Table 3.
Result of False-positive probability analysis at six prior probability levels.
| Model | Subgroup | P value | OR (95% CI) | Statistical Power† | Prior probability | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| 0.25 | 0.1 | 0.01 | 0.001 | 0.0001 | 0.00001 | |||||
| Rs4939827 | ||||||||||
| CC + CT vs TT | Remove HWE | .008 | 0.89 (0.83, 0.97) | 1.000 | 0.023 | 0.067 | 0.441 | 0.888 | 0.988 | 0.999 |
| Caucasian | <.001 | 0.87 (0.8, 0.94) | 1.000 | 0.001 | 0.004 | 0.040 | 0.296 | 0.808 | 0.977 | |
| NA | .001 | 0.83 (0.75, 0.93) | 1.000 | 0.004 | 0.012 | 0.116 | 0.570 | 0.930 | 0.993 | |
| LAGER | <.001 | 0.90 (0.83, 0.97) | 1.000 | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 | |
| CC vs CT + TT | Remove HWE | .003 | 0.89 (0.83, 0.96) | 1.000 | 0.008 | 0.022 | 0.202 | 0.718 | 0.962 | 0.996 |
| Caucasian | .002 | 0.87 (0.79, 0.95) | 1.000 | 0.006 | 0.017 | 0.159 | 0.657 | 0.950 | 0.995 | |
| PB | .03 | 0.90 (0.82, 0.99) | 1.000 | 0.083 | 0.014 | 0.750 | 0.968 | 0.997 | 1.000 | |
| NA | <.001 | 0.81 (0.74, 0.88) | 1.000 | <0.001 | <0.001 | <0.001 | 0.001 | 0.006 | 0.059 | |
| LAGER | .001 | 0.88 (0.82, 0.95) | 1.000 | 0.003 | 0.009 | 0.095 | 0.515 | 0.914 | 0.991 | |
| CC vs TT | Remove HWE | <.001 | 0.84 (0.76, 0.93) | 1.000 | 0.002 | 0.007 | 0.072 | 0.440 | 0.887 | 0.987 |
| Caucasian | <.001 | 0.79 (0.7, 0.89) | 0.997 | <0.001 | 0.001 | 0.010 | 0.096 | 0.515 | 0.914 | |
| PB | .002 | 0.80 (0.71, 0.92) | 0.995 | 0.005 | 0.016 | 0.148 | 0.638 | 0.946 | 0.994 | |
| NA | <.001 | 0.73 (0.65, 0.83) | 0.917 | <0.001 | <0.001 | <0.001 | 0.002 | 0.017 | 0.145 | |
| LAGER | <.001 | 0.84 (0.76, 0.93) | 1.000 | 0.002 | 0.007 | 0.072 | 0.440 | 0.887 | 0.987 | |
| CT vs TT | Remove HWE | .004 | 0.91 (0.85, 0.97) | 1.000 | 0.011 | 0.033 | 0.273 | 0.791 | 0.974 | 0.997 |
| Caucasian | <.001 | 0.88 (0.83, 0.94) | 1.000 | <0.001 | 0.001 | 0.014 | 0.127 | 0.593 | 0.936 | |
| NA | .006 | 0.87 (0.79, 0.96) | 1.000 | 0.016 | 0.048 | 0.355 | 0.847 | 0.982 | 0.998 | |
| LAGER | .01 | 0.92 (0.86, 0.98) | 1.000 | 0.028 | 0.080 | 0.490 | 0.906 | 0.990 | 0.999 | |
| C vs T | Remove HWE | <.001 | 0.91 (0.87, 0.96) | 1.000 | 0.002 | 0.005 | 0.052 | 0.354 | 0.846 | 0.982 |
| Caucasian | <.001 | 0.89 (0.84, 0.95) | 1.000 | 0.001 | 0.004 | 0.044 | 0.317 | 0.823 | 0.979 | |
| PB | .001 | 0.9 (0.84, 0.96) | 1.000 | 0.004 | 0.012 | 0.120 | 0.579 | 0.932 | 0.993 | |
| NA | <.001 | 0.87 (0.8, 0.93) | 1.000 | <0.001 | <0.001 | 0.004 | 0.041 | 0.299 | 0.810 | |
| LAGER | <.001 | 0.91 (0.87, 0.96) | 1.000 | 0.002 | 0.005 | 0.052 | 0.354 | 0.846 | 0.982 | |
| Rs4464148* | ||||||||||
| CC + CT vs TT | Caucasian | .003 | 1.15 (1.06, 1.26) | 1.000 | 0.008 | 0.024 | 0.212 | 0.730 | 0.964 | 0.996 |
| CT vs TT | Remove HWE | .01 | 1.13 (1.04, 1.24) | 1.000 | 0.029 | 0.082 | 0.495 | 0.908 | 0.990 | 0.999 |
| Caucasian | .018 | 1.12 (1.02, 1.23) | 1.000 | 0.051 | 0.138 | 0.637 | 0.947 | 0.994 | 0.999 | |
| C vs T | Include HWE | .001 | 1.12 (1.05, 1.20) | 1.000 | 0.004 | 0.011 | 0.113 | 0.562 | 0.928 | 0.992 |
| PB | .03 | 1.10 (1.01, 1.2) | 1.000 | 0.087 | 0.023 | 0.759 | 0.969 | 0.997 | 1.000 | |
| NA | <.001 | 1.14 (1.1, 1.19) | 1.000 | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 | |
| LAGER | <.001 | 1.14 (1.1, 1.19) | 1.000 | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 | |
| Rs12953717 | ||||||||||
| TT + TC vs CC | Remove HWE | .03 | 1.11 (1.01, 1.22) | 1.000 | 0.084 | 0.015 | 0.751 | 0.968 | 0.997 | 1.000 |
| Caucasian | .05 | 1.13 (1.01, 1.28) | 1.000 | 0.141 | 0.030 | 0.844 | 0.982 | 0.998 | 1.000 | |
| NA | .01 | 1.17 (1.04, 1.32) | 1.000 | 0.031 | 0.088 | 0.515 | 0.915 | 0.991 | 0.999 | |
| LAGER | <.001 | 1.17 (1.10, 1.25) | 1.000 | <0.001 | <0.001 | <0.001 | 0.003 | 0.032 | 0.247 | |
| TT vs CC + TC | Include HWE | <.001 | 1.17 (1.07, 1.28) | 1.000 | 0.002 | 0.006 | 0.057 | 0.381 | 0.860 | 0.984 |
| NA | <.001 | 1.18 (1.10, 1.27) | 1.000 | <0.001 | 0.001 | 0.001 | 0.010 | 0.092 | 0.504 | |
| TT vs CC | Remove HWE | <.001 | 1.25 (1.13, 1.38) | 1.000 | <0.001 | <0.001 | 0.001 | 0.010 | 0.090 | 0.496 |
| Include HWE | .007 | 1.18 (1.05, 1.33) | 1.000 | 0.020 | 0.057 | 0.399 | 0.870 | 0.985 | 0.999 | |
| Caucasian | <.001 | 1.34 (1.21, 1.48) | 0.987 | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 | |
| NA | .009 | 1.28 (1.07, 1.54) | 0.954 | 0.027 | 0.077 | 0.480 | 0.903 | 0.989 | 0.999 | |
| LAGER | <.001 | 1.26 (1.13, 1.41) | 0.999 | <0.001 | 0.001 | 0.006 | 0.053 | 0.361 | 0.850 | |
| TC vs CC | LAGER | <.001 | 1.12 (1.07, 1.17) | 1.000 | <0.001 | <0.001 | <0.001 | <0.001 | 0.004 | 0.035 |
| T vs C | Remove HWE | <.001 | 1.11 (1.05, 1.17) | 1.000 | <0.001 | 0.001 | 0.010 | 0.093 | 0.505 | 0.911 |
| Include HWE | .016 | 1.08 (1.01, 1.15) | 1.000 | 0.047 | 0.128 | 0.618 | 0.942 | 0.994 | 0.999 | |
| Caucasian | <.001 | 1.14 (1.07, 1.22) | 1.000 | <0.001 | 0.001 | 0.015 | 0.132 | 0.604 | 0.939 | |
| NA | .01 | 1.13 (1.04, 1.24) | 1.000 | 0.029 | 0.082 | 0.495 | 0.908 | 0.990 | 0.999 | |
| LAGER | <.001 | 1.11 (1.04, 1.17) | 1.000 | <0.001 | 0.001 | 0.010 | 0.093 | 0.505 | 0.911 | |
CI = confidence interval, GC = gastric cancer, HWE = Hardy-Weinberg equilibrium, LAGER = the total sample size in the study was greater than 1000, NA = control source unknow, OR = odds ratio, PB = population based.
*
No statistically significant ORs for the recessive and Homozygous models in RS4464148.
†
The statistical power is measured at an odd ratio of 1.5.