Two-stage analyses of sequence variants in association with quantitative traits

BMC Proceedings

Table 1 Analysis of genes in relation to trait Q1 using the simple strategy, the alternative strategy based on more specific hypotheses, and the combined analysis with appropriate adjustment for multiple testing

				Number of significant replicates
Gene	Chromosome	Number of variants in gene	Number of times passing stage 1 threshold	Simple strategy	Alternative strategy	Joint analysis
*FLT1*	13	35	195	188	187	195
OR2T34	1	16	166	79	77	140
*KDR*	4	16	165	75	39	146
PRR4	12	34	159	57	60	117
JAK1	1	12	150	49	45	105
CYP4F3	19	12	149	37	38	97
TAS2R48	12	12	148	41	53	102
ZNF91	19	9	145	45	42	87
HLA-B	6	28	143	33	36	89
INSR	19	16	138	42	39	91
LOC645118	19	5	125	24	21	73
CES1	16	30	123	28	32	64

Only genes significant in the first analysis (at the 1% level) in at least 120 of the 200 replicates are shown. The two genes in bold were simulated to be associated with the trait. All analyses are adjusted for population stratification.

ISSN: 1753-6561