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Table 2 Association with T1D conditional on the presence of the respective HLA-Bw4 epitope, tested in the joint copy number group KIR3DS1 - KIR3DL1 (a), and in the marginal KIR3DL1 (b) and KIR3DS1 (c) copy number groups

From: A hybrid qPCR/SNP array approach allows cost efficient assessment of KIR gene copy numbers in large samples

a) HLA-Bw4 subset

qPCR

SNP

KIR3DS1-KIR3DL1

Case:control

Total

OR

95% CI

p-value

Case:control

Total

OR

95% CI

p-value

0-2

259:286

545

1.00

  

1027:1157

2184

1

  

1-1

123:128

251

1.06

0.79-1.43

0.6976

555:582

1137

1.08

0.93-1.24

0.3119

2-0

16:15

31

1.22

0.58-2.57

0.5985

59:88

147

0.76

0.54-1.07

0.1133

2-1

7:13

20

0.59

0.23-1.51

0.2754

34:40

74

0.93

0.58-1.48

0.7529

1-2

8:8

16

1.10

0.41-2.98

0.8450

24:33

57

0.85

0.5-1.45

0.5502

0-1

10:7

17

1.58

0.59-4.20

0.3621

36:24

60

1.69

1-2.85

0.0491

1-0

2:1

3

2.21

0.20-24.50

0.5187

7:4

11

1.97

0.58-6.76

0.2793

3-0

3:0

3

   

5:0

5

   

Overall

428:458

886

  

0.8978

1747:1928

3675

  

0.2173

b) HLA-Bw4 subset

qPCR

SNP

KIR3DL1

Case:control

Total

OR

95% CI

p-value

Case:control

Total

OR

95% CI

p-value

2

267:294

561

1.00

  

1051:1190

2241

1

  

1

140:148

288

1.04

0.78-1.38

0.7787

625:646

1271

1.09

0.95-1.26

0.1975

0

21:16

37

1.45

0.74-2.83

0.2822

71:92

163

0.88

0.64-1.21

0.4181

Overall

428:458

886

  

0.5563

1747:1928

3675

  

0.2586

c) HLA-Bw4-80I subset

qPCR

SNP

KIR3DS1

Case:control

Total

OR

95% CI

p-value

Case:control

Total

OR

95% CI

p-value

0

159:187

346

1.00

  

649:733

1382

1

  

1

93:83

176

1.32

0.92-1.90

0.1370

383:366

749

1.18

0.99-1.41

0.0628

2

12:14

26

1.01

0.45-2.24

0.9842

61:75

136

0.91

0.64-1.3

0.607

3

2:0

2

   

3:0

3

   

Overall

266:284

550

  

0.5209

1096:1174

2270

  

0.2416

  1. Association is tested in the subset of individuals carriers of an HLA-Bw4 epitope for the joint KIR3DS1-KIR3DL1 (a) and marginal KIR3DL1 (b) copy number groups and, also tested in the subset of individuals carriers of the HLA-Bw4-80I epitope for the marginal KIR3DS1 (c) copy number group. Case-control counts shown are derived from the most likely copy number assignment across the ten multiply imputed qPCR and SNP datasets. Statistical inference for association is derived from the multiply imputed datasets using the R mitools package [13]. The last row of each table contains the pooled p-value for each association test using the R mice package [14].
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BMC Genomics

ISSN: 1471-2164

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