Identification of multiple rare variants associated with a disease

BMC Proceedings

Table 2 Genes associated with disease liability, Q1, and Q2 for the pooled populations at the significance levels of 0.05 and 1.56 × 10⁻⁵

Trait	All SNPs (nonsynonymous and synonymous)			Nonsynonymous SNPs
	Gene	Replicates significant at 0.05 (%)^a	Replicates significant at 1.56 × 10⁻⁵ (%)^b	Gene	Replicates significant at 0.05 (%)^a	Replicates significant at 1.56 × 10⁻⁵ (%)^b
Disease liability (case-control)	CYSLTR2	77.5	68.5	AKR1D1	72.5	36.5
	MGEA5	84	79.5	AQP3	74	66.5
	NF2	85.5	76.5	CAPNS1	74	64
	PTPN11	83.5	71	EIF6	84	77.5
	UGT1A1	72.5	55	FLT1	72.5	5
				LYPD6	77.5	72.5
				PCDHGA4	77	69.5
				PRKCG	70	65
				UGT1A1	71.5	55.5
Q1	CYSLTR2	62.5	45	*FLT1*	96.5	97.5
	*FLT1*	100	92	SLC2A13	69.5	0
	PTPN11	64.5	42.5
Q2	PIK3R1	66.5	29	*VNN1*	62	0
	PTGIS	62.5	41.5
	PTPN11	71.5	51.5

Listed genes were significant in at least 70% of replicates. Genes in boldface are the true causal genes in the simulation model.
^a Percentage of replicates in which the gene was significantly associated with disease liability, Q1, or Q2 at the significance level of 0.05.
^b Percentage of replicates in which the gene was significantly associated with disease liability, Q1, or Q2 at the significance level of 1.56 × 10⁻⁵

ISSN: 1753-6561