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Table 3 Genotype-based associations with RA (case-control comparison, reference is major allele homozygote)

From: Meta-genetic association of rheumatoid arthritis and PTPN22using PedGenie 2.1

 

PedGenie 2.1

   
 

NARAC Study 1a

NARAC Study 2b

Meta-analysis

Previously publishedc

PTPN22

Genotyped

OR

95% CI

p-trende

OR

95% CI

p-trende

OR

95% CI

p-trendf

OR

95% CI

p-trend

rs3789604

AC

0.94

0.69–1.26

 

1.16

0.93–1.46

 

1.07

0.91–1.26

 

1.15

0.93–1.42

 
 

CC

1.68

0.83–3.38

0.39

1.25

0.70–2.21

0.18

1.43

0.93–2.18

0.12

1.78

1.13–2.79

0.014

rs1217413

TC

1.44

1.11–1.87

 

1.34

1.08–1.66

 

1.38

1.17–1.63

    
 

CC

1.71

1.06–2.75

0.003

1.52

1.00–2.31

0.002

1.59

1.14–2.22

<0.001

   

rs1217388

TC

1.49

1.14–1.93

 

1.30

1.05–1.61

 

1.37

1.15–1.63

    
 

CC

1.30

0.78–2.17

0.017

1.27

0.86–1.87

0.026

1.28

0.94–1.74

0.003

   

ss38346943

TC

0.32

0.15–0.69

 

0.88

0.48–1.61

 

0.61

0.39–0.95

    
 

CC

--

--

--

--

--

--

--

--

--

   

rs1310182

CT

1.55

1.13–2.13

 

1.39

1.11–1.73

 

1.45

1.20–1.75

 

1.22

0.98–1.77

 
 

TT

1.57

1.07–2.30

0.011

1.62

1.18–2.22

<0.01

1.60

1.25–2.03

<0.001

1.32

0.97–1.54

0.052

rs2476601

CT

1.92

1.41–2.60

 

2.36

1.84–3.04

 

2.18

1.80–2.65

 

2.19

1.73–2.78

 

(R620W)

TT

1.96

0.74–5.21

<0.001

2.91

1.26–6.74

<0.001

2.53

1.32–4.84

<0.001

2.90

1.37–6.18

<0.001

rs12730735

AG

1.00

0.75–1.31

 

1.10

0.89–1.36

 

1.06

0.89–1.25

    
 

GG

0.48

0.29–0.80

0.08

0.56

0.37–0.83

0.14

0.53

0.39–0.72

0.024

   

rs12760457

AG

1.01

0.75–1.36

 

1.09

0.87–1.37

 

1.06

0.89–1.26

    
 

GG

0.48

0.28–0.82

0.09

0.55

0.37–0.82

0.14

0.52

0.38–0.72

0.023

   

rs2488458

GA

1.51

1.15–1.97

 

1.33

1.07–1.66

 

1.40

1.18–1.67

    
 

AA

1.27

0.79–2.05

0.014

1.20

0.81–1.78

0.037

1.23

0.91–1.67

0.003

   

rs1217414

CT

1.02

0.77–1.35

 

0.85

0.69–1.04

 

0.91

0.78–1.06

    
 

TT

0.60

0.34–1.03

0.20

0.70

0.46–1.06

0.053

0.65

0.46–0.92

0.018

   
  1. aProblem 2 data, 446 family cases and 103 family controls in 202 affected NARAC pedigrees, 664 independent NYC controls; excludes Plenge et al. [6] samples.
  2. bProblem 2 data, samples in Plenge et al. [6] candidate gene file, 839 family cases in 463 pedigrees and 854 independent NYC controls.
  3. cCarlton et al. [5] sample set 2, 661 random independent cases from NARAC pedigrees and 1322 NYC controls; adjusted for R620W or rs3789604 (R620W).
  4. dMinor allele heterozygote and homozygote genotypes according to Carlton et al. [5] Table 1.
  5. eEmpirical confidence intervals and chi-square p-values, 1000 simulations; p < 0.05 in bold.
  6. fEmpirical confidence intervals and CMH chi-square trend test p-values, 1000 simulations; p < 0.05 in bold.
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BMC Proceedings

ISSN: 1753-6561

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