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

From: Distance-based phenotypic association analysis of DNA sequence data

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
  1. 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.