Application of collapsing methods for continuous traits to the Genetic Analysis Workshop 17 exome sequence data

BMC Proceedings

Table 1 Averaged −log(P) across 200 replicates from collapsing methods for Q1 and Q2 at the true causal genes

Gene	All SNPs			Rare SNPs			Rare nonsynonymous SNPs			Best single
	N (true)	Prop	Y/N	N	Prop	Y/N	N	Prop	Y/N
Q1
ARNT	18 (5)	0.45	0.40	17	1.88	1.88	9	2.24	2.50	3.94
ELAVL4	10 (2)	2.47	2.38	8	0.85	0.85	4	0.76	0.76	2.28
FLT1	35 (11)	6.61	2.59	32	9.70	6.84	19	17.81	15.04	24.26
FLT4	10 (2)	2.70	2.98	10	2.70	2.98	5	1.44	1.50	1.77
HIF1A	8 (4)	3.03	3.31	8	3.03	3.31	6	3.24	3.48	3.39
HIF3A	21 (3)	0.62	0.37	17	0.34	0.36	8	0.55	0.58	1.02
KDR	16 (10)	8.78	3.84	15	8.24	8.18	10	8.77	8.10	5.63
VEGFA	6 (1)	1.47	1.64	6	1.47	1.64	2	0.87	0.87	1.21
Q2
BCHE	29 (13)	0.71	0.57	28	1.22	1.43	25	1.32	1.59	1.58
INSIG1	5 (3)	0.53	0.50	5	0.53	0.50	4	0.39	0.39	0.57
LPL	20 (3)	0.37	0.37	17	0.64	0.63	8	1.38	1.27	1.88
PDGFD	11 (4)	0.44	0.50	9	0.72	0.94	7	1.66	1.66	1.81
PLAT	29 (8)	0.41	0.37	27	0.42	0.46	11	0.86	0.89	0.95
RARB	11 (2)	0.66	0.62	11	0.66	0.62	3	1.26	1.26	1.22
SIRT1	24 (9)	1.89	1.25	23	1.60	1.04	14	1.34	1.20	2.03
SREBF1	24 (10)	0.52	0.89	23	0.91	0.87	18	0.80	0.76	1.12
VLDLR	27 (8)	0.41	0.40	24	0.65	0.61	15	1.23	1.22	0.83
VNN1	7 (2)	3.24	2.90	6	0.37	0.46	2	0.96	0.96	3.42
VNN3	15 (7)	1.29	0.80	12	0.94	0.91	9	1.03	1.01	2.08
VWF	8 (2)	0.89	0.54	8	0.89	0.54	4	0.75	0.59	0.90

Boldface indicates the best result among the collapsing methods for each gene. Rare SNPs are defined as SNPs with MAF < 0.05. Prop is the proportion test; Y/N is the presence test. “Best Single” is the best signal from a single-marker analysis among all SNPs within each gene.

ISSN: 1753-6561