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Table 4 Type I error estimate at alpha = 1e-6 using 100 replicates of phenotype without QTL effect and real 550K genotype data of 34,265 SNPs (HWE p-value > 1e-6, call rate > 95%, MAF > 0.01) on chromosome 1.

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

MAF Polygenic Variance LM LME FBAT LM-LME 1 Three-stage
0.1 0.3 0.22 0.01 0.02 0.01 0.01
0.1 0.6 0.78 0.01 0.02 0.01 0
  1. Marginal phenotype distribution follows the standard normal distribution.
  2. LM_LME1: two-stage approach with LM at first stage with p-value cut-off 0.1 and LME at second stage with p-value cut-off 1e-6.
  3. Three-stage: LM at first stage with p-value cut-off 0.1, LME at second stage with p-value cut-off 1e-6 and FBAT at third stage with p-value cut-off 0.05/n, where n is the number of SNPs entering the third stage.