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Table 3 Power (%) of seven methods to detect association of rare variants under seven scenarios for underlying genetic architecture using data simulated for TERT in 2000 cases and 2000 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 T1 T5 WST VTT EREC RAML SKAT-O T1 T5 WST VTT EREC RAML SKAT-O T1 T5 WST VTT EREC
1 0.05 15.5 10.5 3.5 4.0 4.0 6.5 10.5 34.0 22.5 14.0 16.0 14.5 15.0 20.5 48.5 36.0 25.5 22.5 24.0 30.0 34.0
2 0.05 19.5 13.0 5.0 4.0 3.5 7.0 13.5 28.5 21.5 11.5 11.0 12.0 14.5 19.0 42.5 38.5 24.0 21.5 24.0 25.0 36.5
3 0.05 18.0 10.5 6.5 4.5 3.5 5.5 6.5 33.5 17.5 12.5 7.0 11.0 12.0 18.5 47.0 35.5 26.0 18.0 25.0 25.5 33.5
4 0.05 13.0 5.0 2.0 1.0 1.0 1.0 3.0 22.5 13.5 7.0 4.0 5.0 6.0 9.0 38.5 27.5 14.0 14.5 14.5 12.5 25.5
5 0.05 21.5 13.5 4.5 4.5 3.0 6.0 9.0 32.5 21.0 10.0 8.5 9.0 14.0 17.5 49.0 35.5 19.5 20.0 20.0 20.5 36.5
6 0.05 15.0 8.5 3.0 4.0 2.0 5.0 6.5 26.5 13.5 7.5 7.0 7.0 10.0 12.0 39.0 25.0 16.5 12.5 13.5 15.5 22.0
7 0.05 10.5 4.5 0.0 2.0 1.5 2.5 4.5 24.0 10.5 3.0 7.5 4.0 4.5 10.0 38.5 25.0 11.0 13.0 10.5 16.0 22.5
1 0.10 23.0 18.5 12.5 15.0 13.0 16.0 19.0 41.0 32.0 26.0 24.5 27.5 31.0 34.0 63.0 51.0 43.5 39.5 48.0 44.0 53.5
2 0.10 14.5 9.0 7.0 3.5 5.0 7.0 7.5 25.0 20.5 15.5 8.0 12.0 13.0 19.5 42.5 36.0 23.5 23.5 24.0 25.0 34.0
3 0.10 17.5 11.5 6.5 6.5 7.0 8.5 10.5 33.0 23.5 19.5 14.5 18.5 22.0 22.0 47.5 39.0 33.0 27.0 33.5 32.5 39.5
4 0.10 10.5 10.0 4.5 5.5 4.5 5.0 7.5 24.5 18.0 11.0 11.0 10.5 12.0 16.5 42.5 32.5 20.0 21.0 20.5 22.5 34.0
5 0.10 12.5 11.0 3.5 6.0 5.5 5.5 10.0 27.0 20.0 10.5 14.0 11.0 13.0 22.5 39.5 35.5 28.0 27.0 23.5 26.0 34.5
6 0.10 6.5 6.0 3.0 0.0 2.0 2.5 4.5 23.0 14.0 7.0 6.5 6.0 7.5 12.5 40.0 27.5 17.0 13.5 17.0 18.5 26.0
7 0.10 10.5 7.0 2.0 0.5 2.0 2.0 6.0 21.0 15.0 5.5 7.5 7.0 6.5 12.5 35.5 25.5 13.5 14.0 13.5 16.0 24.0
1 0.20 31.0 33.5 31.5 24.5 30.5 30.5 30.5 55.0 58.0 53.0 48.5 61.0 55.5 58.5 75.0 72.0 73.5 67.5 75.5 70.5 73.0
2 0.20 12.5 12.0 9.5 6.5 9.5 10.0 12.5 34.0 30.5 25.0 20.0 26.0 26.0 29.5 63.5 53.5 45.5 37.0 45.0 42.0 55.0
3 0.20 18.0 14.5 11.0 11.0 14.5 15.5 16.0 39.0 36.5 32.0 23.5 33.0 31.5 35.0 58.5 58.5 49.5 45.0 49.5 45.5 56.5
4 0.20 12.5 10.5 5.5 3.0 3.0 4.5 7.5 23.5 18.5 16.0 16.0 16.0 17.5 20.0 46.0 40.5 31.5 28.5 31.5 31.0 39.0
5 0.20 14.5 10.5 6.5 4.5 5.0 6.5 10.5 28.5 27.0 20.0 17.5 19.0 17.5 26.5 48.5 47.0 36.5 30.0 32.5 36.0 43.0
6 0.20 11.5 6.0 2.0 3.0 1.0 2.0 4.0 27.0 15.5 7.0 7.5 8.0 8.0 17.5 43.0 38.0 19.5 21.0 20.0 21.5 33.5
7 0.20 9.5 4.0 1.0 2.0 1.0 1.0 4.5 22.0 17.5 5.5 5.5 6.0 5.5 13.0 44.5 30.0 15.0 13.0 11.5 17.5 28.5
  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.