The effects of linkage disequilibrium in large scale SNP datasets for MDR

Table 1 Sensitivity of MDR to detect one-locus disease models

Scenario	Relative LD	Effect Size	Exact Sensitivity	Signal Sensitivity	Signal Sensitivity when Functional SNP Dropped
SNP at Edge of LD Block	40%	1.5 OR	86	87	4
		2.0 OR	96	96	7
		3.0 OR	94	94	10
	60%	1.5 OR	85	93	71
		2.0 OR	97	99	67
		3.0 OR	96	96	49
	80%	1.5 OR	23	90	90
		2.0 OR	22	91	91
		3.0 OR	28	92	92
	95%	1.5 OR	14	82	84
		2.0 OR	25	90	90
		3.0 OR	24	94	95
SNP in Middle of LD Block	40%	1.5 OR	76	80	14
		2.0 OR	92	92	10
		3.0 OR	95	95	5
	60%	1.5 OR	58	90	92
		2.0 OR	75	99	99
		3.0 OR	73	93	94
	80%	1.5 OR	54	88	87
		2.0 OR	72	93	96
		3.0 OR	84	94	93
	95%	1.5 OR	0	92	92
		2.0 OR	0	83	83
		3.0 OR	0	93	93

The exact sensitivity, signal sensitivity and sensitivity with functional SNP removed, for MDR to identify a disease signal in data with 40% to 95% LD under two one-locus scenarios.

ISSN: 1756-0381