Figure 5.

Manhattan plots for the different combinations of methods and nuclear family designs from the multiethnic GENEVA study on CL/P. The gTDT and the TDT are applicable to case–parent trio design ($n=1487$) only. The 1‐TDT (a generalization of TDT) is applicable to both case–mother dyad design ($n=1487$) and the combined case–mother dyad case–parent trio design ($n_1=371$ trios, $n_2=1116$ dyads). The GDT‐PO and HAPLIN methods are applicable to all three designs. Here, HAPLIN (2‐df test of offspring genotypic effect) was applied on each racial/ethnic group separately and then meta‐analyzed. The red and blue horizontal lines in each plot correspond to the genome‐wide ($5\times {10}^{-8}$) and a suggestive (${10}^{-6}$) significance levels, respectively. The genome‐wide significant loci for each method‐design pair are annotated in dark gray and the suggestively significant loci in light gray. The gene names provided are labels for the genetic loci based on nearest gene mapping approach and do not necessarily represent causal genes. GDT, generalized disequilibrium test; gTDT, genotypic TDT; TDT, transmission disequilibrium test