Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression
Figure 3
Causal variant detection in the exome sequencing data analysis.
(A): NOD2 data; (B): ITPA data. The two top panels are from one replicate of the simulation. For single variant test, SNP effect size was represented by −log10 of p value from logistic regression model; for Bayesian liability model, it was represented by the standardized effect estimated at each SNP. Red dots indicate two causal variants (see Table 1 for more information). Blue vertical bars show values of SNP weights (r × phastCons). The horizontal dashed line indicates effect size at the significance threshold (permutation p value = 0.01). The bottom panel shows proportion of simulations where a variant was detected (i.e., significant at permutation p = 0.01 level). Causal variants are marked in red color.