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Table 6 Power (%) of RAML and SKAT methods to detect association of rare variants under seven scenarios for underlying genetic architecture using data simulated for TERT in 4000 cases and 4000 controls

From: The admixture maximum likelihood test to test for association between rare variants and disease phenotypes

   Threshold for significance
   P < 0.001 P < 0.01 P < 0.05
Scenario* Proportion of variants associated RAML SKAT-O RAML SKAT-O RAML SKAT-O
1 0.05 75.5 53 87 66 90 80.5
2 0.05 72.5 42.5 85 66 90 78
3 0.05 68 42.5 79 57.5 88.5 73
4 0.05 62.5 35 76 50.5 86 64
5 0.05 57 36.5 74.5 50 84.5 61.5
6 0.05 57.5 35.5 71 52.5 84.5 67.5
7 0.05 58 34 73.5 48.5 83.5 64.5
1 0.10 84 62 90 79 93.5 89.5
2 0.10 68 47.5 80.5 66.5 87.5 77.5
3 0.10 68.5 50 81 65 89.5 78
4 0.10 56 37 70.5 53.5 80 68.5
5 0.10 66.5 42.5 80.5 59 90.5 78
6 0.10 57.5 38.5 79.5 53.5 88 70
7 0.10 63 41 83.5 61 91.5 73.5
1 0.20 90.5 87 96.5 96 99.5 98
2 0.20 70.5 57.5 84 75.5 93.5 85.5
3 0.20 74.5 65.5 89 79 96.5 89.5
4 0.20 66.5 54 80 72 92 84
5 0.20 72.5 58 86 72.5 92 87.5
6 0.20 57.5 41 76 61 90.5 80
7 0.20 60 41.5 74 59 86.5 76.5
  1. Method with greatest power emboldened.
  2. * See text for description of genetic architecture for each scenario.
  3. RAML Rare admixture maximum likelihood, SKAT-O sequence kernel association test, T1 fixed threshold test 1 per cent MAF, T5 fixed threshold test 5 per cent MAF, WST weighted sum test, VTT variable threshold test, EREC estimated regression coefficient test.