Search for compound heterozygous effects in exome sequence of unrelated subjects

BMC Proceedings

Table 4 Genes found by each analysis approach

	Analysis of first simulation replicate			Analysis of average values of all 200 simulation replicates
Trait	Additive model, Beagle	Additive model, fastPHASE	Dominant model (no phase)	Additive model, Beagle	Additive model, fastPHASE	Dominant model (no phase)
Affected	FLT1*	FLT1*	FLT1*	FLT1*	FLT1*	FLT1*
Q1	FLT1*	FLT1*	FLT1*	FLT1*	FLT1*	FLT1*
				KDR*	KDR*	SLC2A13
				SLC2A13	SLC2A13	PSKH2
				MAP3K12	MAP3K12	LIMK2
				PATE	PATE	JAK1
				JAK1	JAK1
Q2	None	None	None	VNN1*	VNN1*	VNN1*
				RARB*	RARB*	RARB*
				SIRT1*	SIRT1*	SIRT1*
				GCKR*	GCKR*	GCKR*
				TXNL1	TXNL1	TXNL1
				OR5B2	OR5B2	OR5B2
				MAF	MAF	MAF
				PCDHGB2	PCDHGB2	PCDHGB2
				C3ORF30	C3ORF30
				TRPV6
Q4	None	None	None	None	None	None

Given the Bonferroni significance threshold for 2,196 tests (p < 2.27 × 10⁻⁵), we show the genes identified as significant for each phenotype using each analysis approach. Genes involved in the GAW17 phenotype simulation are marked with an asterisk.

ISSN: 1753-6561