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

BMC Bioinformatics

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

		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

Method with greatest power emboldened.
* See text for description of genetic architecture for each scenario.
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.

ISSN: 1471-2105