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Table 3 Genotype and allele frequencies of the RA cases and controls for the three candidate genotypes (PTPN22, CTLA-4, and PADI-4) and genotype frequencies of HLA-SE

From: Genetic polymorphisms in PTPN22, PADI-4, and CTLA-4 and risk for rheumatoid arthritis in two longitudinal cohort studies: evidence of gene-environment interactions with heavy cigarette smoking

Gene

Genotype/allele

NHS blood (219 matched pairs)

NHS cheek cell (169 matched pairs)

NHSII blood (49 matched pairs)

  

Cases

Controls

Cases

Controls

Cases

Controls

PTPN22 a

Genotype

      
 

   CC

160 (74%)

178 (82%)

125 (77%)

131 (80%)

37 (79%)

44 (94%)

 

   CT

50 (23%)

38 (18%)

30 (18%)

31 (19%)

7 (15%)

3 (6%)

 

   TT

5 (2%)

1 (0.5%)

8 (5%)

1 (1%)

3 (6%)

0 (0%)

 

   Missing

4

2

6

6

2

2

 

   Pe

0.08

 

0.07

 

0.06

 
 

Allele

      
 

   C

370 (86%)

394 (91%)

280 (86%)

293 (90%)

81 (86%)

91 (97%)

 

   T

60 (14%)

40 (9%)

46 (14%)

33 (10%)

13 (14%)

3 (3%)

 

   Pf

0.03

 

0.12

 

0.009

 

CTLA-4 b

Genotype

      
 

   AA

35 (17%)

46 (22%)

40 (25%)

29 (18%)

7 (15%)

12 (25%)

 

   AG

106 (50%)

96 (45%)

69 (42%)

80 (50%)

26 (54%)

19 (40%)

 

   GG

71 (33%)

70 (33%)

54 (33%)

51 (32%)

15 (31%)

17 (35%)

 

   Missing

7

7

6

9

1

1

 

   Pf

0.37

 

0.27

 

0.28

 
 

Allele

      
 

   A

176 (42%)

188 (44%)

149 (46%)

138 (43%)

40 (42%)

43 (45%)

 

   G

248 (58%)

236 (56%)

177 (54%)

182 (57%)

56 (58%)

53 (55%)

 

   Pf

0.41

 

0.51

 

0.66

 

PADI-4 c

Genotype

      
 

   GG

76 (35%)

76 (36%)

57 (35%)

64 (39%)

22 (45%)

18 (38%)

 

   GA

107 (49%)

101 (47%)

68 (41%)

73 (44%)

16 (33%)

21 (45%)

 

   AA

34 (16%)

37 (17%)

39 (24%)

28 (17%)

11 (22%)

8 (17%)

 

   Missing

2

5

5

4

0

2

 

   Pf

0.87

 

0.30

 

0.47

 
 

Allele

      
 

   G

259 (60%)

253 (59%)

182 (55%)

201 (61%)

60 (61%)

57 (61%)

 

   A

175 (40%)

175 (41%)

146 (45%)

129 (39%)

38 (39%)

37 (39%)

 

   Pf

0.87

 

0.16

 

0.93

 

HLA-SE d

0 copy

84 (38%)

122 (56%)

99 (60%)

114 (70%)

23 (47%)

30 (63%)

 

1 copies

99 (45%)

83 (38%)

52 (32%)

40 (24%)

17 (35%)

17 (35%)

 

2 copies

36 (16%)

14 (6%)

13 (8%)

10 (6%)

9 (18%)

1 (2%)

 

Missing

0

0

5

5

0

1

 

P f

0.0001

 

0.22

 

0.03

 
  1. aUnable to genotype 12 cases and 10 controls. bUnable to genotype 14 cases and 17 controls. cUnable to genotype 7 cases and 11 controls. dUnable to genotype 5 cases and 5 controls. eP values estimated from the Fisher's exact test. fP values estimated from the χ2 test. NHS, Nurses' Health Study; RA, rheumatoid arthritis. OK
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Arthritis Research & Therapy

ISSN: 1478-6362

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