Exploration and comparison of methods for combining population- and family-based genetic association using the Genetic Analysis Workshop 17 mini-exome

Table 2 Empirical rejection rates for top causal SNPs

Causal SNP	Gene	Effect size	MAF	Chen and Lin	Zhang et al.	Zhu et al.
C1S3181	ELAVL4	0.30946	0.000717	0	0.235	0
C1S3181	ELAVL4	0.76911	0.000717	0	0.235	0
C1S9189	PIK3C2B	0.19102	0.006456	0	0.395	0.380
C3S4880	BCHE	0.20651	0.001435	0	0.005	0.275
C4S1873	KDR	0.58301	0.000717	0.300	0.420	0
C4S1878	KDR	0.13573	0.164993	0	0.305	0.120
C4S4935	VEGFC	1.35726	0.000717	0.045	0.805	0.690
C5S5133	FLT4	0.15986	0.001435	0	0.275	0
C6S2981	VEGFA	1.20645	0.002152	0.195	0.935	0.825
C6S5380	VNN1	0.24437	0.170732	0	0.580	0.450
C8S442	LPL	0.49459	0.015782	0.050	0.280	0.260
C9S444	VLDLR	0.86528	0.001435	0.020	0.430	0.195
C10S3050	SIRT1	0.97060	0.002152	0.025	0.215	0.040
C10S3109	SIRT1	0.51421	0.000717	0	0.730	0.640
C13S431	FLT1	0.74136	0.017217	0	0.075	0.385
C13S522	FLT1	0.61830	0.027977	0	0.550	0.400
C13S523	FLT1	0.64997	0.066714	0.055	0.685	0.660
C14S1382	SOS2	0.28058	0.003587	0	0.230	0.015
C17S1043	SREBF1	0.49941	0.004304	0	0.270	0.155
C17S1046	SREBF1	0.62779	0.002869	0	0.015	0.350
C17S1048	SREBF1	0.28739	0.001435	0	0	0.245
C17S4578	PRKCA	0.17038	0.166428	0.010	0.355	0.520

Gene, effect size, minor allele frequency (MAF), and empirical rejection rate over the 200 replications from each method for the 21 causal SNPs conferring ≥20% empirical rejection rate from at least one of the three methods. The maximum empirical rejection rate over the three methods is in boldface for each causal SNP. There are 160 causal SNPs, 2 of which confer susceptibility through two different components of the latent disease susceptibility distribution.

ISSN: 1753-6561