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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 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