Search for compound heterozygous effects in exome sequence of unrelated subjects

BMC Proceedings

Table 3 Results of association testing for averaged phenotypes across all 200 simulation replicates

	Additive model, Beagle		Additive model, fastPHASE		Dominant model (no phase)
Phenotype	Gene	p-value	Gene	p-value	Gene	p-value
Affected	FLT1*	4.70 × 10⁻⁸	FLT1*	1.08 × 10⁻⁷	FLT1*	2.90 × 10⁻⁷
	PIK3C2B*	3.75 × 10⁻⁵	HPDL	5.44 × 10⁻⁵	HPDL	5.44 × 10⁻⁵
	HPDL	5.44 × 10⁻⁵	GRIA4	9.43 × 10⁻⁵	GRIA4	9.43 × 10⁻⁵
Q1	FLT1*	7.43 × 10⁻⁶¹	FLT1*	9.61 × 10⁻⁵⁷	FLT1*	2.04 × 10⁻⁵⁸
	SLC2A13	7.22 × 10⁻⁸	SLC2A13	3.02 × 10⁻⁷	SLC2A13	7.22 × 10⁻⁸
	KDR*	1.45 × 10⁻⁶	KDR*	1.12 × 10⁻⁶	PSKH2	2.26 × 10⁻⁶
Q2	VNN1*	1.98 × 10⁻¹⁶	VNN1*	9.42 × 10⁻¹⁷	VNN1*	5.89 × 10⁻¹³
	RARB*	7.64 × 10⁻⁷	RARB*	7.64 × 10⁻⁷	RARB*	7.64 × 10⁻⁷
	TXNL1	1.26 × 10⁻⁶	TXNL1	1.25 × 10⁻⁶	SIRT1	7.95 × 10⁻⁷
Q4	ICAM4	3.35 × 10⁻⁴	GLP2R	1.38 × 10⁻⁴	LP2R	6.22 × 10⁻⁵
	GLP2R	3.62 × 10⁻⁴	GOLGA1	2.25 × 10⁻⁴	YP3A43	1.11 × 10⁻⁴
	PBX3	5.79 × 10⁻⁴	ICAM4	3.35 × 10⁻⁴	LC22A1	2.22 × 10⁻⁴

Tests were run using the average phenotype values from the 200 simulation replicates. The three genes with the smallest p-values are listed for each test. Genes involved in the GAW17 phenotype simulation are marked with an asterisk.

ISSN: 1753-6561