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

Table 2 Sensitivity of MDR to detect two-locus disease models

Scenario	Relative LD	Broad-Sense Heritability	Exact Sensitivity	Signal Sensitivity	Signal Sensitivity when SNP1 Dropped	Signal Sensitivity when SNP2 Dropped	Signal Sensitivity when both SNPs Dropped
One SNP in LD Block and One Outside	40%	5%	77	81	22	44	7
		15%	100	100	3	31	1
		25%	100	100	0	23	0
	60%	5%	83	96	91	100	97
		15%	97	100	98	100	97
		25%	99	100	100	100	100
	80%	5%	11	65	63	60	63
		15%	77	97	99	84	86
		25%	86	98	99	83	86
	95%	5%	0	80	63	80	63
		15%	0	95	88	95	88
		25%	0	89	87	89	87
Two SNPs in Separa te LD Blocks	40%	5%	91	97	8	52	1
		15%	100	100	3	34	1
		25%	100	100	2	26	0
	60%	5%	88	98	100	95	96
		15%	91	96	100	97	100
		25%	94	97	100	95	99
	80%	5%	6	64	67	64	67
		15%	36	89	92	87	92
		25%	49	93	96	93	96
	95%	5%	19	79	79	79	79
		15%	23	91	91	92	92
		25%	28	93	93	94	94
Two SNPs in Same LD Block	60%	5%	96	96	96	97	99
		15%	97	97	98	96	100
		25%	98	98	98	96	100
	80%	5%	78	95	95	95	93
		15%	17	72	72	72	77
		25%	54	91	91	91	93
	95%	5%	57	91	91	91	91
		15%	29	86	86	86	86
		25%	41	94	94	94	94

Detection sensitivity of MDR to identify functional SNPs from 40% to 95% LD amounts in epistatic two-locus models.

ISSN: 1756-0381