Identification of genes and variants associated with quantitative traits using Bayesian factor screening

BMC Proceedings

Table 2 SNPs with high marginal posterior probabilities

SNP	Gene	Posterior probability > 0.5	Posterior probability > 0.1
C13S431	FLT1	1	4
C13S522	FLT1	6	8
C13S523	FLT1	9	9
C13S534	FLT1	0	1
C4S1878	KDR	0	2
C4S1884	KDR	2	4
C6S2981	VEGFA	0	1
Other Q1		0	0
Non-Q1		3	36
False-positive discovery rate		3/21	36/65

The first column lists Q1-associated SNP variants that have marginal posterior probabilities larger that 0.1 in any of the 10 replicates. The second column gives the genes on which these variants sit. The third and fourth columns are frequency of their posterior probabilities larger than 0.1 and 0.5, respectively; they summarize all variants not associated with Q1 but with a posterior probability greater than 0.1 or 0.5. The false discovery rates are given in the last row.

ISSN: 1753-6561