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Table 1 Power (%) of seven methods to detect association of rare variants under seven scenarios for underlying genetic architecture using data simulated for BRCA1 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 5.0 4.5 3.0 2.5 2.0 3.0 3.0 15.0 11.0 10.0 7.5 8.0 7.0 10.0 30.0 29.0 22.5 18.5 20.5 19.5 26.0
2 0.05 5.0 6.5 1.5 2.0 1.0 1.5 3.0 11.5 11.5 4.5 6.0 5.5 9.0 8.0 28.0 21.5 14.5 10.5 13.5 17.0 16.0
3 0.05 7.5 5.0 2.5 0.5 1.5 1.5 4.0 13.5 11.0 7.0 6.0 7.0 7.0 8.0 25.5 26.0 16.0 19.5 17.0 17.5 22.5
4 0.05 7.0 4.0 2.0 1.0 1.0 1.0 2.5 14.0 12.5 5.0 3.5 5.0 4.5 8.0 26.0 23.5 12.5 12.0 9.5 10.0 21.0
5 0.05 6.5 5.0 2.0 2.0 1.5 2.0 3.5 14.5 9.5 5.0 2.5 3.5 5.5 6.5 27.5 18.0 11.5 8.0 10.0 13.5 14.5
6 0.05 9.0 4.5 1.0 0.5 0.5 1.0 3.5 16.0 11.0 5.0 4.0 3.0 3.0 8.5 26.0 20.5 12.5 10.5 11.0 10.5 18.5
7 0.05 8.5 5.0 1.0 1.5 0.5 1.5 4.0 16.0 8.0 3.0 4.0 3.5 4.0 7.5 24.5 21.5 8.0 8.5 6.5 10.0 16.5
1 0.10 7.5 6.0 6.0 2.0 5.0 4.5 5.5 14.5 16.0 11.0 8.0 10.0 11.0 15.0 30.0 30.0 24.5 21.5 20.0 20.5 25.0
2 0.10 2.5 3.5 1.5 2.0 1.5 0.5 1.5 8.5 8.5 6.0 5.5 7.0 6.5 10.5 26.0 24.0 19.5 17.5 17.5 17.5 20.5
3 0.10 4.5 5.0 3.0 2.5 3.0 1.5 3.5 10.5 8.5 7.0 4.5 5.5 7.5 8.5 22.0 19.5 15.0 11.5 14.0 15.5 18.5
4 0.10 3.5 3.0 2.0 2.0 1.5 1.5 2.5 9.5 10.5 6.0 3.0 4.5 3.5 7.5 22.0 18.5 13.5 13.0 13.0 12.5 17.5
5 0.10 4.0 4.5 3.0 1.0 1.5 3.0 2.5 10.5 9.0 5.5 3.0 5.0 5.5 9.0 23.0 21.0 13.0 11.5 14.0 14.5 22.0
6 0.10 2.5 3.5 1.5 1.0 1.5 1.0 1.5 9.0 9.0 5.0 2.5 5.5 3.5 5.5 21.0 18.0 10.0 9.0 9.0 11.0 16.5
7 0.10 4.0 3.0 1.0 1.0 0.5 2.0 3.5 11.0 10.5 2.5 5.0 3.0 3.0 7.5 25.5 20.0 11.5 11.5 12.0 12.5 17.0
1 0.20 6.5 7.5 7.5 4.0 5.5 4.5 7.5 23.5 27.5 23.5 18.5 24.5 20.5 25.5 40.0 44.5 44.0 40.0 44.5 39.0 43.5
2 0.20 4.0 6.5 4.5 2.0 4.5 4.0 4.5 14.0 12.5 14.0 7.0 10.0 9.5 12.5 23.0 26.5 23.5 16.5 22.5 23.0 24.0
3 0.20 5.0 6.0 5.5 3.5 5.0 5.5 5.0 14.5 17.0 15.0 12.5 16.5 13.0 17.0 27.5 36.5 31.0 28.5 34.0 30.0 35.5
4 0.20 2.5 3.0 1.5 1.5 1.5 1.0 2.0 7.5 10.5 5.0 6.5 5.5 5.0 8.0 18.5 21.5 16.0 14.0 16.5 17.0 18.5
5 0.20 4.5 5.0 1.0 1.0 1.5 1.0 2.5 10.5 9.0 7.0 4.0 4.5 6.0 8.0 24.0 25.5 17.5 13.5 15.0 14.5 20.5
6 0.20 0.5 1.0 0.0 0.0 0.5 0.0 0.5 6.5 6.5 3.5 2.5 2.0 1.5 4.5 17.0 20.0 10.0 12.0 11.0 8.5 18.5
7 0.20 3.0 3.5 0.5 0.5 1.0 0.5 0.5 9.0 9.5 3.0 4.0 2.5 3.5 6.5 23.5 21.5 12.0 9.5 12.0 12.0 17.5
  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, T1fixed 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.