Figure 2

Odds ratio (OR) vs. "critical sens/spec" of detected pairs in seven WTCCC datasets in our study and reported in literature to date. Odds ratio (OR) vs. "critical sens/spec", i.e. sensitivity for contributing genotypes (log₂ OR > 0) or vs. specificity for protective genotypes (log₂ OR < 0). We show pairs from seven WTCCC datasets reported by GWIS or in previous literature. Results from GBOOST, an implementation of log-linear regression method, have been indicated by circles. Here we show all pairs from the full set of previous literature results that we have compiled. Each pair is represented by a point whose style indicates the methods it was reported by. There are nine pairs in the literature which pass the formal Bonferroni threshold for the gain test, $\mathsf{\text{fl}}{\mathsf{\text{t}}}_{\mathsf{\text{GSS}}}>{\text{log}}_{10}\left(\begin{array}{c}\hfill 459,012\hfill \\ \hfill 2\hfill \end{array}\right)\approx 11$ but were not detected by GWIS (black diamonds); the literature pairs which did not pass this formal requirement are marked by cyan diamonds. There are few pairs that were only detected by GBOOST (empty green circles). There is a substantial number of pairs with high odds ratios and coverage which were detected only by GWIS (red dots with no surrounding green circle) while many more were detected both in the literature and by GWIS (blue dots). The left most vertical dotted line marks the formal minimum requirement of critical sens/spec ≥ 2%, while such horizontal lines are for log₂OR = ±1 corresponding to OR = 2 or OR = 1/2, respectively.