The scale of a GWAS can be overwhelming, and many find it useful to use graphics to depict certain results. Figure 3b shows a quantile-quantile plot, a scatter plot of the p-values observed in a GWAS versus that expected by chance. To spread the graph out, the points are transformed using –log10(p-value) (e.g., 0.0001 or 10−4 becomes +4.0). In this instance, the plot shows that the observed p-values conform closely to the expected suggesting that no finding is individually impressive after accounting for multiple comparisons. Figure 3c shows a “Manhattan plot” (to some eyes, this resembles the night skyline of the Manhattan borough of New York City viewed from across the Hudson River), a depiction of all small p-values by genomic position. These results (from a different study than in Figure 3b), suggest that genomic regions on chromosomes 4, 6, 7, 10, and 12 exceed genome-wide significance. Figure 3d (again from a different study) shows an expanded view of a genomic region of interest (NRG1, neuregulin 1). The region of maximum signal on the right-hand side of the graph is quite far from the region suggested as a risk factor for schizophrenia (on the far left-hand side of the figure).
