Skip to main content

Table 4 Power (%) of RAML and SKAT methods to detect association of rare variants under seven scenarios for underlying genetic architecture using data simulated for BRCA1 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 47.5 31.5 61.0 44.0 73.5 58.5
2 0.05 39.5 24.0 53.5 36.0 64.5 49.0
3 0.05 43.0 29.5 61.5 43.0 70.5 55.0
4 0.05 33.5 22.5 49.5 29.0 59.5 42.5
5 0.05 39.5 25.5 57.0 39.5 62.0 51.5
6 0.05 33.5 21.5 43.0 29.5 57.0 41.5
7 0.05 37.5 30.5 51.0 38.0 56.5 45.5
1 0.10 40.0 34.5 58.0 50.0 76.0 66.0
2 0.10 36.0 29.0 50.5 42.5 65.5 58.0
3 0.10 32.5 28.5 53.0 42.5 67.5 58.0
4 0.10 31.0 22.0 45.5 35.5 59.0 48.5
5 0.10 33.5 25.0 55.0 39.5 71.0 59.5
6 0.10 32.5 21.5 48.5 31.5 62.0 48.5
7 0.10 31.5 23.0 44.0 35.0 60.5 46.5
1 0.20 47.5 50.0 71.0 67.5 83.5 81.0
2 0.20 26.5 34.5 49.0 46.0 69.5 68.0
3 0.20 41.0 40.5 59.5 52.5 74.0 67.0
4 0.20 26.0 26.0 44.5 40.0 67.5 55.5
5 0.20 35.0 26.5 51.5 44.5 70.0 64.5
6 0.20 27.5 24.5 45.5 37.0 62.5 55.0
7 0.20 23.5 19.0 46.0 35.5 63.0 59.5
  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.