Supplementary Figure 2: Association with T2D of nonsynonymous variants from the initial sequencing experiment.
From: Loss-of-function mutations in SLC30A8 protect against type 2 diabetes
Based on data from the initial sequencing experiment, we performed two types of as- sociation tests for all low-frequency (below 1%) nonsynonymous variants. First, variants were tested individually using a linear mixed model. Second, variants were collapsed within each gene and tested for aggregate association using the same mixed model approach. Shown are QQ plots of association for each approach: the x-axis plots the expected distribution of (−log10) P-values under the null model whereby no association exists across the entire experiment (e.g. the uniform distribution); the y-axis plots the observed distribution of (−log10) p-values. The blue lines show estimated 95% confidence intervals for observed distributions under the null model. For each plot, only variants (or, analogously, genes) for which ten or more carriers are observed are plotted: for variants with small numbers of counts, the uniform distribution is not a good approximation to the P -value distribution expected under the null model.
