Skip to main content

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.