Influence of genotyping error in linkage mapping for complex traits – an analytic study

BMC Genomic Data

Table 2 Impact of genotyping error (rate = ϵ) on type I error and power

Error rate ϵ	Selection	ρ	EC		ED		$I$
			Power	Type I Error × 10^-4	Power	Type I Error × 10^-4	Power	Type I Error × 10^-4
0.005	1%	0.1	0.87	0.6	0.92	1.6	0.90	1.1
		0.2	0.87	0.6	0.92	1.5	0.91	1.3
		0.3	0.87	0.5	0.91	1.5	0.91	1.3
		0.4	0.87	0.5	0.91	1.4	0.91	1.3
		0.5	0.87	0.5	0.91	1.4	0.91	1.3
		0.6	0.87	0.5	0.91	1.3	0.91	1.2
	10%	0.1	0.85	0.4	0.93	2.2	0.90	1.1
		0.2	0.85	0.4	0.93	2.0	0.91	1.2
		0.3	0.84	0.3	0.92	1.9	0.91	1.3
		0.4	0.84	0.3	0.92	1.7	0.91	1.4
		0.5	0.84	0.3	0.92	1.6	0.91	1.4
		0.6	0.85	0.4	0.91	1.5	0.91	1.3
	30%	0.1	0.83	0.3	0.94	2.8	0.90	1.1
		0.2	0.82	0.2	0.93	2.4	0.90	1.1
		0.3	0.82	0.2	0.93	2.1	0.91	1.2
		0.4	0.82	0.2	0.92	1.9	0.91	1.2
		0.5	0.83	0.3	0.92	1.6	0.91	1.2
		0.6	0.85	0.4	0.91	1.5	0.91	1.2
0.01	1%	0.1	0.84	0.3	0.93	2.4	0.91	1.3
		0.2	0.83	0.3	0.93	2.2	0.92	1.7
		0.3	0.83	0.3	0.93	2.1	0.92	1.8
		0.4	0.83	0.3	0.92	1.9	0.92	1.7
		0.5	0.83	0.3	0.92	1.7	0.92	1.6
		0.6	0.83	0.3	0.92	1.6	0.91	1.5
	10%	0.1	0.78	0.1	0.95	4.5	0.91	1.3
		0.2	0.78	0.1	0.95	3.9	0.91	1.5
		0.3	0.77	0.1	0.94	3.4	0.92	1.7
		0.4	0.77	0.1	0.94	2.9	0.92	1.9
		0.5	0.77	0.1	0.93	2.5	0.92	1.9
		0.6	0.78	0.1	0.93	2.1	0.92	1.8
	30%	0.1	0.73	0.1	0.96	7.1	0.90	1.2
		0.2	0.71	0.1	0.96	5.6	0.91	1.3
		0.3	0.71	0.0	0.95	4.4	0.91	1.4
		0.4	0.71	0.1	0.94	3.4	0.91	1.5
		0.5	0.74	0.1	0.93	2.6	0.91	1.5
		0.6	0.78	0.1	0.93	2.1	0.91	1.5

Impact of genotyping error (rate = ϵ) on power and type I error of linkage test in selective designs (indexed by degree of Selection and sib-sib trait correlation ρ) – Nominal error rate = 10^-4, QTL effect γ = 0.1 and sample size equivalent to a Fisher's information = 2500 in each design (provides 90% power in absence of genotyping error)

ISSN: 2730-6844