201033_x_at ribosomal protein, large, P0 RPLP0 12q24.2 1.35
208856_x_at ribosomal protein, large, P0 RPLP0 12q24.2 1.35
208692_at ribosomal protein S3 RPS3 11q13.3-q13.5 1.28
211927_x_at eukaryotic translation elongation factor 1 gamma EEF1G 11q12.3 1.27
200689_x_at eukaryotic translation elongation factor 1 gamma EEF1G 11q12.3 1.35
211345_x_at eukaryotic translation elongation factor 1 gamma EEF1G 11q12.3 1.32
213588_x_at ribosomal protein L14 RPL14 3p22-p21.2 1.44
200705_s_at eukaryotic translation elongation factor 1 beta 2 EEF1B2 2q33-q34 1.52
215963_x_at ribosomal protein L3 RPL3 22q13 1.57
201217_x_at ribosomal protein L3 RPL3 22q13 1.58
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
211710_x_at ribosomal protein L4 RPL4 15q22 1.47
201154_x_at ribosomal protein L4 RPL4 15q22 1.39
211542_x_at ribosomal protein S10, clone MGC:10943, mRNA unknown6 --- 1.23
200817_x_at ribosomal protein S10 RPS10 6p21.31 1.30
213890_x_at ribosomal protein S16 RPS16 19q13.1 1.27
200781_s_at ribosomal protein S15a RPS15A 16p 1.27
200926_at ribosomal protein S23 RPS23 5q14.1 1.29
200909_s_at ribosomal protein, large P2 RPLP2 11p15.5-p15.4 1.45
208904_s_at ribosomal protein S28 RPS28 19p13.2 1.29
203034_s_at ribosomal protein L27a RPL27A 11p15 1.31
201492_s_at ribosomal protein L41 RPL41 12q13 1.26
201429_s_at ribosomal protein L37a RPL37A 2q35 1.24
208825_x_at ribosomal protein L23a RPL23A 17q11 1.28
208834_x_at

cadherin 1, type 1, E-cadherin (epithelial)

CDH1 16q22.1 1.31
213377_x_at ribosomal protein S12 RPS12 6q23.1 1.30
201049_s_at ribosomal protein S18 RPS18 6p21.3 1.31
200963_x_at ribosomal protein L31 RPL31 2q12.1 1.29
200763_s_at ribosomal protein, large, P1 RPLP1 15q22 1.26
200061_s_at ribosomal protein S24 RPS24 10q22-q23 1.22
213583_x_at eukaryotic translation elongation factor 1 alpha 1 EEF1A1 6q14.1 1.17
204892_x_at eukaryotic translation elongation factor 1 alpha 1 EEF1A1 6q14.1 1.24
206559_x_at eukaryotic translation elongation factor 1 alpha 1 EEF1A1 6q14.1 1.25
213614_x_at eukaryotic translation elongation factor 1 alpha 1 EEF1A1 6q14.1 1.15
212433_x_at ribosomal protein S2 RPS2 16p13.3 1.27
210646_x_at ribosomal protein L13a RPL13A 19q13.3 1.34
212790_x_at ribosomal protein L13a RPL13A 19q13.3 1.35
221798_x_at ribosomal protein S2 RPS2 16p13.3 1.26
203107_x_at ribosomal protein S2 RPS2 16p13.3 1.17
211942_x_at ribosomal protein L13a RPL13A 19q13.3 1.32
200031_s_at ribosomal protein S11 RPS11 19q13.3 1.24
200716_x_at ribosomal protein L13a RPL13A 19q13.3 1.32
214042_s_at Similar to ribosomal protein L22 (LOC389175), mRNA unknown2 3q26.31 1.48
207132_x_at prefoldin 5 PFDN5 12q12 1.27
221700_s_at

ubiquitin A-52 residue ribosomal protein fusion product 1

UBA52 19p13.1-p12 1.21
200013_at MAM domain containing 2 MAMDC2 9q21.13-q21.2 1.29
214143_x_at ribosomal protein L24 RPL24 3q12 1.28
200082_s_at ribosomal protein S7 RPS7 2p25 1.21
213941_x_at ribosomal protein S7 RPS7 2p25 1.41
200012_x_at CDNA clone MGC:71781 IMAGE:5287560 unknown3 4q12 1.28
200091_s_at ribosomal protein S25 RPS25 11q23.3 1.22
221775_x_at ribosomal protein L22 RPL22 1p36.3-p36.2 1.28
208768_x_at ribosomal protein L22 RPL22 1p36.3-p36.2 1.29
213687_s_at ribosomal protein L35a RPL35A 3q29-qter 1.29
211487_x_at ribosomal protein S17, clone MGC:11144, mRNA unknown5 --- 1.27
201665_x_at ribosomal protein S17 RPS17 15q 1.21
200062_s_at ribosomal protein L30 RPL30 8q22 1.29
208645_s_at ribosomal protein S14 RPS14 5q31-q33 1.26
200018_at ribosomal protein S13 RPS13 11p15 1.30
200092_s_at ribosomal protein L37 RPL37 5p13 1.21
216380_x_at ribosomal protein S28 RPS28 19p13.2 1.26
217807_s_at

glioma tumor suppressor candidate region gene 2

GLTSCR2 19q13.3 1.42
217747_s_at ribosomal protein S9 RPS9 19q13.4 1.33
214317_x_at ribosomal protein S9 RPS9 19q13.4 1.38
217313_at AC004692 PAC clone RP5-1107K12 from 7p12-p14 unknown1 --- 1.24
200022_at ribosomal protein L18 RPL18 19q13 1.34
200003_s_at ribosomal protein L28 RPL28 19q13.4 1.35
200869_at ribosomal protein L18a RPL18A 19p13 1.35
211475_s_at BCL2-associated athanogene BAG1 9p12 1.40
209087_x_at melanoma cell adhesion molecule MCAM 11q23.3 1.98
210869_s_at melanoma cell adhesion molecule MCAM 11q23.3 1.48
212481_s_at tropomyosin 4 TPM4 19p13.1 1.53
209604_s_at GATA binding protein 3 GATA3 10p15 2.74
209602_s_at GATA binding protein 3 GATA3 10p15 8.01
217787_s_at polypeptide UDP-N-acetylgalactosaminyltransferase 2 GALNT2 1q41-q42 2.30
204897_at prostaglandin E receptor 4 (subtype EP4) PTGER4 5p13.1 2.73
217523_at CD44 antigen (homing function and Indian blood group) CD44 11p13 2.33
212886_at DKFZP434C171 protein DKFZP434C171 5q33.1 1.85
205434_s_at AP2 associated kinase 1 AAK1 2p24.3-p14 1.45
220306_at FLJ20202 protein FLJ20202 1p12 1.84
60528_at phospholipase A2, group IVB (cytosolic) PLA2G4B 15q11.2-q21.3 1.20
202315_s_at breakpoint cluster region BCR 22q11.23 1.48
213897_s_at mitochondrial ribosomal protein L23 MRPL23 11p15.5-p15.4 1.70
201163_s_at insulin-like growth factor binding protein 7 IGFBP7 4q12 1.93
201403_s_at microsomal glutathione S-transferase 3 MGST3 1q23 1.51
217809_at basic leucine zipper and W2 domains 2 BZW2 7p21.2 1.52
211709_s_at stem cell growth factor; lymphocyte secreted C-type lectin SCGF 19q13.3 3.20
205131_x_at stem cell growth factor; lymphocyte secreted C-type lectin SCGF 19q13.3 3.73
209073_s_at numb homolog (Drosophila) NUMB 14q24.3 0.71
209806_at histone 1, H2be HIST1H2BE 6p21.3 0.58
215245_x_at fragile X mental retardation 1 FMR1 xq27.3 0.60
212476_at centaurin, beta 2 CENTB2 3q29 0.56
209004_s_at F-box and leucine-rich repeat protein 5 FBXL5 4p15.33 0.64
218951_s_at hypothetical protein FLJ11323 FLJ11323 xp22.33; yp11.32 0.60
206219_s_at vav 1 oncogene VAV1 19p13.2 0.74
219131_at transitional epithelia response protein TERE1 1pter 0.65
212438_at putative nucleic acid binding protein RY-1 RY1 2p13.3 0.65
200709_at FK506 binding protein 1A, 12kDa FKBP1A 20p13 0.72
203611_at telomeric repeat binding factor 2 TERF2 16q22.1 0.38
205267_at POU domain, class 2, associating factor 1 POU2AF1 11q23.1 0.39
213039_at rho/rac guanine nucleotide exchange factor (GEF) 18 ARHGEF18 19p13.3 0.57
39318_at T-cell leukemia/lymphoma 1A TCL1A 14q32.1 0.46
209995_s_at T-cell leukemia/lymphoma 1A TCL1A 14q32.1 0.42
208990_s_at heterogeneous nuclear ribonucleoprotein H3 (2H9) HNRPH3 10q22 0.58
203302_at deoxycytidine kinase DCK 4q13.3-q21.1 0.63
221725_at WAS protein family, member 2 WASF2 1p36.11-p34.3 0.67
212492_s_at jumonji domain containing 2B JMJD2B 19p13.3 0.75
221011_s_at likely ortholog of mouse limb-bud and heart gene LBH 2p23.3 0.68
218642_s_at coiled-coil-helix-coiled-coil-helix domain containing 7 CHCHD7 8q11.23 0.63
219253_at family with sequence similarity 11, member B FAM11B 2q14.2 0.72
204698_at interferon stimulated gene 20kDa ISG20 15q26 0.37
33304_at interferon stimulated gene 20kDa ISG20 15q26 0.58
218076_s_at Rho GTPase activating protein 17 ARHGAP17 16p12.2 0.65
204849_at transcription factor-like 5 (basic helix-loop-helix) TCFL5 20q13.3-qter 0.15
219753_at stromal antigen 3 STAG3 7q22.1 0.36
202838_at fucosidase, alpha-L- 1, tissue FUCA1 1p34 0.48
221747_at tensin TNS 2q35-q36 0.52
221748_s_at tensin TNS 2q35-q36 0.48
209695_at protein tyrosine phosphatase type IVA, member 3 PTP4A3 8q24.3 0.49
44790_s_at chromosome 13 open reading frame 18 C13orf18 13q14.11 0.38
219471_at chromosome 13 open reading frame 18 C13orf18 13q14.11 0.38
203388_at arrestin, beta 2 ARRB2 17p13 0.54
200696_s_at gelsolin (amyloidosis, Finnish type) GSN 9q33 0.57
217984_at ribonuclease T2 RNASET2 6q27 0.59
217983_s_at ribonuclease T2 RNASET2 6q27 0.63
204265_s_at G-protein signalling modulator 3 GPSM3 6p21.3 0.70
221601_s_at regulator of Fas-induced apoptosis TOSO 1q32.1 0.49
221602_s_at regulator of Fas-induced apoptosis TOSO 1q32.1 0.26
219256_s_at SH3 domain and tetratricopeptide repeats 1 SH3TC1 4p16.1 0.50
221757_at LIM domain kinase 2 LIMK2 22q12.2 0.54
221756_at LIM domain kinase 2 LIMK2 22q12.2 0.57
203710_at inositol 1,4,5-triphosphate receptor, type 1 ITPR1 3p26-p25 0.54
205928_at zinc finger protein 443 ZNF443 19p13.2 0.45
204689_at hematopoietically expressed homeobox HHEX 10q23.33 0.62
215933_s_at hematopoietically expressed homeobox HHEX 10q23.33 0.66
209431_s_at zinc finger protein 278 ZNF278 22q12.2 0.69
214958_s_at epidermodysplasia verruciformis 1 EVER1 17q25.3 0.56
201015_s_at junction plakoglobin JUP 17q21 0.78
212070_at G protein-coupled receptor 56 GPR56 16q13 0.30
221773_at ELK3, ETS-domain protein (SRF accessory protein 2) ELK3 12q23 0.44
209568_s_at ral guanine nucleotide dissociation stimulator-like 1 RGL1 1q25.2 0.48
221641_s_at acyl-Coenzyme A thioesterase 2, mitochondrial ACATE2 xp22.13 0.35
207571_x_at chromosome 1 open reading frame 38 C1orf38 1p35.3 0.50
210785_s_at chromosome 1 open reading frame 38 C1orf38 1p35.3 0.44
212956_at KIAA0882 protein KIAA0882 4q31.1 0.19
220230_s_at cytochrome b5 reductase b5R.2 CYB5R2 11p15.4 0.52
204011_at sprouty homolog 2 (Drosophila) SPRY2 13q22.2 0.45
201663_s_at SMC4 structural maintenance of chromosomes 4-like 1 SMC4L1 3q26.1 0.72
201260_s_at synaptophysin-like protein SYPL 7q22.2 0.71
203978_at nucleotide binding protein 1 (MinD homolog, E. coli) NUBP1 16p13.2 0.72
207390_s_at smoothelin SMTN 22q12.2 0.41
203680_at protein kinase, cAMP-dependent, regulatory, type II PRKAR2B 7q22 0.48

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