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Table 1 Estimated type I error rates at nominal level 0.05, 1000 replicate simulation data sets

From: Genome-wide association tests by two-stage approaches with unified analysis of families and unrelated individuals

    Two children in each familyb One child in each familyb
Sample size Minor allele frequency α a PDT T pc T cc T cb PDT T pc T cc T cb
100 families, 120 controls 0.1 0.05 0.014 0.032 0.043 0.042 0.031 0.033 0.044 0.043
   0.1   0.023 0.028 0.032   0.029 0.041 0.029
   0.2   0.025 0.027 0.027   0.031 0.031 0.026
  0.3 0.05 0.024 0.042 0.049 0.047 0.036 0.05 0.045 0.053
   0.1   0.04 0.043 0.035   0.051 0.047 0.046
   0.2   0.046 0.038 0.037   0.054 0.047 0.053
500 families, 600 controls 0.1 0.05 0.048 0.051 0.051 0.059 0.053 0.052 0.054 0.051
   0.1   0.04 0.052 0.042   0.052 0.041 0.045
   0.2   0.042 0.046 0.044   0.04 0.047 0.05
  0.3 0.05 0.059 0.053 0.047 0.045 0.042 0.046 0.04 0.042
   0.1   0.054 0.042 0.046   0.048 0.034 0.044
   0.2   0.053 0.034 0.048   0.047 0.043 0.041
  1. aα, the cut-off p-value of the test in the first stage
  2. bPDT, pedigree disequilibrium test; T pc , test comparing all parents to controls; T cc , test comparing affected and unaffected parents; T cb , combined T pc and T cc