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Table 1 Type I error estimate at alpha = 0.05 with 10,000 replicates for quantitative phenotype and single SNP genotype data with MAF = 0.1.

From: A three-stage approach for genome-wide association studies with family data for quantitative traits

Phenotype Distribution Polygenic Variance LM LME FBAT LM-LME 1 LM-LME 2
Normal 0.3 0.084 0.051 0.050 0.049 0.051
Normal 0.6 0.115 0.052 0.049 0.046 0.050
Abs Normal 0.3 0.055 0.053 0.049 0.053 0.053
Abs Normal 0.6 0.064 0.050 0.049 0.050 0.050
Chi-square(1) 0.3 0.076 0.052 0.050 0.052 0.052
Chi-square(1) 0.6 0.104 0.049 0.051 0.045 0.047
Lognormal 0.3 0.059 0.054 0.046 0.054 0.054
Lognormal 0.6 0.066 0.049 0.047 0.049 0.049
  1. The SNP explains 0% phenotype variation.
  2. Normal: marginal phenotype follows the standard normal distribution
  3. Abs Normal: marginal phenotype follows the absolute standard normal distribution
  4. Chi-square(1): marginal phenotype follows a Chi-square distribution with 1 degree of freedom
  5. Lognormal: marginal phenotype follows a Lognormal distribution
  6. LM_LME1: two-stage approach with LM (p-value cut-off 0.1) at first stage
  7. LM_LME2: two-stage approach with LM (p-value cut-off 0.2) at first stage