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Table 5 Sensitivity results of MB-MDR to detect two locus model of pure epistatic interaction in 1200 simulated datasets with real human genome LD patterns, for 3 effect sizes and after 5 LD pruning levels

From: Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies

LD block setting LD pruning Effect Size Exact Signal Sensitivity
    Sensitivity −−−−−−−−−−−−−−−−−−
     tag-SNP condition tag-SNP condition
     LD r2≥0.45 LD r2≥0.20
A unpruned β3=0.90 0.61 0.67 0.73
Two SNPs   β3=0.75 0.55 0.65 0.77
in same   β3=0.50 0.70 0.85 0.89
LD block LD r2≤0.75 β3=0.90 0.01 0.90 0.91
   β3=0.75 0.04 0.92 0.94
   β3=0.50 0.03 0.93 0.93
  LD r2≤0.60 β3=0.90 0.01 0.93 0.94
   β3=0.75 0.00 0.94 0.94
   β3=0.50 0.01 0.92 0.94
  LD r2≤0.50 β3=0.90 0.00 0.91 0.92
   β3=0.75 0.00 0.90 0.91
   β3=0.50 0.01 0.91 0.95
  LD r2≤0.20 β3=0.90 0.00 0.61 0.74
   β3=0.75 0.00 0.69 0.80
   β3=0.50 0.01 0.66 0.84
B unpruned β3=0.90 0.54 0.75 0.75
Two SNPs   β3=0.75 0.46 0.70 0.71
in middle   β3=0.50 0.41 0.75 0.76
of two LD r2≤0.75 β3=0.90 0.64 0.91 0.91
separate   β3=0.75 0.58 0.91 0.91
LD blocks   β3=0.50 0.44 0.93 0.94
  LD r2≤0.60 β3=0.90 0.49 0.92 0.92
   β3=0.75 0.41 0.93 0.93
   β3=0.50 0.27 0.94 0.95
  LD r2≤0.50 β3=0.90 0.39 0.92 0.92
   β3=0.75 0.32 0.93 0.93
   β3=0.50 0.23 0.94 0.95
  LD r2≤0.20 β3=0.90 0.19 0.57 0.81
   β3=0.75 0.16 0.69 0.91
   β3=0.50 0.21 0.83 0.92
C unpruned β3=0.90 0.18 0.33 0.43
One SNP   β3=0.75 0.23 0.36 0.49
in a block   β3=0.50 0.18 0.36 0.51
and one LD r2≤0.75 β3=0.90 0.0 0.65 0.74
in the edge   β3=0.75 0.0 0.72 0.83
of a separate   β3=0.50 0.0 0.57 0.76
LD block LD r2≤0.60 β3=0.90 0.0 0.56 0.74
   β3=0.75 0.0 0.59 0.81
   β3=0.50 0.0 0.47 0.74
  LD r2≤0.50 β3=0.90 0.0 0.48 0.71
   β3=0.75 0.0 0.50 0.81
   β3=0.50 0.0 0.36 0.70
  LD r2≤0.20 β3=0.90 0.0 0.07 0.60
   β3=0.75 0.0 0.05 0.62
   β3=0.50 0.0 0.04 0.57
D unpruned β3=0.90 0.39 0.68 0.82
Two SNPs   β3=0.75 0.40 0.69 0.81
on LD blocks   β3=0.50 0.58 0.76 0.84
of separate LD r2≤0.75 β3=0.90 0.18 0.86 0.94
chromosomes   β3=0.75 0.18 0.93 0.99
   β3=0.50 0.23 0.84 0.90
  LD r2≤0.60 β3=0.90 0.14 0.87 0.94
   β3=0.75 0.13 0.93 0.98
   β3=0.50 0.17 0.85 0.90
  LD r2≤0.50 β3=0.90 0.13 0.85 0.92
   β3=0.75 0.13 0.93 0.97
   β3=0.50 0.16 0.83 0.89
  LD r2≤0.20 β3=0.90 NA NA NA
   β3=0.75 0.10 0.67 0.86
   β3=0.50 0.17 0.75 0.84