Linkage analysis merging replicate phenotypes: an application to three quantitative phenotypes in two African samples

Table 1 True positives and false positives from Fisher’s method and GLMM analyses

Trait	Gene	Chromosome	Position	Families	GLMM analysis,	Fisher’s method,
	−log₁₀(p-value)		−log₁₀(p-value)
						Combined	Min–max	Median
True positives
Q1	VEGFA	6	43,846,955	Luhya	34.30	70.23	0.78–4.95	2.33
Q1	FLT1	13	27,775,331	Yoruba	20.85	30.56	0.00–3.47	1.42
Q1	KDR	4	55,650,982	Luhya	2.91	5.39	0.00–3.36	0.65
Q1	VEGFC	4	177,845,572	Yoruba	3.50	4.43	0.00–3.28	0.58
Q2	PLAT	8	42,152,676	Luhya	5.39	4.12	0.00–1.88	0.65
Q2	SREBF1	17	17,658,674	Yoruba	4.65	2.44	0.00–2.87	0.45
False positives
Q1	LAMB3	1	207,855,310	Yoruba	1.69	5.07	0.00–2.62	0.67
Q1	VCAN	5	82,868,901	Luhya	5.25	15.64	0.00–5.64	1.03
Q1	UPP1	7	48,100,910	Luhya	2.12	4.12	0.00–3.53	0.43
Q1	LMTK2	7	97,660,051	Yoruba	2.76	4.88	0.00–3.98	0.55
Q1	CDCA2	8	24,830,588	Yoruba	5.41	12.10	0.00–3.52	0.73
Q1	WDR40A	9	34,097,504	Yoruba	3.40	4.88	0.00–3.40	0.49
Q1	PPP2R4	9	130,913,706	Yoruba	2.87	4.08	0.00–2.88	0.47
Q1	NPTX1	17	76,060,297	Luhya	8.71	17.20	0.00–3.81	1.11
Q4	LOC643659	20	20,004,221	Luhya	0.89	4.29	0.00–3.15	0.49
Q4	RNF145	5	159,708,779	Yoruba	4.52	0.65	0.00–2.51	0.00

ISSN: 1753-6561