Distance-based phenotypic association analysis of DNA sequence data

BMC Proceedings

Table 1 True positive rates of five different strategies for the 13 Q2 risk genes

Gene	Setting	MDMR using all variants	Mantel test using all variants	MDMR using only rare variants	Mantel test using only rare variants	Collapsing analysis using only rare variants
BCHE	1c + 28r (13s)	0.045	0.170	0.320	0.310	0.455
GCKR	1c (1s)	0.405	0.150	NA	NA	NA
INSIG1	1c + 4r (3s)	0.090	0.020	0.040	0.040	0.035
LPL	5c (1s) + 15r (2s)	0.045	0.135	0.060	0.125	0.040
PDGFD	5c + 6r (4s)	0.065	0.035	0.685	0.290	0.745
PLAT	4c + 25r (8s)	0.035	0.030	0.055	0.040	0.110
RARB	2c + 9r (2s)	0.105	0.145	0.410	0.115	0.155
SIRT1	1c + 23r (9s)	0.365	0.285	0.605	0.320	0.330
SREBF1	3c + 21r (10s)	0.030	0.110	0.380	0.205	0.690
VLDLR	4c + 23r (8s)	0.055	0.065	0.140	0.140	0.140
VNN1	1c (1s) + 6r (1s)	0.940	0.250	0.200	0.085	0.050
VNN3	6c (3s) + 9r (4s)	0.190	0.175	0.025	0.055	0.030
VWF	2c + 6r (2s)	0.180	0.080	0.285	0.080	0.190
Mean		0.196	0.127	0.267	0.150	0.248

The true positive rate was determined as the frequency of observing p-values less than 0.05 among 200 (replication) p-values for each gene. The “Setting” column shows the composition of SNPs within a gene: c, r, and s stand for common, rare, and signal SNPs, respectively. For example, VNN1 has 1 common causal SNP and 6 rare SNPs, one of which is a signal. SNPs with MAF > 0.01 are defined as common.

ISSN: 1753-6561