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Table 5 Power estimate at alpha = 1e-6 using 100 replicates of phenotype with 1% QTL (rs1570092 with MAF 0.31) effect and 30% of polygenic 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

LD group # SNPs in LD group LM LME FBAT LM-LME 1 Three-stage
0 <r2 ≤ 0.01 34025 0.20 0 0.01 0 0
0.01 <r2 ≤ 0.1 209 0.02 0.01 0 0.01 0
0.1 <r2 ≤ 0.3 6 0.70 0.54 0 0.54 0.50
0.3 <r2 ≤ 0.8 15 1 1 0.39 1 0.99
0.8 <r2 ≤ 1 10 1 1 0.51 1 0.99
  1. rs1570092 explains 1% phenotype variation.
  2. Marginal phenotype distribution follows a normal distribution with variance 1. The additive genetic effect is sqrt(0.01/2/0.31/0.69) = 0.153.
  3. 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.
  4. 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.