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Table 1 Contribution of HW disequilibrium to p value distribution, evaluated by regression analysis. Significant F tests (p < 0.05) demonstrating evidence of the contribution of HW disequilibrium to the p value distributions are shown in bold font

From: Assessing transmission ratio distortion in extended families: a comparison of analysis methods

  Allb, c Sequenceda, c Nuclearb, c
Method TDT PDT FBAT TDT PDT FBAT TDT PDT FBAT
Regression model of - log10 p values at all SNPs
R 2 full –R 2 reduced 4.4 × \( {10}^{-4} \) 3.6 × \( {10}^{-7} \) 1.5 × \( {10}^{-6} \) 0.0018 3.6 × \( {10}^{-8} \) 2 × \( {10}^7 \) 2.9 × \( {10}^{-6} \) 8.26 × \( {10}^{-9} \) 3.5 × \( {10}^{-7} \)
 # SNPse 6.1 × \( {10}^6 \) 5.6 × \( {10}^6 \) 2.1 × \( {10}^6 \) 3.2 × \( {10}^6 \) 3 × \( {10}^6 \) 8 × \( {10}^5 \) 3.6 × \( {10}^6 \) 2.1 × \( {10}^6 \) 5 × \( {10}^5 \)
Regression models of - log10 p values greater than 3 only    
R 2 full –R 2 reduced 0.002 8.4 × \( {10}^{-5} \) 8.8 × \( {10}^{-4} \) 0.0015 \( {\mathrm{NA}}^f \) 0.006 0.014 0.01 0.01
# SNPse 8 × \( {10}^4 \) 517 870 1777 11 19 3.3 × \( {10}^4 \) 53 54
F-test p-valuesd
 All SNPs 0.00 0.16 0.07 0.00 0.74 0.69 0.00 0.89 0.68
P< \( {10}^{-3} \) 0.00 0.84 0.38 0.10 NAf 0.82 0.00 0.49 0.50
  1. aFull model is given by Eq. (1)
  2. bFull model is given by Eq. (2)
  3. cReduced model excludes \( -{ \log}_{10}\left({\mathrm{HWE}}_{p\mathrm{value}}\right) \)
  4. dTest to see if there is a significant difference between the full model and the reduced model. Numbers presented correspond to pvalues of the F test where the null hypothesis is \( {\beta}_{\mathrm{HWE}}=0 \)
  5. eThe number of informative SNPs
  6. fNot enough data points to fit the model