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Table 1 Significant SNPs (FDR q value < 0.005) associated with paclitaxel response along with statistical information

From: Bioinformatic analyses identifies novel protein-coding pharmacogenomic markers associated with paclitaxel sensitivity in NCI60 cancer cell lines

CHR

Marker

RS_ID

Gene Name

Gene Description

A1

AF_R

AF_S

A2

UNADJ

BONF

FDR_BH

CHISQ

OR

L95

U95

1p31.1

91699

rs371363

LPHN2

Latrophilin 2, G-protein coupled receptor

A

0.5

0.0714

G

2.58E-06

0.2051

0.00477

22.11

13

3.741

45.17

2q14

1413956

rs1898705

  

A

0.571

0.0851

G

1.76E-06

0.1405

0.003902

22.84

14.33

3.975

51.69

2q14.3

1421343

   

C

0.438

0.0313

A

1.32E-07

0.01052

0.001169

27.84

24.11

5.296

109.8

2q31.2

1481588

   

T

0.25

0

C

1.02E-06

0.08144

0.003192

23.88

NA

NA

NA

2q33.1

1503580

   

A

0.5

0.0375

G

1.26E-06

0.1006

0.003354

23.48

25.67

4.721

139.5

2q35

1523870

rs6739040

  

A

0.286

0

G

1.39E-06

0.1104

0.003451

23.3

NA

NA

NA

2q36.3

1538316

   

T

0.375

0.0213

C

4.74E-07

0.03773

0.002331

25.37

27.6

4.902

155.4

3p24.3

1743877

   

C

0.286

0

A

2.32E-07

0.0185

0.001542

26.74

NA

NA

NA

3p14.2

1785132

   

G

0.333

0.0106

C

6.86E-07

0.05459

0.002481

24.66

46.5

4.628

467.2

3p12.3

1805457

rs1032966

ROBO1

roundabout, axon guidance receptor, homolog 1 (Drosophila)

A

0.333

0.0111

G

1.20E-06

0.09528

0.003354

23.58

44.5

4.428

447.3

3q26.1

1876142

rs2404571

  

G

0.667

0.0854

A

2.81E-07

0.02238

0.001721

26.38

21.43

5.136

89.41

4p15.3

1929743

rs685064

  

C

0.313

0.0114

T

2.01E-06

0.1602

0.004162

22.58

39.55

4.224

370.3

5q23.2

2254477

rs959300

  

G

0.714

0.1111

A

9.98E-08

0.007946

0.001135

28.38

20

5.274

75.84

5q33.3

2292501

rs7715464

SGCD

sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)

A

0.563

0.0851

G

1.04E-06

0.08298

0.003192

23.85

13.82

4.06

47.05

5q33.3

2294131

   

A

0.313

0.0102

G

5.15E-07

0.04098

0.002331

25.21

44.09

4.714

412.4

6p25.1

2325528

rs2073042

  

A

0.786

0.1622

G

1.12E-06

0.08914

0.003301

23.71

18.94

4.587

78.25

6p22.3

2343860

   

A

0.917

0.141

C

5.87E-09

0.000467

0.000156

33.88

67

7.85

571.8

6q14

2403189

   

A

0.333

0.0116

G

2.09E-06

0.1665

0.004162

22.51

42.5

4.227

427.3

6q22.1

2440993

rs594930

  

C

0.4

0.0217

T

1.38E-06

0.1098

0.003451

23.31

30

4.542

198.2

7q31.2

2626491

rs213988

CFTR

Cystic fibrosis transmembrane conductance regulator

G

0.438

0.0444

A

2.03E-06

0.1616

0.004162

22.57

16.72

4.093

68.31

8p12

2715222

   

G

0.25

0

A

1.72E-06

0.1373

0.003902

22.88

NA

NA

NA

8q11.22

2727769

rs2385525

  

C

0.429

0.0217

T

7.93E-08

0.006315

0.001052

28.82

33.75

5.829

195.4

8q11.22

2727770

rs2132528

  

G

0.5

0.0256

A

3.77E-08

0.003005

0.00063

30.26

38

6.591

219.1

8q11.22

2727954

   

T

0.583

0.0778

G

1.75E-06

0.1392

0.003902

22.85

16.6

4.165

66.17

8q11.22

2728154

rs318885

SNTG1

syntrophin, gamma 1

G

0.6

0.025

T

1.70E-09

0.000136

6.78E-05

36.29

58.5

8.841

387.1

8q24.21

2806750

rs2568409

  

G

0.643

0.0455

T

4.79E-10

3.81E-05

3.81E-05

38.76

37.8

8.573

166.7

9p23

2835786

   

G

0.25

0

A

6.07E-07

0.04836

0.002418

24.89

NA

NA

NA

9p23

2836025

rs7470838

PTPRD

protein tyrosine phosphatase, receptor type, D

T

0.857

0.2245

C

1.47E-06

0.1168

0.003538

23.19

20.73

4.311

99.66

9p23

2836880

   

T

0.714

0.1413

C

1.26E-06

0.1005

0.003354

23.48

15.19

4.143

55.72

9p22.2

2845463

   

G

0.25

0

A

7.88E-07

0.06275

0.002728

24.39

NA

NA

NA

9p21.2

2856599

rs2060439

  

G

0.25

0

A

6.07E-07

0.04836

0.002418

24.89

NA

NA

NA

9q21.33

2897567

   

G

0.6

0.0488

A

1.24E-07

0.009894

0.001169

27.95

29.25

5.814

147.2

11q14.1

494182

rs7927911

  

A

0.429

0.0256

C

8.37E-07

0.06661

0.002775

24.27

28.5

4.912

165.4

12q21

629187

   

G

0.25

0

A

3.61E-07

0.02874

0.002053

25.89

NA

NA

NA

13q13.3

709113

rs7335400

  

A

0.563

0.0714

C

1.58E-07

0.01257

0.001251

27.49

16.71

4.781

58.43

13q21.33

748668

   

G

0.857

0.1628

A

3.96E-08

0.003151

0.00063

30.17

30.86

6.213

153.2

13q32.1

779846

rs727299

DCT

dopachrome tautomerase

T

0.313

0.01

C

3.92E-07

0.03122

0.002081

25.73

45

4.812

420.8

16p13.3

997458

rs714181

BTBD12

BTB (POZ) domain containing 12

A

0.313

0.0104

G

6.76E-07

0.05379

0.002481

24.68

43.18

4.616

404

16p13.12

1011445

rs251919

  

C

0.438

0.0385

T

2.41E-06

0.1918

0.004566

22.24

19.44

4.257

88.81

16q23.3

1071765

   

G

0.571

0.0745

C

5.27E-07

0.04196

0.002331

25.16

16.57

4.476

61.35

18p11.22

1162169

rs3975417

  

T

0.333

0.0116

C

2.09E-06

0.1665

0.004162

22.51

42.5

4.227

427.3

19q13.12

1266548

rs958305

ZNF607

zinc finger protein 607

C

0.5

0.061

T

2.18E-06

0.1738

0.004239

22.43

15.4

4.058

58.44

21q21.3

1647581

rs457531

GRIK1

glutamate receptor, ionotropic, kainate 1

T

0.5

0.0349

C

1.73E-07

0.01377

0.001251

27.31

27.67

5.504

139.1

  1. Significant SNPs were traced back to their genes using dbSNP Build 131 in order to identify which protein-coding genes they belonged to. (CHR = Chromosome loci, Marker = SNP ID number on Affymetrix 125 k SNP Array, RS_ID = SNP rs number, Gene Name = Notation for gene as found on Human Genome Organization Gene Nomenclature Committee website, A1 = Associated SNP allele, A2 = Alternate variant allele, AF_R = Frequency of associated allele in resistant cell lines, AF_S = frequency of associated allele in sensitive cell lines, UNADJ = unadjusted p value, BONF = Bonferroni correction value, FDR_BH = FDR correction value, CHISQ = Chi-Squared Value, OR = Odds Ratio, L95 = Lower Bound of 95% confidence interval for odds ratio, U95 = Upper Bound of 95% confidence interval for odds ratio). Statistics with NA written indicate that the statistic could not be calculated. This GWAS was performed using only 58 of the 62 cell lines which had drug response data available since the remaining 4 cell lines lacked available genotype data.
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BMC Medical Genomics

ISSN: 1755-8794

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