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Table 2 Power (%) of seven methods to detect association of rare variants under seven scenarios for underlying genetic architecture using data simulated for BRCA2 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 19.5 2.5 0.5 2.5 1.5 4.5 5.5 41.0 7.5 6.0 7.0 6.0 14.5 11.0 57.5 18.0 21.5 15.0 15.5 29.5 18.5
2 0.05 15.5 4.5 1.5 3.0 2.0 3.0 5.0 26.5 9.5 3.0 6.0 7.0 7.5 10.0 44.0 21.0 14.0 15.0 11.5 18.5 18.0
3 0.05 13.0 2.5 0.5 2.0 2.0 2.5 2.5 27.5 4.0 4.0 4.0 2.5 3.5 4.5 45.5 13.5 15.5 8.0 9.0 17.0 11.5
4 0.05 14.0 3.5 1.5 2.5 1.5 3.5 3.0 27.0 9.5 4.0 6.5 6.0 7.5 8.5 39.5 18.5 7.5 13.5 13.5 16.0 16.0
5 0.05 14.5 3.0 0.5 2.0 1.5 2.5 3.5 31.0 8.0 3.0 5.5 3.5 7.0 8.0 47.0 12.5 15.0 10.5 9.0 17.0 13.0
6 0.05 15.0 2.5 0.5 0.5 1.0 1.5 1.0 30.0 9.5 4.0 7.0 7.0 4.0 9.0 45.5 21.0 8.0 17.0 15.0 14.0 21.0
7 0.05 18.0 0.5 0.0 0.5 0.0 1.5 1.5 29.5 2.5 3.0 1.0 1.0 3.0 2.5 44.0 9.0 8.5 5.0 3.5 9.0 10.0
1 0.10 14.5 1.5 3.0 1.5 2.5 7.5 3.5 30.5 8.0 13.0 6.0 8.0 15.5 8.5 48.5 19.0 24.0 14.5 20.5 31.0 20.0
2 0.10 9.5 2.0 1.0 1.5 2.0 3.5 3.0 24.5 10.5 4.5 7.0 7.5 8.5 9.0 40.0 22.0 15.5 18.0 19.5 18.5 23.0
3 0.10 11.5 1.5 1.5 1.0 2.0 3.0 2.5 27.0 5.0 9.0 4.0 4.5 8.5 6.0 41.5 12.5 20.5 10.5 10.5 22.5 13.5
4 0.10 11.0 3.0 2.0 2.5 1.0 2.5 2.5 20.5 7.0 4.0 5.0 3.5 9.5 5.5 39.5 18.0 13.0 11.5 12.5 16.0 14.0
5 0.10 13.5 2.5 3.0 1.5 2.0 3.5 2.5 24.0 6.0 6.0 4.0 3.0 9.0 7.0 40.5 18.0 15.5 12.0 13.5 18.0 14.5
6 0.10 6.5 0.5 0.0 0.0 0.0 0.0 0.5 17.0 4.5 1.0 2.5 3.0 3.0 3.5 36.0 13.0 7.0 7.5 8.5 11.5 10.5
7 0.10 7.5 1.5 1.5 2.0 1.0 3.0 2.0 22.5 4.0 5.0 4.0 4.0 8.0 4.0 40.5 15.5 13.5 9.0 10.5 17.0 13.0
1 0.20 20.0 9.0 12.0 9.5 12.0 22.5 11.0 41.0 18.0 27.0 17.0 25.0 39.5 21.0 59.0 31.5 47.5 28.0 38.0 55.0 30.0
2 0.20 8.5 1.0 2.5 0.5 1.5 4.5 2.5 22.0 5.5 11.0 5.0 8.0 13.5 7.0 45.0 18.5 27.0 12.0 21.5 30.0 17.0
3 0.20 9.0 3.0 5.0 3.0 6.5 9.0 4.0 25.5 9.0 17.5 9.0 13.0 20.0 10.5 44.5 17.0 34.0 16.0 22.0 34.5 19.5
4 0.20 8.5 1.0 1.0 0.5 1.0 1.5 1.0 21.5 6.5 6.0 4.0 6.0 9.0 5.5 38.0 15.0 16.0 13.0 12.0 20.5 17.5
5 0.20 12.5 4.0 2.5 4.0 1.0 4.5 4.0 29.0 8.0 5.5 6.0 6.0 12.5 8.5 43.5 17.5 17.5 14.0 15.0 24.0 18.0
6 0.20 5.5 2.0 1.0 2.5 1.0 2.5 3.0 21.5 4.0 3.0 5.0 3.5 7.0 6.0 35.0 15.5 12.0 10.0 11.0 15.5 15.0
7 0.20 8.5 2.5 1.0 1.5 1.0 1.5 3.0 21.0 6.0 3.0 5.0 5.0 3.5 7.0 42.0 16.5 9.0 13.0 12.5 14.0 16.0
  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.