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Table 2 8-SNP haplotype association tests for the best haplotype pattern (rs7550106, rs499697, rs17659389, rs17670505) derived by multi-locus stepwise regression (MSR) with four known FLG mutations (S3247X, R2447X, 2282del4, R501X) added in that order for case control set and replicated by family set.

From: Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis

  

Case control set

Family set

  

Freq. (n = 1914)

FLG (n = 1914)

NON-FLG (n = 1605)

FLG (268 families)

NON-FLG (162 families)

Haplotypes

Cases

Controls

OR

p value

OR

p value

Freq.

T:U

OR

p value

T:U

OR

p value

2222

2222

0.3656

0.4028

0.83

1.05 E-02

1.07

4.10E-01

0.3992

206.3:256.1

0.81

2.08 E-02

138.6:152.4

0.91

4.18 E-01

2222

2212

0.0102

0.0035

4.92

2.67 E-03

  

0.0039

2.0:6.0

0.33

1.58 E-01

   

2222

2221

0.0052

0.0062

0.80

6.50 E-01

  

0.0011

2.1:0.1

38.89

1.66 E-01

   

2222

2122

0.0030

0.0041

0.63

4.80 E-01

  

NA

NA

NA

NA

   

2222

Total

0.3841

0.4166

0.85

2.43 E-02

  

0.4042

210.4:262.1

0.80

1.74 E-02

   

2212

2222

0.1180

0.1392

0.78

2.43 E-02

0.95

6.34E-01

0.1077

110.6:91.8

1.20

1.86 E-01

66.5:59.6

1.11

5.42 E-01

2212

2212

0.0014

0.0018

0.53

6.35 E-01

  

NA

NA

NA

NA

   

2212

2221

0.0010

0.0012

0.63

7.79 E-01

  

0.0011

1.1:1.1

1.00

1.00 E+00

   

2212

Total

0.1204

0.1422

0.76

1.28 E-02

  

0.1088

111.7:92.9

1.20

1.89 E-01

   

2122

2222

0.1289

0.1488

0.81

4.78 E-02

0.90

3.44E-01

0.1205

93.7:126.6

0.74

2.66 E-02

64.1:79.9

0.80

1.87 E-01

2122

2221

0.0241

0.0032

12.65

1.75 E-10

  

0.0267

35.2:18.3

1.92

2.07 E-02

   

2122

2212

0.0123

0.0037

7.00

1.21 E-04

  

0.0068

7.0:8.0

0.87

7.91 E-01

   

2122

2122

0.0114

0.0012

22.62

7.16 E-07

  

0.0115

15.0:9.0

1.67

2.21 E-01

   

2122

2211

0.0034

0.0000

NA

NA

  

NA

NA

NA

NA

   

2122

Total

0.1800

0.1569

1.23

2.69 E-02

  

0.1655

150.9:161.9

0.93

5.34 E-01

   

2121

2212

0.0448

0.0028

31.26

3.10 E-24

  

0.0538

74.0:38.0

1.95

6.61 E-04

   

2121

2222

0.0267

0.0295

0.88

5.63 E-01

0.97

8.94E-01

0.0123

11.8:13.8

0.85

6.92 E-01

5.7:9.7

0.59

3.08 E-01

2121

2221

0.0075

0.0000

NA

NA

  

0.0019

2.0:2.0

1.00

1.00 E+00

   

2121

Total

0.0790

0.0322

2.65

5.22 E-10

  

0.0680

87.7:53.7

1.63

4.22 E-03

   

2112

2222

0.0562

0.0892

0.49

2.43 E-06

0.59

8.22E-04

0.0582

46.8:68.0

0.69

4.73 E-02

24.2:36.3

0.67

1.19 E-01

2112

2212

0.0041

0.0016

6.23

4.20 E-02

  

0.0048

4.0:6.0

0.67

5.27 E-01

   

2112

2221

0.0015

0.0010

2.59

4.73 E-01

  

0.0029

2.1:3.0

0.69

6.75 E-01

   

2112

Total

0.0618

0.0917

0.60

3.89 E-04

  

0.0659

52.8:77.1

0.69

3.37 E-02

   

1222

2222

0.0982

0.0785

1.36

1.69 E-02

1.71

5.55E-05

0.1186

124.8:88.6

1.41

1.30 E-02

92.0:54.9

1.68

2.19 E-03

1222

1222

0.0061

0.0010

8.05

2.77 E-03

  

NA

NA

NA

NA

   

1222

Total

0.1043

0.0795

1.42

4.81 E-03

  

0.1186

124.8:88.6

1.41

1.30 E-02

   
  1. Logistic regression was used for testing a single haplotype for the case control set and the weighted TDT statistic was used for a single haplotype by computing transmitted (T) versus non-transmitted (U) haplotypes. Calculations were carried out for the full set (FLG) and the FLG reduced sets (NON-FLG). The minor allele was coded as 1 and the major one as 2. For the sake of following the rare FLG mutations the frequency threshold for the 8-SNP haplotype estimation had been lowered to 0.001, however, only combined with best pattern haplotypes down to a total frequency > 0.05 in the full case set.
  2. Abbreviations are as follows: Freq., haplotype frequency; OR, odds ratio; FLG, Filaggrin gene; T:U, transmitted:non-transmitted; NA, not available.
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